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value: - cli_version: 0.25.0 - e: - f0ugcbwht0bzsznis5d33rdup7dudruj: - args: - - --model_name_or_path - - /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 - - --tokenizer_path - - /home/n5huang/dna_token/tokenizer_evaluation/baseline_bpe/tokenizer.json - - --trust_remote_code - - "True" - - --data_path - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/enhancers/split - - --kmer - - "-1" - - --run_name - - hg38_BPE_base__baseline_bpe_tokenizer_3e-5_enhancers_seed42 - - --model_max_length - - "100" - - --per_device_train_batch_size - - "128" - - --per_device_eval_batch_size - - "128" - - --gradient_accumulation_steps - - "1" - - --learning_rate - - "3e-5" - - --num_train_epochs - - "4" - - --fp16 - - --save_steps - - "200" - - --output_dir - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "546900058112" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:01:22.935924Z" - writerId: f0ugcbwht0bzsznis5d33rdup7dudruj - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 41 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 41 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_040122-aq8j72f1/files/output.log b/wandb/run-20260305_040122-aq8j72f1/files/output.log deleted file mode 100644 index b5f9132702b494b30fe21ef3d5a9d9ed391eb551..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040122-aq8j72f1/files/output.log +++ /dev/null @@ -1,37 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 diff --git a/wandb/run-20260305_040122-aq8j72f1/files/requirements.txt b/wandb/run-20260305_040122-aq8j72f1/files/requirements.txt deleted file mode 100644 index e3d9629db6fa5f00aab96101b087d1d57a440fb4..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040122-aq8j72f1/files/requirements.txt +++ /dev/null @@ -1,90 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -idna==3.11 -pycparser==2.23 -triton==3.1.0 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -charset-normalizer==3.4.4 -wandb==0.25.0 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -accelerate==1.13.0 -torch==2.5.1 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -torchvision==0.20.1 -shellingham==1.5.4 -torchaudio==2.5.1 -sympy==1.13.1 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -click==8.3.1 -MarkupSafe==3.0.2 -urllib3==2.6.3 -propcache==0.4.1 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_040122-aq8j72f1/files/wandb-metadata.json b/wandb/run-20260305_040122-aq8j72f1/files/wandb-metadata.json deleted file mode 100644 index d7b27a6dbedb2f2b97a34e8bb34df02c46d08bdd..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040122-aq8j72f1/files/wandb-metadata.json +++ /dev/null @@ -1,134 +0,0 @@ -{ - "os": "Linux-5.15.0-72-generic-x86_64-with-glibc2.35", - "python": "CPython 3.10.19", - "startedAt": "2026-03-05T04:01:22.935924Z", - "args": [ - "--model_name_or_path", - "/home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000", - "--tokenizer_path", - "/home/n5huang/dna_token/tokenizer_evaluation/baseline_bpe/tokenizer.json", - "--trust_remote_code", - "True", - "--data_path", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/enhancers/split", - "--kmer", - "-1", - "--run_name", - "hg38_BPE_base__baseline_bpe_tokenizer_3e-5_enhancers_seed42", - "--model_max_length", - "100", - "--per_device_train_batch_size", - "128", - "--per_device_eval_batch_size", - "128", - "--gradient_accumulation_steps", - "1", - "--learning_rate", - "3e-5", - "--num_train_epochs", - "4", - "--fp16", - "--save_steps", - "200", - "--output_dir", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers", - "--evaluation_strategy", - "steps", - "--eval_steps", - "200", - "--warmup_steps", - "30", - "--logging_steps", - "100000", - "--log_level", - "info", - "--seed", - "42", - "--find_unused_parameters", - "False", - "--project_name", - "genomic_bench_tune_hg38_1024" - ], - "program": 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/home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 - - --tokenizer_path - - /home/n5huang/dna_token/tokenizer_evaluation/baseline_bpe/tokenizer.json - - --trust_remote_code - - "True" - - --data_path - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/enhancers_types/split - - --kmer - - "-1" - - --run_name - - hg38_BPE_base__baseline_bpe_tokenizer_3e-5_enhancers_types_seed42 - - --model_max_length - - "100" - - --per_device_train_batch_size - - "128" - - --per_device_eval_batch_size - - "128" - - --gradient_accumulation_steps - - "1" - - --learning_rate - - "3e-5" - - --num_train_epochs - - "4" - - --fp16 - - --save_steps - - "200" - - --output_dir - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers_types - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "546902056960" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB 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/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:01:36.144515Z" - writerId: t1x05ahrojkswcdknlxxvq1epngyd9kc - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 41 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 41 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_040136-qpc17ycl/files/output.log b/wandb/run-20260305_040136-qpc17ycl/files/output.log deleted file mode 100644 index b5f9132702b494b30fe21ef3d5a9d9ed391eb551..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040136-qpc17ycl/files/output.log +++ /dev/null @@ -1,37 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 diff --git a/wandb/run-20260305_040136-qpc17ycl/files/requirements.txt b/wandb/run-20260305_040136-qpc17ycl/files/requirements.txt deleted file mode 100644 index e3d9629db6fa5f00aab96101b087d1d57a440fb4..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040136-qpc17ycl/files/requirements.txt +++ /dev/null @@ -1,90 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -idna==3.11 -pycparser==2.23 -triton==3.1.0 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -charset-normalizer==3.4.4 -wandb==0.25.0 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -accelerate==1.13.0 -torch==2.5.1 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -torchvision==0.20.1 -shellingham==1.5.4 -torchaudio==2.5.1 -sympy==1.13.1 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -click==8.3.1 -MarkupSafe==3.0.2 -urllib3==2.6.3 -propcache==0.4.1 -regex==2026.2.28 -xxhash==3.6.0 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"/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/enhancers_types/split", - "--kmer", - "-1", - "--run_name", - "hg38_BPE_base__baseline_bpe_tokenizer_3e-5_enhancers_types_seed42", - "--model_max_length", - "100", - "--per_device_train_batch_size", - "128", - "--per_device_eval_batch_size", - "128", - "--gradient_accumulation_steps", - "1", - "--learning_rate", - "3e-5", - "--num_train_epochs", - "4", - "--fp16", - "--save_steps", - "200", - "--output_dir", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers_types", - "--evaluation_strategy", - "steps", - "--eval_steps", - "200", - "--warmup_steps", - "30", - "--logging_steps", - "100000", - "--log_level", - "info", - "--seed", - "42", - "--find_unused_parameters", - "False", - "--project_name", - "genomic_bench_tune_hg38_1024" - ], - "program": 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/home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 - - --tokenizer_path - - /home/n5huang/dna_token/tokenizer_evaluation/baseline_bpe/tokenizer.json - - --trust_remote_code - - "True" - - --data_path - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/promoter_all/split - - --kmer - - "-1" - - --run_name - - hg38_BPE_base__baseline_bpe_tokenizer_3e-5_promoter_all_seed42 - - --model_max_length - - "80" - - --per_device_train_batch_size - - "128" - - --per_device_eval_batch_size - - "128" - - --gradient_accumulation_steps - - "1" - - --learning_rate - - "3e-5" - - --num_train_epochs - - "2" - - --fp16 - - --save_steps - - "200" - - --output_dir - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/promoter_all - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "546902155264" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:01:49.227236Z" - writerId: sglafjcvr8er2m8m2ct1kp5m6yzyiu0z - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 41 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 41 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_040149-wwzikjfe/files/output.log b/wandb/run-20260305_040149-wwzikjfe/files/output.log deleted file mode 100644 index b5f9132702b494b30fe21ef3d5a9d9ed391eb551..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040149-wwzikjfe/files/output.log +++ /dev/null @@ -1,37 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 diff --git a/wandb/run-20260305_040149-wwzikjfe/files/requirements.txt b/wandb/run-20260305_040149-wwzikjfe/files/requirements.txt deleted file mode 100644 index e3d9629db6fa5f00aab96101b087d1d57a440fb4..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040149-wwzikjfe/files/requirements.txt +++ /dev/null @@ -1,90 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -idna==3.11 -pycparser==2.23 -triton==3.1.0 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -charset-normalizer==3.4.4 -wandb==0.25.0 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -accelerate==1.13.0 -torch==2.5.1 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -torchvision==0.20.1 -shellingham==1.5.4 -torchaudio==2.5.1 -sympy==1.13.1 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -click==8.3.1 -MarkupSafe==3.0.2 -urllib3==2.6.3 -propcache==0.4.1 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_040149-wwzikjfe/files/wandb-metadata.json b/wandb/run-20260305_040149-wwzikjfe/files/wandb-metadata.json deleted file mode 100644 index 7fcf95e03e67a95d9c8bdddc285bd151b4b6f4a2..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040149-wwzikjfe/files/wandb-metadata.json +++ /dev/null @@ -1,134 +0,0 @@ -{ - "os": "Linux-5.15.0-72-generic-x86_64-with-glibc2.35", - "python": "CPython 3.10.19", - "startedAt": "2026-03-05T04:01:49.227236Z", - "args": [ - "--model_name_or_path", - "/home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000", - "--tokenizer_path", - "/home/n5huang/dna_token/tokenizer_evaluation/baseline_bpe/tokenizer.json", - "--trust_remote_code", - "True", - "--data_path", - 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--warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "546902290432" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB 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/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:02:01.072664Z" - writerId: vfpu61gd7bux48d6r9tpwknkwvqgw5gv - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 41 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 41 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_040201-sq11rclj/files/output.log b/wandb/run-20260305_040201-sq11rclj/files/output.log deleted file mode 100644 index b5f9132702b494b30fe21ef3d5a9d9ed391eb551..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040201-sq11rclj/files/output.log +++ /dev/null @@ -1,37 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 diff --git a/wandb/run-20260305_040201-sq11rclj/files/requirements.txt b/wandb/run-20260305_040201-sq11rclj/files/requirements.txt deleted file mode 100644 index e3d9629db6fa5f00aab96101b087d1d57a440fb4..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040201-sq11rclj/files/requirements.txt +++ /dev/null @@ -1,90 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -idna==3.11 -pycparser==2.23 -triton==3.1.0 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -charset-normalizer==3.4.4 -wandb==0.25.0 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -accelerate==1.13.0 -torch==2.5.1 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -torchvision==0.20.1 -shellingham==1.5.4 -torchaudio==2.5.1 -sympy==1.13.1 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -click==8.3.1 -MarkupSafe==3.0.2 -urllib3==2.6.3 -propcache==0.4.1 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_040201-sq11rclj/files/wandb-metadata.json b/wandb/run-20260305_040201-sq11rclj/files/wandb-metadata.json deleted file mode 100644 index c65e000976a435d197caac4373a52480d495e465..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040201-sq11rclj/files/wandb-metadata.json +++ /dev/null @@ -1,134 +0,0 @@ -{ - "os": "Linux-5.15.0-72-generic-x86_64-with-glibc2.35", - "python": "CPython 3.10.19", - "startedAt": "2026-03-05T04:02:01.072664Z", - "args": [ - "--model_name_or_path", - "/home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000", - "--tokenizer_path", - "/home/n5huang/dna_token/tokenizer_evaluation/baseline_bpe/tokenizer.json", - "--trust_remote_code", - "True", - "--data_path", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/promoter_no_tata/split", - "--kmer", - "-1", - "--run_name", - "hg38_BPE_base__baseline_bpe_tokenizer_3e-5_promoter_no_tata_seed42", - "--model_max_length", - "80", - "--per_device_train_batch_size", - "128", - "--per_device_eval_batch_size", - "128", - "--gradient_accumulation_steps", - "1", - "--learning_rate", - "3e-5", - "--num_train_epochs", - "2", - "--fp16", - "--save_steps", - "200", - "--output_dir", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/promoter_no_tata", - "--evaluation_strategy", - "steps", - "--eval_steps", - "200", - "--warmup_steps", - "30", - "--logging_steps", - "100000", - "--log_level", - "info", - "--seed", - "42", - "--find_unused_parameters", - "False", - "--project_name", - "genomic_bench_tune_hg38_1024" - ], - "program": 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/home/n5huang/dna_token/tokenizer_evaluation/baseline_bpe/tokenizer.json - - --trust_remote_code - - "True" - - --data_path - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/promoter_tata/split - - --kmer - - "-1" - - --run_name - - hg38_BPE_base__baseline_bpe_tokenizer_3e-5_promoter_tata_seed42 - - --model_max_length - - "80" - - --per_device_train_batch_size - - "128" - - --per_device_eval_batch_size - - "128" - - --gradient_accumulation_steps - - "1" - - --learning_rate - - "3e-5" - - --num_train_epochs - - "2" - - --fp16 - - --save_steps - - "200" - - --output_dir - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/promoter_tata - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "546902446080" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:02:14.197174Z" - writerId: ffxm8q6qp1l1piwxz1h1pyrnbob5nzwb - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 41 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 41 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_040214-vyqcoynz/files/output.log b/wandb/run-20260305_040214-vyqcoynz/files/output.log deleted file mode 100644 index b5f9132702b494b30fe21ef3d5a9d9ed391eb551..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040214-vyqcoynz/files/output.log +++ /dev/null @@ -1,37 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 diff --git a/wandb/run-20260305_040214-vyqcoynz/files/requirements.txt b/wandb/run-20260305_040214-vyqcoynz/files/requirements.txt deleted file mode 100644 index e3d9629db6fa5f00aab96101b087d1d57a440fb4..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040214-vyqcoynz/files/requirements.txt +++ /dev/null @@ -1,90 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -idna==3.11 -pycparser==2.23 -triton==3.1.0 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -charset-normalizer==3.4.4 -wandb==0.25.0 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -accelerate==1.13.0 -torch==2.5.1 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -torchvision==0.20.1 -shellingham==1.5.4 -torchaudio==2.5.1 -sympy==1.13.1 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -click==8.3.1 -MarkupSafe==3.0.2 -urllib3==2.6.3 -propcache==0.4.1 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_040214-vyqcoynz/files/wandb-metadata.json b/wandb/run-20260305_040214-vyqcoynz/files/wandb-metadata.json deleted file mode 100644 index 823e797fb7cf6a5a299e7997813599ec3d17aba4..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040214-vyqcoynz/files/wandb-metadata.json +++ /dev/null @@ -1,134 +0,0 @@ -{ - "os": "Linux-5.15.0-72-generic-x86_64-with-glibc2.35", - "python": "CPython 3.10.19", - "startedAt": "2026-03-05T04:02:14.197174Z", - "args": [ - "--model_name_or_path", - "/home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000", - "--tokenizer_path", - "/home/n5huang/dna_token/tokenizer_evaluation/baseline_bpe/tokenizer.json", - "--trust_remote_code", - "True", - "--data_path", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/promoter_tata/split", - "--kmer", - "-1", - "--run_name", - "hg38_BPE_base__baseline_bpe_tokenizer_3e-5_promoter_tata_seed42", - "--model_max_length", - "80", - "--per_device_train_batch_size", - "128", - "--per_device_eval_batch_size", - "128", - "--gradient_accumulation_steps", - "1", - "--learning_rate", - "3e-5", - "--num_train_epochs", - "2", - "--fp16", - "--save_steps", - "200", - "--output_dir", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/promoter_tata", - "--evaluation_strategy", - "steps", - "--eval_steps", - "200", - "--warmup_steps", - "30", - "--logging_steps", - "100000", - "--log_level", - "info", - "--seed", - "42", - "--find_unused_parameters", - "False", - "--project_name", - "genomic_bench_tune_hg38_1024" - ], - "program": 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[service_client.py:_forward_responses():134] Reached EOF. -2026-03-05 04:02:15,894 INFO wandb-AsyncioManager-main:862282 [mailbox.py:close():155] Closing mailbox, abandoning 1 handles. diff --git a/wandb/run-20260305_040214-vyqcoynz/run-vyqcoynz.wandb b/wandb/run-20260305_040214-vyqcoynz/run-vyqcoynz.wandb deleted file mode 100644 index 87c3dd8da3c3e52c644e75acb4c75a3dc2d03265..0000000000000000000000000000000000000000 Binary files a/wandb/run-20260305_040214-vyqcoynz/run-vyqcoynz.wandb and /dev/null differ diff --git a/wandb/run-20260305_040223-yfxomrbt/files/config.yaml b/wandb/run-20260305_040223-yfxomrbt/files/config.yaml deleted file mode 100644 index 743d2654abff0477d96468d19c8886486835cda4..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040223-yfxomrbt/files/config.yaml +++ /dev/null @@ -1,141 +0,0 @@ -_wandb: - value: - cli_version: 0.25.0 - e: - 4wgvlh1jxxjwyr68cc0n54olcpzgaplm: - args: - - --model_name_or_path - - /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 - - --tokenizer_path - - /home/n5huang/dna_token/tokenizer_evaluation/baseline_bpe/tokenizer.json - - --trust_remote_code - - "True" - - --data_path - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/splice_sites_acceptors/split - - --kmer - - "-1" - - --run_name - - hg38_BPE_base__baseline_bpe_tokenizer_3e-5_splice_sites_acceptors_seed42 - - --model_max_length - - "140" - - --per_device_train_batch_size - - "128" - - --per_device_eval_batch_size - - "128" - - --gradient_accumulation_steps - - "1" - - --learning_rate - - "3e-5" - - --num_train_epochs - - "4" - - --fp16 - - --save_steps - - "200" - - --output_dir - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_acceptors - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "546902515712" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:02:23.923029Z" - writerId: 4wgvlh1jxxjwyr68cc0n54olcpzgaplm - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 41 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 41 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_040223-yfxomrbt/files/output.log b/wandb/run-20260305_040223-yfxomrbt/files/output.log deleted file mode 100644 index b5f9132702b494b30fe21ef3d5a9d9ed391eb551..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040223-yfxomrbt/files/output.log +++ /dev/null @@ -1,37 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 diff --git a/wandb/run-20260305_040223-yfxomrbt/files/requirements.txt b/wandb/run-20260305_040223-yfxomrbt/files/requirements.txt deleted file mode 100644 index e3d9629db6fa5f00aab96101b087d1d57a440fb4..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040223-yfxomrbt/files/requirements.txt +++ /dev/null @@ -1,90 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -idna==3.11 -pycparser==2.23 -triton==3.1.0 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -charset-normalizer==3.4.4 -wandb==0.25.0 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -accelerate==1.13.0 -torch==2.5.1 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -torchvision==0.20.1 -shellingham==1.5.4 -torchaudio==2.5.1 -sympy==1.13.1 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -click==8.3.1 -MarkupSafe==3.0.2 -urllib3==2.6.3 -propcache==0.4.1 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_040223-yfxomrbt/files/wandb-metadata.json b/wandb/run-20260305_040223-yfxomrbt/files/wandb-metadata.json deleted file mode 100644 index eb9ca4e48355c8bde9676ffdec5319530db0ed5e..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040223-yfxomrbt/files/wandb-metadata.json +++ /dev/null @@ -1,134 +0,0 @@ -{ - "os": "Linux-5.15.0-72-generic-x86_64-with-glibc2.35", - "python": "CPython 3.10.19", - "startedAt": "2026-03-05T04:02:23.923029Z", - "args": [ - "--model_name_or_path", - "/home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000", - "--tokenizer_path", - "/home/n5huang/dna_token/tokenizer_evaluation/baseline_bpe/tokenizer.json", - "--trust_remote_code", - "True", - "--data_path", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/splice_sites_acceptors/split", - "--kmer", - "-1", - "--run_name", - "hg38_BPE_base__baseline_bpe_tokenizer_3e-5_splice_sites_acceptors_seed42", - "--model_max_length", - "140", - "--per_device_train_batch_size", - "128", - "--per_device_eval_batch_size", - "128", - "--gradient_accumulation_steps", - "1", - "--learning_rate", - "3e-5", - "--num_train_epochs", - "4", - "--fp16", - "--save_steps", - "200", - "--output_dir", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_acceptors", - "--evaluation_strategy", - "steps", - "--eval_steps", - "200", - "--warmup_steps", - "30", - "--logging_steps", - "100000", - "--log_level", - "info", - "--seed", - "42", - "--find_unused_parameters", - "False", - "--project_name", - "genomic_bench_tune_hg38_1024" - ], - 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--find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "546904584192" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:02:37.566296Z" - writerId: xw9kpceisjkpb8c6x4f5skdmkmbgdo5c - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 41 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 41 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_040237-5e1o7f0w/files/output.log b/wandb/run-20260305_040237-5e1o7f0w/files/output.log deleted file mode 100644 index b5f9132702b494b30fe21ef3d5a9d9ed391eb551..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040237-5e1o7f0w/files/output.log +++ /dev/null @@ -1,37 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 diff --git a/wandb/run-20260305_040237-5e1o7f0w/files/requirements.txt b/wandb/run-20260305_040237-5e1o7f0w/files/requirements.txt deleted file mode 100644 index e3d9629db6fa5f00aab96101b087d1d57a440fb4..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040237-5e1o7f0w/files/requirements.txt +++ /dev/null @@ -1,90 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -idna==3.11 -pycparser==2.23 -triton==3.1.0 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -charset-normalizer==3.4.4 -wandb==0.25.0 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -accelerate==1.13.0 -torch==2.5.1 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -torchvision==0.20.1 -shellingham==1.5.4 -torchaudio==2.5.1 -sympy==1.13.1 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -click==8.3.1 -MarkupSafe==3.0.2 -urllib3==2.6.3 -propcache==0.4.1 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_040237-5e1o7f0w/files/wandb-metadata.json b/wandb/run-20260305_040237-5e1o7f0w/files/wandb-metadata.json deleted file mode 100644 index a7bc70df7bfe3c079c146d8479f9680cad7e1b8c..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040237-5e1o7f0w/files/wandb-metadata.json +++ /dev/null @@ -1,134 +0,0 @@ -{ - "os": "Linux-5.15.0-72-generic-x86_64-with-glibc2.35", - "python": "CPython 3.10.19", - "startedAt": "2026-03-05T04:02:37.566296Z", - "args": [ - "--model_name_or_path", - "/home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000", - "--tokenizer_path", - "/home/n5huang/dna_token/tokenizer_evaluation/baseline_bpe/tokenizer.json", - "--trust_remote_code", - "True", - "--data_path", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/splice_sites_all/split", - "--kmer", - "-1", - "--run_name", - "hg38_BPE_base__baseline_bpe_tokenizer_3e-5_splice_sites_all_seed42", - "--model_max_length", - "140", - "--per_device_train_batch_size", - "128", - "--per_device_eval_batch_size", - "128", - "--gradient_accumulation_steps", - "1", - "--learning_rate", - "3e-5", - "--num_train_epochs", - "4", - "--fp16", - "--save_steps", - "200", - "--output_dir", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_all", - "--evaluation_strategy", - "steps", - "--eval_steps", - "200", - "--warmup_steps", - "30", - "--logging_steps", - "100000", - "--log_level", - "info", - "--seed", - "42", - "--find_unused_parameters", - "False", - "--project_name", - "genomic_bench_tune_hg38_1024" - ], - "program": 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/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_donors - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "546904743936" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:02:51.983308Z" - writerId: h3za1x5i2ufl9fgvy56mt6br6j5n5j8g - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 41 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 41 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_040251-0vl8szmy/files/output.log b/wandb/run-20260305_040251-0vl8szmy/files/output.log deleted file mode 100644 index b5f9132702b494b30fe21ef3d5a9d9ed391eb551..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040251-0vl8szmy/files/output.log +++ /dev/null @@ -1,37 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 diff --git a/wandb/run-20260305_040251-0vl8szmy/files/requirements.txt b/wandb/run-20260305_040251-0vl8szmy/files/requirements.txt deleted file mode 100644 index e3d9629db6fa5f00aab96101b087d1d57a440fb4..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040251-0vl8szmy/files/requirements.txt +++ /dev/null @@ -1,90 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -idna==3.11 -pycparser==2.23 -triton==3.1.0 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -charset-normalizer==3.4.4 -wandb==0.25.0 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -accelerate==1.13.0 -torch==2.5.1 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -torchvision==0.20.1 -shellingham==1.5.4 -torchaudio==2.5.1 -sympy==1.13.1 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -click==8.3.1 -MarkupSafe==3.0.2 -urllib3==2.6.3 -propcache==0.4.1 -regex==2026.2.28 -xxhash==3.6.0 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GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:03:05.814107Z" - writerId: b9i2pyb4uwtesy7gw7w7lmnebnso6tfb - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 41 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 41 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_040305-mrgs4onp/files/output.log b/wandb/run-20260305_040305-mrgs4onp/files/output.log deleted file mode 100644 index b5f9132702b494b30fe21ef3d5a9d9ed391eb551..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040305-mrgs4onp/files/output.log +++ /dev/null @@ -1,37 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 diff --git a/wandb/run-20260305_040305-mrgs4onp/files/requirements.txt b/wandb/run-20260305_040305-mrgs4onp/files/requirements.txt deleted file mode 100644 index e3d9629db6fa5f00aab96101b087d1d57a440fb4..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040305-mrgs4onp/files/requirements.txt +++ /dev/null @@ -1,90 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -idna==3.11 -pycparser==2.23 -triton==3.1.0 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -charset-normalizer==3.4.4 -wandb==0.25.0 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -accelerate==1.13.0 -torch==2.5.1 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -torchvision==0.20.1 -shellingham==1.5.4 -torchaudio==2.5.1 -sympy==1.13.1 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -click==8.3.1 -MarkupSafe==3.0.2 -urllib3==2.6.3 -propcache==0.4.1 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_040305-mrgs4onp/files/wandb-metadata.json b/wandb/run-20260305_040305-mrgs4onp/files/wandb-metadata.json deleted file mode 100644 index 4197cb55977b2aeadf6ad2925720b89777431b55..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040305-mrgs4onp/files/wandb-metadata.json +++ /dev/null @@ -1,134 +0,0 @@ -{ - "os": "Linux-5.15.0-72-generic-x86_64-with-glibc2.35", - "python": "CPython 3.10.19", - "startedAt": "2026-03-05T04:03:05.814107Z", - "args": [ - "--model_name_or_path", - "/home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000", - "--tokenizer_path", - "/home/n5huang/dna_token/tokenizer_evaluation/baseline_bpe/tokenizer.json", - "--trust_remote_code", - "True", - "--data_path", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/H2AFZ/split", - "--kmer", - "-1", - "--run_name", - "hg38_BPE_base__baseline_bpe_tokenizer_3e-5_H2AFZ_seed42", - "--model_max_length", - "220", - "--per_device_train_batch_size", - "128", - "--per_device_eval_batch_size", - "128", - "--gradient_accumulation_steps", - "1", - "--learning_rate", - "3e-5", - "--num_train_epochs", - "2", - "--fp16", - "--save_steps", - "200", - "--output_dir", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H2AFZ", - "--evaluation_strategy", - "steps", - "--eval_steps", - "200", - "--warmup_steps", - "30", - "--logging_steps", - "100000", - "--log_level", - "info", - "--seed", - "42", - "--find_unused_parameters", - "False", - "--project_name", - "genomic_bench_tune_hg38_1024" - ], - "program": 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a/wandb/run-20260305_040322-rukkaeg2/files/config.yaml +++ /dev/null @@ -1,141 +0,0 @@ -_wandb: - value: - cli_version: 0.25.0 - e: - tbl3ls86yduhmso7201pfcivy7thpp0z: - args: - - --model_name_or_path - - /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 - - --tokenizer_path - - /home/n5huang/dna_token/tokenizer_evaluation/baseline_bpe/tokenizer.json - - --trust_remote_code - - "True" - - --data_path - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/H3K27ac/split - - --kmer - - "-1" - - --run_name - - hg38_BPE_base__baseline_bpe_tokenizer_3e-5_H3K27ac_seed42 - - --model_max_length - - "220" - - --per_device_train_batch_size - - "128" - - --per_device_eval_batch_size - - "128" - - --gradient_accumulation_steps - - "1" - - --learning_rate - - "3e-5" - - --num_train_epochs - - "2" - - --fp16 - - --save_steps - - "200" - - --output_dir - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K27ac - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "546904989696" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:03:22.607725Z" - writerId: tbl3ls86yduhmso7201pfcivy7thpp0z - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 41 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 41 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_040322-rukkaeg2/files/output.log b/wandb/run-20260305_040322-rukkaeg2/files/output.log deleted file mode 100644 index b5f9132702b494b30fe21ef3d5a9d9ed391eb551..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040322-rukkaeg2/files/output.log +++ /dev/null @@ -1,37 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 diff --git a/wandb/run-20260305_040322-rukkaeg2/files/requirements.txt b/wandb/run-20260305_040322-rukkaeg2/files/requirements.txt deleted file mode 100644 index e3d9629db6fa5f00aab96101b087d1d57a440fb4..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040322-rukkaeg2/files/requirements.txt +++ /dev/null @@ -1,90 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -idna==3.11 -pycparser==2.23 -triton==3.1.0 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -charset-normalizer==3.4.4 -wandb==0.25.0 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -accelerate==1.13.0 -torch==2.5.1 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -torchvision==0.20.1 -shellingham==1.5.4 -torchaudio==2.5.1 -sympy==1.13.1 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -click==8.3.1 -MarkupSafe==3.0.2 -urllib3==2.6.3 -propcache==0.4.1 -regex==2026.2.28 -xxhash==3.6.0 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"/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/H3K27ac/split", - "--kmer", - "-1", - "--run_name", - "hg38_BPE_base__baseline_bpe_tokenizer_3e-5_H3K27ac_seed42", - "--model_max_length", - "220", - "--per_device_train_batch_size", - "128", - "--per_device_eval_batch_size", - "128", - "--gradient_accumulation_steps", - "1", - "--learning_rate", - "3e-5", - "--num_train_epochs", - "2", - "--fp16", - "--save_steps", - "200", - "--output_dir", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K27ac", - "--evaluation_strategy", - "steps", - "--eval_steps", - "200", - "--warmup_steps", - "30", - "--logging_steps", - "100000", - "--log_level", - "info", - "--seed", - "42", - "--find_unused_parameters", - "False", - "--project_name", - "genomic_bench_tune_hg38_1024" - ], - "program": 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a/wandb/run-20260305_040339-i9hgz2b9/files/config.yaml +++ /dev/null @@ -1,141 +0,0 @@ -_wandb: - value: - cli_version: 0.25.0 - e: - 3r99jqa8qq41i76cc0rz9aty3e1ejq3r: - args: - - --model_name_or_path - - /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 - - --tokenizer_path - - /home/n5huang/dna_token/tokenizer_evaluation/baseline_bpe/tokenizer.json - - --trust_remote_code - - "True" - - --data_path - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/H3K27me3/split - - --kmer - - "-1" - - --run_name - - hg38_BPE_base__baseline_bpe_tokenizer_3e-5_H3K27me3_seed42 - - --model_max_length - - "220" - - --per_device_train_batch_size - - "128" - - --per_device_eval_batch_size - - "128" - - --gradient_accumulation_steps - - "1" - - --learning_rate - - "3e-5" - - --num_train_epochs - - "2" - - --fp16 - - --save_steps - - "200" - - --output_dir - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K27me3 - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "546907082752" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:03:39.457382Z" - writerId: 3r99jqa8qq41i76cc0rz9aty3e1ejq3r - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 41 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 41 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_040339-i9hgz2b9/files/output.log b/wandb/run-20260305_040339-i9hgz2b9/files/output.log deleted file mode 100644 index b5f9132702b494b30fe21ef3d5a9d9ed391eb551..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040339-i9hgz2b9/files/output.log +++ /dev/null @@ -1,37 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 diff --git a/wandb/run-20260305_040339-i9hgz2b9/files/requirements.txt b/wandb/run-20260305_040339-i9hgz2b9/files/requirements.txt deleted file mode 100644 index e3d9629db6fa5f00aab96101b087d1d57a440fb4..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040339-i9hgz2b9/files/requirements.txt +++ /dev/null @@ -1,90 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -idna==3.11 -pycparser==2.23 -triton==3.1.0 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -charset-normalizer==3.4.4 -wandb==0.25.0 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -accelerate==1.13.0 -torch==2.5.1 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -torchvision==0.20.1 -shellingham==1.5.4 -torchaudio==2.5.1 -sympy==1.13.1 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -click==8.3.1 -MarkupSafe==3.0.2 -urllib3==2.6.3 -propcache==0.4.1 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_040339-i9hgz2b9/files/wandb-metadata.json b/wandb/run-20260305_040339-i9hgz2b9/files/wandb-metadata.json deleted file mode 100644 index d31274dc20fb3e10ec5e0bded7c3b02180324bfc..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040339-i9hgz2b9/files/wandb-metadata.json +++ /dev/null @@ -1,134 +0,0 @@ -{ - "os": "Linux-5.15.0-72-generic-x86_64-with-glibc2.35", - "python": "CPython 3.10.19", - "startedAt": "2026-03-05T04:03:39.457382Z", - "args": [ - "--model_name_or_path", - "/home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000", - "--tokenizer_path", - "/home/n5huang/dna_token/tokenizer_evaluation/baseline_bpe/tokenizer.json", - "--trust_remote_code", - "True", - "--data_path", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/H3K27me3/split", - "--kmer", - "-1", - "--run_name", - "hg38_BPE_base__baseline_bpe_tokenizer_3e-5_H3K27me3_seed42", - "--model_max_length", - "220", - "--per_device_train_batch_size", - "128", - "--per_device_eval_batch_size", - "128", - "--gradient_accumulation_steps", - "1", - "--learning_rate", - "3e-5", - "--num_train_epochs", - "2", - "--fp16", - "--save_steps", - "200", - "--output_dir", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K27me3", - "--evaluation_strategy", - "steps", - "--eval_steps", - "200", - "--warmup_steps", - "30", - "--logging_steps", - "100000", - "--log_level", - "info", - "--seed", - "42", - "--find_unused_parameters", - "False", - "--project_name", - "genomic_bench_tune_hg38_1024" - ], - "program": 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/home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 - - --tokenizer_path - - /home/n5huang/dna_token/tokenizer_evaluation/baseline_bpe/tokenizer.json - - --trust_remote_code - - "True" - - --data_path - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/H3K36me3/split - - --kmer - - "-1" - - --run_name - - hg38_BPE_base__baseline_bpe_tokenizer_3e-5_H3K36me3_seed42 - - --model_max_length - - "220" - - --per_device_train_batch_size - - "128" - - --per_device_eval_batch_size - - "128" - - --gradient_accumulation_steps - - "1" - - --learning_rate - - "3e-5" - - --num_train_epochs - - "2" - - --fp16 - - --save_steps - - "200" - - --output_dir - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K36me3 - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "546907222016" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:03:55.925997Z" - writerId: 2ogamslvyt9pon8flwmuwmgegzlhrvvm - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 41 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 41 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_040355-h2kktals/files/output.log b/wandb/run-20260305_040355-h2kktals/files/output.log deleted file mode 100644 index b5f9132702b494b30fe21ef3d5a9d9ed391eb551..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040355-h2kktals/files/output.log +++ /dev/null @@ -1,37 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 diff --git a/wandb/run-20260305_040355-h2kktals/files/requirements.txt b/wandb/run-20260305_040355-h2kktals/files/requirements.txt deleted file mode 100644 index e3d9629db6fa5f00aab96101b087d1d57a440fb4..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040355-h2kktals/files/requirements.txt +++ /dev/null @@ -1,90 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -idna==3.11 -pycparser==2.23 -triton==3.1.0 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -charset-normalizer==3.4.4 -wandb==0.25.0 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -accelerate==1.13.0 -torch==2.5.1 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -torchvision==0.20.1 -shellingham==1.5.4 -torchaudio==2.5.1 -sympy==1.13.1 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -click==8.3.1 -MarkupSafe==3.0.2 -urllib3==2.6.3 -propcache==0.4.1 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_040355-h2kktals/files/wandb-metadata.json b/wandb/run-20260305_040355-h2kktals/files/wandb-metadata.json deleted file mode 100644 index 0509cf2e1e82e724181e6e39239c8fb014333258..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040355-h2kktals/files/wandb-metadata.json +++ /dev/null @@ -1,134 +0,0 @@ -{ - "os": "Linux-5.15.0-72-generic-x86_64-with-glibc2.35", - "python": "CPython 3.10.19", - "startedAt": "2026-03-05T04:03:55.925997Z", - "args": [ - "--model_name_or_path", - "/home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000", - "--tokenizer_path", - "/home/n5huang/dna_token/tokenizer_evaluation/baseline_bpe/tokenizer.json", - "--trust_remote_code", - "True", - "--data_path", - 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/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K4me1 - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "546907357184" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:04:13.365399Z" - writerId: w56830c9pgy1p5f2rgm93itgrjfifh32 - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 41 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 41 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_040413-z2mqv3tt/files/output.log b/wandb/run-20260305_040413-z2mqv3tt/files/output.log deleted file mode 100644 index b5f9132702b494b30fe21ef3d5a9d9ed391eb551..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040413-z2mqv3tt/files/output.log +++ /dev/null @@ -1,37 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 diff --git a/wandb/run-20260305_040413-z2mqv3tt/files/requirements.txt b/wandb/run-20260305_040413-z2mqv3tt/files/requirements.txt deleted file mode 100644 index e3d9629db6fa5f00aab96101b087d1d57a440fb4..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040413-z2mqv3tt/files/requirements.txt +++ /dev/null @@ -1,90 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -idna==3.11 -pycparser==2.23 -triton==3.1.0 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -charset-normalizer==3.4.4 -wandb==0.25.0 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -accelerate==1.13.0 -torch==2.5.1 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -torchvision==0.20.1 -shellingham==1.5.4 -torchaudio==2.5.1 -sympy==1.13.1 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -click==8.3.1 -MarkupSafe==3.0.2 -urllib3==2.6.3 -propcache==0.4.1 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_040413-z2mqv3tt/files/wandb-metadata.json b/wandb/run-20260305_040413-z2mqv3tt/files/wandb-metadata.json deleted file mode 100644 index b18fa3742ad9854859d394e997e6888de3790263..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040413-z2mqv3tt/files/wandb-metadata.json +++ /dev/null @@ -1,134 +0,0 @@ -{ - "os": "Linux-5.15.0-72-generic-x86_64-with-glibc2.35", - "python": "CPython 3.10.19", - "startedAt": "2026-03-05T04:04:13.365399Z", - "args": [ - "--model_name_or_path", - "/home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000", - "--tokenizer_path", - "/home/n5huang/dna_token/tokenizer_evaluation/baseline_bpe/tokenizer.json", - "--trust_remote_code", - "True", - "--data_path", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/H3K4me1/split", - "--kmer", - "-1", - "--run_name", - "hg38_BPE_base__baseline_bpe_tokenizer_3e-5_H3K4me1_seed42", - "--model_max_length", - "220", - "--per_device_train_batch_size", - "128", - "--per_device_eval_batch_size", - "128", - "--gradient_accumulation_steps", - "1", - "--learning_rate", - "3e-5", - "--num_train_epochs", - "2", - "--fp16", - "--save_steps", - "200", - "--output_dir", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K4me1", - "--evaluation_strategy", - "steps", - "--eval_steps", - "200", - "--warmup_steps", - "30", - "--logging_steps", - "100000", - "--log_level", - "info", - "--seed", - "42", - "--find_unused_parameters", - "False", - "--project_name", - "genomic_bench_tune_hg38_1024" - ], - "program": 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a/wandb/run-20260305_040429-j7d07s7m/files/config.yaml +++ /dev/null @@ -1,141 +0,0 @@ -_wandb: - value: - cli_version: 0.25.0 - e: - 3fj2ctrr3p8fyhh0w2vicg7g97qpebks: - args: - - --model_name_or_path - - /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 - - --tokenizer_path - - /home/n5huang/dna_token/tokenizer_evaluation/baseline_bpe/tokenizer.json - - --trust_remote_code - - "True" - - --data_path - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/H3K4me2/split - - --kmer - - "-1" - - --run_name - - hg38_BPE_base__baseline_bpe_tokenizer_3e-5_H3K4me2_seed42 - - --model_max_length - - "220" - - --per_device_train_batch_size - - "128" - - --per_device_eval_batch_size - - "128" - - --gradient_accumulation_steps - - "1" - - --learning_rate - - "3e-5" - - --num_train_epochs - - "2" - - --fp16 - - --save_steps - - "200" - - --output_dir - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K4me2 - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "546907500544" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:04:29.337815Z" - writerId: 3fj2ctrr3p8fyhh0w2vicg7g97qpebks - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 41 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 41 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_040429-j7d07s7m/files/output.log b/wandb/run-20260305_040429-j7d07s7m/files/output.log deleted file mode 100644 index b5f9132702b494b30fe21ef3d5a9d9ed391eb551..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040429-j7d07s7m/files/output.log +++ /dev/null @@ -1,37 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 diff --git a/wandb/run-20260305_040429-j7d07s7m/files/requirements.txt b/wandb/run-20260305_040429-j7d07s7m/files/requirements.txt deleted file mode 100644 index e3d9629db6fa5f00aab96101b087d1d57a440fb4..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040429-j7d07s7m/files/requirements.txt +++ /dev/null @@ -1,90 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -idna==3.11 -pycparser==2.23 -triton==3.1.0 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -charset-normalizer==3.4.4 -wandb==0.25.0 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -accelerate==1.13.0 -torch==2.5.1 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -torchvision==0.20.1 -shellingham==1.5.4 -torchaudio==2.5.1 -sympy==1.13.1 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -click==8.3.1 -MarkupSafe==3.0.2 -urllib3==2.6.3 -propcache==0.4.1 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_040429-j7d07s7m/files/wandb-metadata.json b/wandb/run-20260305_040429-j7d07s7m/files/wandb-metadata.json deleted file mode 100644 index 54eef29922eceb95f558f99c26f3a4d825bafd1f..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040429-j7d07s7m/files/wandb-metadata.json +++ /dev/null @@ -1,134 +0,0 @@ -{ - "os": "Linux-5.15.0-72-generic-x86_64-with-glibc2.35", - "python": "CPython 3.10.19", - "startedAt": "2026-03-05T04:04:29.337815Z", - "args": [ - "--model_name_or_path", - "/home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000", - "--tokenizer_path", - "/home/n5huang/dna_token/tokenizer_evaluation/baseline_bpe/tokenizer.json", - "--trust_remote_code", - "True", - "--data_path", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/H3K4me2/split", - "--kmer", - "-1", - "--run_name", - "hg38_BPE_base__baseline_bpe_tokenizer_3e-5_H3K4me2_seed42", - "--model_max_length", - "220", - "--per_device_train_batch_size", - "128", - "--per_device_eval_batch_size", - "128", - "--gradient_accumulation_steps", - "1", - "--learning_rate", - "3e-5", - "--num_train_epochs", - "2", - "--fp16", - "--save_steps", - "200", - "--output_dir", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K4me2", - "--evaluation_strategy", - "steps", - "--eval_steps", - "200", - "--warmup_steps", - "30", - "--logging_steps", - "100000", - "--log_level", - "info", - "--seed", - "42", - "--find_unused_parameters", - "False", - "--project_name", - "genomic_bench_tune_hg38_1024" - ], - "program": 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a/wandb/run-20260305_040445-qeivjux7/files/config.yaml +++ /dev/null @@ -1,141 +0,0 @@ -_wandb: - value: - cli_version: 0.25.0 - e: - 13zvl8us4w5q9awnhtixdunxhhfs9f1g: - args: - - --model_name_or_path - - /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 - - --tokenizer_path - - /home/n5huang/dna_token/tokenizer_evaluation/baseline_bpe/tokenizer.json - - --trust_remote_code - - "True" - - --data_path - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/H3K4me3/split - - --kmer - - "-1" - - --run_name - - hg38_BPE_base__baseline_bpe_tokenizer_3e-5_H3K4me3_seed42 - - --model_max_length - - "220" - - --per_device_train_batch_size - - "128" - - --per_device_eval_batch_size - - "128" - - --gradient_accumulation_steps - - "1" - - --learning_rate - - "3e-5" - - --num_train_epochs - - "2" - - --fp16 - - --save_steps - - "200" - - --output_dir - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K4me3 - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "546909577216" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:04:45.504860Z" - writerId: 13zvl8us4w5q9awnhtixdunxhhfs9f1g - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 41 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 41 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_040445-qeivjux7/files/output.log b/wandb/run-20260305_040445-qeivjux7/files/output.log deleted file mode 100644 index b5f9132702b494b30fe21ef3d5a9d9ed391eb551..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040445-qeivjux7/files/output.log +++ /dev/null @@ -1,37 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 diff --git a/wandb/run-20260305_040445-qeivjux7/files/requirements.txt b/wandb/run-20260305_040445-qeivjux7/files/requirements.txt deleted file mode 100644 index e3d9629db6fa5f00aab96101b087d1d57a440fb4..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040445-qeivjux7/files/requirements.txt +++ /dev/null @@ -1,90 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -idna==3.11 -pycparser==2.23 -triton==3.1.0 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -charset-normalizer==3.4.4 -wandb==0.25.0 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -accelerate==1.13.0 -torch==2.5.1 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -torchvision==0.20.1 -shellingham==1.5.4 -torchaudio==2.5.1 -sympy==1.13.1 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -click==8.3.1 -MarkupSafe==3.0.2 -urllib3==2.6.3 -propcache==0.4.1 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_040445-qeivjux7/files/wandb-metadata.json b/wandb/run-20260305_040445-qeivjux7/files/wandb-metadata.json deleted file mode 100644 index 97f5a3a6da640ac84bd0e7c05f020656c345242f..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040445-qeivjux7/files/wandb-metadata.json +++ /dev/null @@ -1,134 +0,0 @@ -{ - "os": "Linux-5.15.0-72-generic-x86_64-with-glibc2.35", - "python": "CPython 3.10.19", - "startedAt": "2026-03-05T04:04:45.504860Z", - "args": [ - "--model_name_or_path", - "/home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000", - "--tokenizer_path", - "/home/n5huang/dna_token/tokenizer_evaluation/baseline_bpe/tokenizer.json", - "--trust_remote_code", - "True", - "--data_path", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/H3K4me3/split", - "--kmer", - "-1", - "--run_name", - "hg38_BPE_base__baseline_bpe_tokenizer_3e-5_H3K4me3_seed42", - "--model_max_length", - "220", - "--per_device_train_batch_size", - "128", - "--per_device_eval_batch_size", - "128", - "--gradient_accumulation_steps", - "1", - "--learning_rate", - "3e-5", - "--num_train_epochs", - "2", - "--fp16", - "--save_steps", - "200", - "--output_dir", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K4me3", - "--evaluation_strategy", - "steps", - "--eval_steps", - "200", - "--warmup_steps", - "30", - "--logging_steps", - "100000", - "--log_level", - "info", - "--seed", - "42", - "--find_unused_parameters", - "False", - "--project_name", - "genomic_bench_tune_hg38_1024" - ], - "program": 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/home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 - - --tokenizer_path - - /home/n5huang/dna_token/tokenizer_evaluation/baseline_bpe/tokenizer.json - - --trust_remote_code - - "True" - - --data_path - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/H3K9ac/split - - --kmer - - "-1" - - --run_name - - hg38_BPE_base__baseline_bpe_tokenizer_3e-5_H3K9ac_seed42 - - --model_max_length - - "220" - - --per_device_train_batch_size - - "128" - - --per_device_eval_batch_size - - "128" - - --gradient_accumulation_steps - - "1" - - --learning_rate - - "3e-5" - - --num_train_epochs - - "2" - - --fp16 - - --save_steps - - "200" - - --output_dir - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K9ac - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "546909687808" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:04:59.228449Z" - writerId: pl1zfpg2pbci9f47uqj5s76h9tjpcul0 - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 41 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 41 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_040459-6nokzpzy/files/output.log b/wandb/run-20260305_040459-6nokzpzy/files/output.log deleted file mode 100644 index b5f9132702b494b30fe21ef3d5a9d9ed391eb551..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040459-6nokzpzy/files/output.log +++ /dev/null @@ -1,37 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 diff --git a/wandb/run-20260305_040459-6nokzpzy/files/requirements.txt b/wandb/run-20260305_040459-6nokzpzy/files/requirements.txt deleted file mode 100644 index e3d9629db6fa5f00aab96101b087d1d57a440fb4..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040459-6nokzpzy/files/requirements.txt +++ /dev/null @@ -1,90 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -idna==3.11 -pycparser==2.23 -triton==3.1.0 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -charset-normalizer==3.4.4 -wandb==0.25.0 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -accelerate==1.13.0 -torch==2.5.1 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -torchvision==0.20.1 -shellingham==1.5.4 -torchaudio==2.5.1 -sympy==1.13.1 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -click==8.3.1 -MarkupSafe==3.0.2 -urllib3==2.6.3 -propcache==0.4.1 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_040459-6nokzpzy/files/wandb-metadata.json b/wandb/run-20260305_040459-6nokzpzy/files/wandb-metadata.json deleted file mode 100644 index ac3e5e8526c370c9181f9b862100fd5f7005b2ee..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040459-6nokzpzy/files/wandb-metadata.json +++ /dev/null @@ -1,134 +0,0 @@ -{ - "os": "Linux-5.15.0-72-generic-x86_64-with-glibc2.35", - "python": "CPython 3.10.19", - "startedAt": "2026-03-05T04:04:59.228449Z", - "args": [ - "--model_name_or_path", - "/home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000", - "--tokenizer_path", - "/home/n5huang/dna_token/tokenizer_evaluation/baseline_bpe/tokenizer.json", - "--trust_remote_code", - "True", - "--data_path", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/H3K9ac/split", - "--kmer", - "-1", - "--run_name", - "hg38_BPE_base__baseline_bpe_tokenizer_3e-5_H3K9ac_seed42", - "--model_max_length", - "220", - "--per_device_train_batch_size", - "128", - "--per_device_eval_batch_size", - "128", - "--gradient_accumulation_steps", - "1", - "--learning_rate", - "3e-5", - "--num_train_epochs", - "2", - "--fp16", - "--save_steps", - "200", - "--output_dir", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K9ac", - "--evaluation_strategy", - "steps", - "--eval_steps", - "200", - "--warmup_steps", - "30", - "--logging_steps", - "100000", - "--log_level", - "info", - "--seed", - "42", - "--find_unused_parameters", - "False", - "--project_name", - "genomic_bench_tune_hg38_1024" - ], - "program": 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/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K9me3 - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "546909855744" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:05:13.919250Z" - writerId: 97pd3oaaqk9lo73bp6xky80unn8g9azr - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 41 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 41 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_040513-9zlpjo2z/files/output.log b/wandb/run-20260305_040513-9zlpjo2z/files/output.log deleted file mode 100644 index b5f9132702b494b30fe21ef3d5a9d9ed391eb551..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040513-9zlpjo2z/files/output.log +++ /dev/null @@ -1,37 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 diff --git a/wandb/run-20260305_040513-9zlpjo2z/files/requirements.txt b/wandb/run-20260305_040513-9zlpjo2z/files/requirements.txt deleted file mode 100644 index e3d9629db6fa5f00aab96101b087d1d57a440fb4..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040513-9zlpjo2z/files/requirements.txt +++ /dev/null @@ -1,90 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -idna==3.11 -pycparser==2.23 -triton==3.1.0 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -charset-normalizer==3.4.4 -wandb==0.25.0 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -accelerate==1.13.0 -torch==2.5.1 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -torchvision==0.20.1 -shellingham==1.5.4 -torchaudio==2.5.1 -sympy==1.13.1 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -click==8.3.1 -MarkupSafe==3.0.2 -urllib3==2.6.3 -propcache==0.4.1 -regex==2026.2.28 -xxhash==3.6.0 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GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:05:29.093579Z" - writerId: rvj6k13xrkzgke225e5x20ilcbnmehkg - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 41 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 41 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_040529-fw8gr6da/files/output.log b/wandb/run-20260305_040529-fw8gr6da/files/output.log deleted file mode 100644 index b5f9132702b494b30fe21ef3d5a9d9ed391eb551..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040529-fw8gr6da/files/output.log +++ /dev/null @@ -1,37 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 diff --git a/wandb/run-20260305_040529-fw8gr6da/files/requirements.txt b/wandb/run-20260305_040529-fw8gr6da/files/requirements.txt deleted file mode 100644 index e3d9629db6fa5f00aab96101b087d1d57a440fb4..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040529-fw8gr6da/files/requirements.txt +++ /dev/null @@ -1,90 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -idna==3.11 -pycparser==2.23 -triton==3.1.0 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -charset-normalizer==3.4.4 -wandb==0.25.0 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -accelerate==1.13.0 -torch==2.5.1 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -torchvision==0.20.1 -shellingham==1.5.4 -torchaudio==2.5.1 -sympy==1.13.1 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -click==8.3.1 -MarkupSafe==3.0.2 -urllib3==2.6.3 -propcache==0.4.1 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_040529-fw8gr6da/files/wandb-metadata.json b/wandb/run-20260305_040529-fw8gr6da/files/wandb-metadata.json deleted file mode 100644 index 611dcb1a5de6f3b0b2178361d6fc7306b4062375..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040529-fw8gr6da/files/wandb-metadata.json +++ /dev/null @@ -1,134 +0,0 @@ -{ - "os": "Linux-5.15.0-72-generic-x86_64-with-glibc2.35", - "python": "CPython 3.10.19", - "startedAt": "2026-03-05T04:05:29.093579Z", - "args": [ - "--model_name_or_path", - "/home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000", - "--tokenizer_path", - "/home/n5huang/dna_token/tokenizer_evaluation/baseline_bpe/tokenizer.json", - "--trust_remote_code", - "True", - "--data_path", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/H4K20me1/split", - "--kmer", - "-1", - "--run_name", - "hg38_BPE_base__baseline_bpe_tokenizer_3e-5_H4K20me1_seed42", - "--model_max_length", - "220", - "--per_device_train_batch_size", - "128", - "--per_device_eval_batch_size", - "128", - "--gradient_accumulation_steps", - "1", - "--learning_rate", - "3e-5", - "--num_train_epochs", - "2", - "--fp16", - "--save_steps", - "200", - "--output_dir", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H4K20me1", - "--evaluation_strategy", - "steps", - "--eval_steps", - "200", - "--warmup_steps", - "30", - "--logging_steps", - "100000", - "--log_level", - "info", - "--seed", - "42", - "--find_unused_parameters", - "False", - "--project_name", - "genomic_bench_tune_hg38_1024" - ], - "program": 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a/wandb/run-20260305_040545-u9m8i2ye/files/config.yaml +++ /dev/null @@ -1,141 +0,0 @@ -_wandb: - value: - cli_version: 0.25.0 - e: - av3tqu9s9mspsn3jit9j4kuk1r2fhoa0: - args: - - --model_name_or_path - - /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 - - --tokenizer_path - - /home/n5huang/dna_token/tokenizer_evaluation/merge_bpe/merge_tokenizer_unigram_len.json - - --trust_remote_code - - "True" - - --data_path - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/enhancers/split - - --kmer - - "-1" - - --run_name - - hg38_BPE_base__merge_bpe_merge_tokenizer_unigram_len_3e-5_enhancers_seed42 - - --model_max_length - - "100" - - --per_device_train_batch_size - - "128" - - --per_device_eval_batch_size - - "128" - - --gradient_accumulation_steps - - "1" - - --learning_rate - - "3e-5" - - --num_train_epochs - - "4" - - --fp16 - - --save_steps - - "200" - - --output_dir - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_len/enhancers - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "546912059392" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:05:45.101059Z" - writerId: av3tqu9s9mspsn3jit9j4kuk1r2fhoa0 - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 41 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 41 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_040545-u9m8i2ye/files/output.log b/wandb/run-20260305_040545-u9m8i2ye/files/output.log deleted file mode 100644 index b5f9132702b494b30fe21ef3d5a9d9ed391eb551..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040545-u9m8i2ye/files/output.log +++ /dev/null @@ -1,37 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 diff --git a/wandb/run-20260305_040545-u9m8i2ye/files/requirements.txt b/wandb/run-20260305_040545-u9m8i2ye/files/requirements.txt deleted file mode 100644 index e3d9629db6fa5f00aab96101b087d1d57a440fb4..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040545-u9m8i2ye/files/requirements.txt +++ /dev/null @@ -1,90 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -idna==3.11 -pycparser==2.23 -triton==3.1.0 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -charset-normalizer==3.4.4 -wandb==0.25.0 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -accelerate==1.13.0 -torch==2.5.1 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -torchvision==0.20.1 -shellingham==1.5.4 -torchaudio==2.5.1 -sympy==1.13.1 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -click==8.3.1 -MarkupSafe==3.0.2 -urllib3==2.6.3 -propcache==0.4.1 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_040545-u9m8i2ye/files/wandb-metadata.json b/wandb/run-20260305_040545-u9m8i2ye/files/wandb-metadata.json deleted file mode 100644 index 4724fa81cc074a09986396d72dc90c0bfa54130a..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040545-u9m8i2ye/files/wandb-metadata.json +++ /dev/null @@ -1,134 +0,0 @@ -{ - "os": "Linux-5.15.0-72-generic-x86_64-with-glibc2.35", - "python": "CPython 3.10.19", - "startedAt": "2026-03-05T04:05:45.101059Z", - "args": [ - "--model_name_or_path", - "/home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000", - "--tokenizer_path", - "/home/n5huang/dna_token/tokenizer_evaluation/merge_bpe/merge_tokenizer_unigram_len.json", - "--trust_remote_code", - "True", - "--data_path", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/enhancers/split", - "--kmer", - "-1", - "--run_name", - "hg38_BPE_base__merge_bpe_merge_tokenizer_unigram_len_3e-5_enhancers_seed42", - "--model_max_length", - "100", - "--per_device_train_batch_size", - "128", - "--per_device_eval_batch_size", - "128", - "--gradient_accumulation_steps", - "1", - "--learning_rate", - "3e-5", - "--num_train_epochs", - "4", - "--fp16", - "--save_steps", - "200", - "--output_dir", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_len/enhancers", - "--evaluation_strategy", - "steps", - "--eval_steps", - "200", - "--warmup_steps", - "30", - "--logging_steps", - "100000", - "--log_level", - "info", - "--seed", - "42", - "--find_unused_parameters", - "False", - "--project_name", - "genomic_bench_tune_hg38_1024" - ], - "program": 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--log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "546912178176" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:05:58.293515Z" - writerId: btealcw3gko6fqlar9j78vcci2mpw3wx - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 41 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 41 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_040558-ts7j0jsy/files/output.log b/wandb/run-20260305_040558-ts7j0jsy/files/output.log deleted file mode 100644 index b5f9132702b494b30fe21ef3d5a9d9ed391eb551..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040558-ts7j0jsy/files/output.log +++ /dev/null @@ -1,37 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 diff --git a/wandb/run-20260305_040558-ts7j0jsy/files/requirements.txt b/wandb/run-20260305_040558-ts7j0jsy/files/requirements.txt deleted file mode 100644 index e3d9629db6fa5f00aab96101b087d1d57a440fb4..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040558-ts7j0jsy/files/requirements.txt +++ /dev/null @@ -1,90 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -idna==3.11 -pycparser==2.23 -triton==3.1.0 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -charset-normalizer==3.4.4 -wandb==0.25.0 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -accelerate==1.13.0 -torch==2.5.1 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -torchvision==0.20.1 -shellingham==1.5.4 -torchaudio==2.5.1 -sympy==1.13.1 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -click==8.3.1 -MarkupSafe==3.0.2 -urllib3==2.6.3 -propcache==0.4.1 -regex==2026.2.28 -xxhash==3.6.0 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"/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/enhancers_types/split", - "--kmer", - "-1", - "--run_name", - "hg38_BPE_base__merge_bpe_merge_tokenizer_unigram_len_3e-5_enhancers_types_seed42", - "--model_max_length", - "100", - "--per_device_train_batch_size", - "128", - "--per_device_eval_batch_size", - "128", - "--gradient_accumulation_steps", - "1", - "--learning_rate", - "3e-5", - "--num_train_epochs", - "4", - "--fp16", - "--save_steps", - "200", - "--output_dir", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_len/enhancers_types", - "--evaluation_strategy", - "steps", - "--eval_steps", - "200", - "--warmup_steps", - "30", - "--logging_steps", - "100000", - "--log_level", - "info", - "--seed", - "42", - "--find_unused_parameters", - "False", - "--project_name", - "genomic_bench_tune_hg38_1024" - 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--eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "546912309248" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:06:12.327160Z" - writerId: ot7l1k2f0vwbgr03jct88by3426v4nmj - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 41 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 41 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_040612-zhxwwq3h/files/output.log b/wandb/run-20260305_040612-zhxwwq3h/files/output.log deleted file mode 100644 index b5f9132702b494b30fe21ef3d5a9d9ed391eb551..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040612-zhxwwq3h/files/output.log +++ /dev/null @@ -1,37 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 diff --git a/wandb/run-20260305_040612-zhxwwq3h/files/requirements.txt b/wandb/run-20260305_040612-zhxwwq3h/files/requirements.txt deleted file mode 100644 index e3d9629db6fa5f00aab96101b087d1d57a440fb4..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040612-zhxwwq3h/files/requirements.txt +++ /dev/null @@ -1,90 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -idna==3.11 -pycparser==2.23 -triton==3.1.0 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -charset-normalizer==3.4.4 -wandb==0.25.0 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -accelerate==1.13.0 -torch==2.5.1 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -torchvision==0.20.1 -shellingham==1.5.4 -torchaudio==2.5.1 -sympy==1.13.1 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -click==8.3.1 -MarkupSafe==3.0.2 -urllib3==2.6.3 -propcache==0.4.1 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_040612-zhxwwq3h/files/wandb-metadata.json b/wandb/run-20260305_040612-zhxwwq3h/files/wandb-metadata.json deleted file mode 100644 index 422bae9406975bf46d51edeafe5bf7d5d929f521..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040612-zhxwwq3h/files/wandb-metadata.json +++ /dev/null @@ -1,134 +0,0 @@ -{ - "os": "Linux-5.15.0-72-generic-x86_64-with-glibc2.35", - "python": "CPython 3.10.19", - "startedAt": "2026-03-05T04:06:12.327160Z", - "args": [ - "--model_name_or_path", - "/home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000", - "--tokenizer_path", - "/home/n5huang/dna_token/tokenizer_evaluation/merge_bpe/merge_tokenizer_unigram_len.json", - "--trust_remote_code", - "True", - "--data_path", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/promoter_all/split", - "--kmer", - "-1", - "--run_name", - "hg38_BPE_base__merge_bpe_merge_tokenizer_unigram_len_3e-5_promoter_all_seed42", - "--model_max_length", - "80", - "--per_device_train_batch_size", - "128", - "--per_device_eval_batch_size", - "128", - "--gradient_accumulation_steps", - "1", - "--learning_rate", - "3e-5", - "--num_train_epochs", - "2", - "--fp16", - "--save_steps", - "200", - "--output_dir", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_len/promoter_all", - "--evaluation_strategy", - "steps", - "--eval_steps", - "200", - "--warmup_steps", - "30", - "--logging_steps", - "100000", - "--log_level", - "info", - "--seed", - "42", - "--find_unused_parameters", - "False", - "--project_name", - "genomic_bench_tune_hg38_1024" - ], - 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steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "546912436224" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:06:25.226308Z" - writerId: yx02zlyibrhwjgpd21xvfcrpj3j08kwq - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 41 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 41 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_040625-fqulm281/files/output.log b/wandb/run-20260305_040625-fqulm281/files/output.log deleted file mode 100644 index b5f9132702b494b30fe21ef3d5a9d9ed391eb551..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040625-fqulm281/files/output.log +++ /dev/null @@ -1,37 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 diff --git a/wandb/run-20260305_040625-fqulm281/files/requirements.txt b/wandb/run-20260305_040625-fqulm281/files/requirements.txt deleted file mode 100644 index e3d9629db6fa5f00aab96101b087d1d57a440fb4..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040625-fqulm281/files/requirements.txt +++ /dev/null @@ -1,90 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -idna==3.11 -pycparser==2.23 -triton==3.1.0 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -charset-normalizer==3.4.4 -wandb==0.25.0 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -accelerate==1.13.0 -torch==2.5.1 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -torchvision==0.20.1 -shellingham==1.5.4 -torchaudio==2.5.1 -sympy==1.13.1 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -click==8.3.1 -MarkupSafe==3.0.2 -urllib3==2.6.3 -propcache==0.4.1 -regex==2026.2.28 -xxhash==3.6.0 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/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:06:37.521061Z" - writerId: 2y177ybewjkd3hj8nadxto7rxxuywoab - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 41 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 41 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_040637-k6rg2dq5/files/output.log b/wandb/run-20260305_040637-k6rg2dq5/files/output.log deleted file mode 100644 index b5f9132702b494b30fe21ef3d5a9d9ed391eb551..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040637-k6rg2dq5/files/output.log +++ /dev/null @@ -1,37 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 diff --git a/wandb/run-20260305_040637-k6rg2dq5/files/requirements.txt b/wandb/run-20260305_040637-k6rg2dq5/files/requirements.txt deleted file mode 100644 index e3d9629db6fa5f00aab96101b087d1d57a440fb4..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040637-k6rg2dq5/files/requirements.txt +++ /dev/null @@ -1,90 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -idna==3.11 -pycparser==2.23 -triton==3.1.0 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -charset-normalizer==3.4.4 -wandb==0.25.0 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -accelerate==1.13.0 -torch==2.5.1 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -torchvision==0.20.1 -shellingham==1.5.4 -torchaudio==2.5.1 -sympy==1.13.1 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -click==8.3.1 -MarkupSafe==3.0.2 -urllib3==2.6.3 -propcache==0.4.1 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_040637-k6rg2dq5/files/wandb-metadata.json b/wandb/run-20260305_040637-k6rg2dq5/files/wandb-metadata.json deleted file mode 100644 index 2afff8a3c4d9d4b7eb9fcd3eb622a311b3fe01af..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040637-k6rg2dq5/files/wandb-metadata.json +++ /dev/null @@ -1,134 +0,0 @@ -{ - "os": "Linux-5.15.0-72-generic-x86_64-with-glibc2.35", - "python": "CPython 3.10.19", - "startedAt": "2026-03-05T04:06:37.521061Z", - "args": [ - "--model_name_or_path", - "/home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000", - "--tokenizer_path", - "/home/n5huang/dna_token/tokenizer_evaluation/merge_bpe/merge_tokenizer_unigram_len.json", - "--trust_remote_code", - "True", - "--data_path", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/promoter_tata/split", - "--kmer", - "-1", - "--run_name", - "hg38_BPE_base__merge_bpe_merge_tokenizer_unigram_len_3e-5_promoter_tata_seed42", - "--model_max_length", - "80", - "--per_device_train_batch_size", - "128", - "--per_device_eval_batch_size", - "128", - "--gradient_accumulation_steps", - "1", - "--learning_rate", - "3e-5", - "--num_train_epochs", - "2", - "--fp16", - "--save_steps", - "200", - "--output_dir", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_len/promoter_tata", - "--evaluation_strategy", - "steps", - "--eval_steps", - "200", - "--warmup_steps", - "30", - "--logging_steps", - "100000", - "--log_level", - "info", - "--seed", - "42", - "--find_unused_parameters", - "False", - "--project_name", - "genomic_bench_tune_hg38_1024" - ], - 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wandb-AsyncioManager-main:1030901 [service_client.py:_forward_responses():134] Reached EOF. -2026-03-05 04:06:39,273 INFO wandb-AsyncioManager-main:1030901 [mailbox.py:close():155] Closing mailbox, abandoning 1 handles. diff --git a/wandb/run-20260305_040637-k6rg2dq5/run-k6rg2dq5.wandb b/wandb/run-20260305_040637-k6rg2dq5/run-k6rg2dq5.wandb deleted file mode 100644 index 7ab29a56c77151760cdacda0ffb19642b75b203c..0000000000000000000000000000000000000000 Binary files a/wandb/run-20260305_040637-k6rg2dq5/run-k6rg2dq5.wandb and /dev/null differ diff --git a/wandb/run-20260305_040647-dxyhawns/files/config.yaml b/wandb/run-20260305_040647-dxyhawns/files/config.yaml deleted file mode 100644 index 19702f5ab6149eeb61c9ead05a691b2d99e092b3..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040647-dxyhawns/files/config.yaml +++ /dev/null @@ -1,141 +0,0 @@ -_wandb: - value: - cli_version: 0.25.0 - e: - devx5yqs86vwjxmxlriwojdrak1lpwfz: - args: - - --model_name_or_path - - /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 - - --tokenizer_path - - /home/n5huang/dna_token/tokenizer_evaluation/merge_bpe/merge_tokenizer_unigram_len.json - - --trust_remote_code - - "True" - - --data_path - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/splice_sites_acceptors/split - - --kmer - - "-1" - - --run_name - - hg38_BPE_base__merge_bpe_merge_tokenizer_unigram_len_3e-5_splice_sites_acceptors_seed42 - - --model_max_length - - "140" - - --per_device_train_batch_size - - "128" - - --per_device_eval_batch_size - - "128" - - --gradient_accumulation_steps - - "1" - - --learning_rate - - "3e-5" - - --num_train_epochs - - "4" - - --fp16 - - --save_steps - - "200" - - --output_dir - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_len/splice_sites_acceptors - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "546914598912" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:06:47.732595Z" - writerId: devx5yqs86vwjxmxlriwojdrak1lpwfz - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 41 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 41 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_040647-dxyhawns/files/output.log b/wandb/run-20260305_040647-dxyhawns/files/output.log deleted file mode 100644 index b5f9132702b494b30fe21ef3d5a9d9ed391eb551..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040647-dxyhawns/files/output.log +++ /dev/null @@ -1,37 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 diff --git a/wandb/run-20260305_040647-dxyhawns/files/requirements.txt b/wandb/run-20260305_040647-dxyhawns/files/requirements.txt deleted file mode 100644 index e3d9629db6fa5f00aab96101b087d1d57a440fb4..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040647-dxyhawns/files/requirements.txt +++ /dev/null @@ -1,90 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -idna==3.11 -pycparser==2.23 -triton==3.1.0 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -charset-normalizer==3.4.4 -wandb==0.25.0 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -accelerate==1.13.0 -torch==2.5.1 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -torchvision==0.20.1 -shellingham==1.5.4 -torchaudio==2.5.1 -sympy==1.13.1 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -click==8.3.1 -MarkupSafe==3.0.2 -urllib3==2.6.3 -propcache==0.4.1 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_040647-dxyhawns/files/wandb-metadata.json b/wandb/run-20260305_040647-dxyhawns/files/wandb-metadata.json deleted file mode 100644 index 63c07da429e557dd4a95087d30dd967ecf6c95a7..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040647-dxyhawns/files/wandb-metadata.json +++ /dev/null @@ -1,134 +0,0 @@ -{ - "os": "Linux-5.15.0-72-generic-x86_64-with-glibc2.35", - "python": "CPython 3.10.19", - "startedAt": "2026-03-05T04:06:47.732595Z", - "args": [ - "--model_name_or_path", - "/home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000", - "--tokenizer_path", - "/home/n5huang/dna_token/tokenizer_evaluation/merge_bpe/merge_tokenizer_unigram_len.json", - "--trust_remote_code", - "True", - "--data_path", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/splice_sites_acceptors/split", - "--kmer", - "-1", - "--run_name", - "hg38_BPE_base__merge_bpe_merge_tokenizer_unigram_len_3e-5_splice_sites_acceptors_seed42", - "--model_max_length", - "140", - "--per_device_train_batch_size", - "128", - "--per_device_eval_batch_size", - "128", - "--gradient_accumulation_steps", - "1", - "--learning_rate", - "3e-5", - "--num_train_epochs", - "4", - "--fp16", - "--save_steps", - "200", - "--output_dir", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_len/splice_sites_acceptors", - "--evaluation_strategy", - "steps", - "--eval_steps", - "200", - "--warmup_steps", - "30", - "--logging_steps", - "100000", - "--log_level", - "info", - "--seed", - "42", - "--find_unused_parameters", - "False", - "--project_name", - 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a/wandb/run-20260305_040702-8vkcu9i5/files/config.yaml +++ /dev/null @@ -1,141 +0,0 @@ -_wandb: - value: - cli_version: 0.25.0 - e: - edqxebt7cp7f3b138spaj0nyedgafp2h: - args: - - --model_name_or_path - - /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 - - --tokenizer_path - - /home/n5huang/dna_token/tokenizer_evaluation/merge_bpe/merge_tokenizer_unigram_len.json - - --trust_remote_code - - "True" - - --data_path - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/splice_sites_all/split - - --kmer - - "-1" - - --run_name - - hg38_BPE_base__merge_bpe_merge_tokenizer_unigram_len_3e-5_splice_sites_all_seed42 - - --model_max_length - - "140" - - --per_device_train_batch_size - - "128" - - --per_device_eval_batch_size - - "128" - - --gradient_accumulation_steps - - "1" - - --learning_rate - - "3e-5" - - --num_train_epochs - - "4" - - --fp16 - - --save_steps - - "200" - - --output_dir - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_len/splice_sites_all - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "546914713600" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:07:02.249274Z" - writerId: edqxebt7cp7f3b138spaj0nyedgafp2h - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 41 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 41 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_040702-8vkcu9i5/files/output.log b/wandb/run-20260305_040702-8vkcu9i5/files/output.log deleted file mode 100644 index b5f9132702b494b30fe21ef3d5a9d9ed391eb551..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040702-8vkcu9i5/files/output.log +++ /dev/null @@ -1,37 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 diff --git a/wandb/run-20260305_040702-8vkcu9i5/files/requirements.txt b/wandb/run-20260305_040702-8vkcu9i5/files/requirements.txt deleted file mode 100644 index e3d9629db6fa5f00aab96101b087d1d57a440fb4..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040702-8vkcu9i5/files/requirements.txt +++ /dev/null @@ -1,90 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -idna==3.11 -pycparser==2.23 -triton==3.1.0 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -charset-normalizer==3.4.4 -wandb==0.25.0 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -accelerate==1.13.0 -torch==2.5.1 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -torchvision==0.20.1 -shellingham==1.5.4 -torchaudio==2.5.1 -sympy==1.13.1 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -click==8.3.1 -MarkupSafe==3.0.2 -urllib3==2.6.3 -propcache==0.4.1 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_040702-8vkcu9i5/files/wandb-metadata.json b/wandb/run-20260305_040702-8vkcu9i5/files/wandb-metadata.json deleted file mode 100644 index 8054e855d0651d39e6df0f6091e90fd2d2f3645c..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040702-8vkcu9i5/files/wandb-metadata.json +++ /dev/null @@ -1,134 +0,0 @@ -{ - "os": "Linux-5.15.0-72-generic-x86_64-with-glibc2.35", - "python": "CPython 3.10.19", - "startedAt": "2026-03-05T04:07:02.249274Z", - "args": [ - "--model_name_or_path", - "/home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000", - "--tokenizer_path", - "/home/n5huang/dna_token/tokenizer_evaluation/merge_bpe/merge_tokenizer_unigram_len.json", - "--trust_remote_code", - "True", - "--data_path", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/splice_sites_all/split", - "--kmer", - "-1", - "--run_name", - "hg38_BPE_base__merge_bpe_merge_tokenizer_unigram_len_3e-5_splice_sites_all_seed42", - "--model_max_length", - "140", - "--per_device_train_batch_size", - "128", - "--per_device_eval_batch_size", - "128", - "--gradient_accumulation_steps", - "1", - "--learning_rate", - "3e-5", - "--num_train_epochs", - "4", - "--fp16", - "--save_steps", - "200", - "--output_dir", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_len/splice_sites_all", - "--evaluation_strategy", - "steps", - "--eval_steps", - "200", - "--warmup_steps", - "30", - "--logging_steps", - "100000", - "--log_level", - "info", - "--seed", - "42", - "--find_unused_parameters", - "False", - "--project_name", - "genomic_bench_tune_hg38_1024" 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a/wandb/run-20260305_040716-7yorswna/files/config.yaml +++ /dev/null @@ -1,141 +0,0 @@ -_wandb: - value: - cli_version: 0.25.0 - e: - s78dhkfvhhyz777mteqbzzp9oqtgzj28: - args: - - --model_name_or_path - - /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 - - --tokenizer_path - - /home/n5huang/dna_token/tokenizer_evaluation/merge_bpe/merge_tokenizer_unigram_len.json - - --trust_remote_code - - "True" - - --data_path - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/splice_sites_donors/split - - --kmer - - "-1" - - --run_name - - hg38_BPE_base__merge_bpe_merge_tokenizer_unigram_len_3e-5_splice_sites_donors_seed42 - - --model_max_length - - "140" - - --per_device_train_batch_size - - "128" - - --per_device_eval_batch_size - - "128" - - --gradient_accumulation_steps - - "1" - - --learning_rate - - "3e-5" - - --num_train_epochs - - "4" - - --fp16 - - --save_steps - - "200" - - --output_dir - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_len/splice_sites_donors - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "546914881536" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:07:16.601911Z" - writerId: s78dhkfvhhyz777mteqbzzp9oqtgzj28 - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 41 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 41 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_040716-7yorswna/files/output.log b/wandb/run-20260305_040716-7yorswna/files/output.log deleted file mode 100644 index b5f9132702b494b30fe21ef3d5a9d9ed391eb551..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040716-7yorswna/files/output.log +++ /dev/null @@ -1,37 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 diff --git a/wandb/run-20260305_040716-7yorswna/files/requirements.txt b/wandb/run-20260305_040716-7yorswna/files/requirements.txt deleted file mode 100644 index e3d9629db6fa5f00aab96101b087d1d57a440fb4..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040716-7yorswna/files/requirements.txt +++ /dev/null @@ -1,90 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -idna==3.11 -pycparser==2.23 -triton==3.1.0 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -charset-normalizer==3.4.4 -wandb==0.25.0 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -accelerate==1.13.0 -torch==2.5.1 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -torchvision==0.20.1 -shellingham==1.5.4 -torchaudio==2.5.1 -sympy==1.13.1 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -click==8.3.1 -MarkupSafe==3.0.2 -urllib3==2.6.3 -propcache==0.4.1 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_040716-7yorswna/files/wandb-metadata.json b/wandb/run-20260305_040716-7yorswna/files/wandb-metadata.json deleted file mode 100644 index bd9185fc6363a7c6befabb8abe4547bce31b0b19..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040716-7yorswna/files/wandb-metadata.json +++ /dev/null @@ -1,134 +0,0 @@ -{ - "os": "Linux-5.15.0-72-generic-x86_64-with-glibc2.35", - "python": "CPython 3.10.19", - "startedAt": "2026-03-05T04:07:16.601911Z", - "args": [ - "--model_name_or_path", - "/home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000", - "--tokenizer_path", - "/home/n5huang/dna_token/tokenizer_evaluation/merge_bpe/merge_tokenizer_unigram_len.json", - "--trust_remote_code", - "True", - "--data_path", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/splice_sites_donors/split", - "--kmer", - "-1", - "--run_name", - "hg38_BPE_base__merge_bpe_merge_tokenizer_unigram_len_3e-5_splice_sites_donors_seed42", - "--model_max_length", - "140", - "--per_device_train_batch_size", - "128", - "--per_device_eval_batch_size", - "128", - "--gradient_accumulation_steps", - "1", - "--learning_rate", - "3e-5", - "--num_train_epochs", - "4", - "--fp16", - "--save_steps", - "200", - "--output_dir", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_len/splice_sites_donors", - "--evaluation_strategy", - "steps", - "--eval_steps", - "200", - "--warmup_steps", - "30", - "--logging_steps", - "100000", - "--log_level", - "info", - "--seed", - "42", - "--find_unused_parameters", - "False", - "--project_name", - 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/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "546914926592" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:07:27.114707Z" - writerId: nqisqyzv1kihadoh2jlr56eg08s9i29r - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 41 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 41 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_040727-oujgs2el/files/output.log b/wandb/run-20260305_040727-oujgs2el/files/output.log deleted file mode 100644 index b5f9132702b494b30fe21ef3d5a9d9ed391eb551..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040727-oujgs2el/files/output.log +++ /dev/null @@ -1,37 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 diff --git a/wandb/run-20260305_040727-oujgs2el/files/requirements.txt b/wandb/run-20260305_040727-oujgs2el/files/requirements.txt deleted file mode 100644 index e3d9629db6fa5f00aab96101b087d1d57a440fb4..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040727-oujgs2el/files/requirements.txt +++ /dev/null @@ -1,90 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -idna==3.11 -pycparser==2.23 -triton==3.1.0 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -charset-normalizer==3.4.4 -wandb==0.25.0 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -accelerate==1.13.0 -torch==2.5.1 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -torchvision==0.20.1 -shellingham==1.5.4 -torchaudio==2.5.1 -sympy==1.13.1 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -click==8.3.1 -MarkupSafe==3.0.2 -urllib3==2.6.3 -propcache==0.4.1 -regex==2026.2.28 -xxhash==3.6.0 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"/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/enhancers/split", - "--kmer", - "-1", - "--run_name", - "hg38_BPE_base__baseline_bpe_tokenizer_3e-5_enhancers_seed42", - "--model_max_length", - "100", - "--per_device_train_batch_size", - "128", - "--per_device_eval_batch_size", - "128", - "--gradient_accumulation_steps", - "1", - "--learning_rate", - "3e-5", - "--num_train_epochs", - "4", - "--fp16", - "--save_steps", - "200", - "--output_dir", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers", - "--evaluation_strategy", - "steps", - "--eval_steps", - "200", - "--warmup_steps", - "30", - "--logging_steps", - "100000", - "--log_level", - "info", - "--seed", - "42", - "--find_unused_parameters", - "False", - "--project_name", - "genomic_bench_tune_hg38_1024" - ], - "program": 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--warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "546916950016" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:07:39.730040Z" - writerId: h2rtxhj6nh7a0c8cq3qeg9xmts26n6da - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 41 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 41 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_040739-5x72h4h4/files/output.log b/wandb/run-20260305_040739-5x72h4h4/files/output.log deleted file mode 100644 index b5f9132702b494b30fe21ef3d5a9d9ed391eb551..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040739-5x72h4h4/files/output.log +++ /dev/null @@ -1,37 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 diff --git a/wandb/run-20260305_040739-5x72h4h4/files/requirements.txt b/wandb/run-20260305_040739-5x72h4h4/files/requirements.txt deleted file mode 100644 index e3d9629db6fa5f00aab96101b087d1d57a440fb4..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040739-5x72h4h4/files/requirements.txt +++ /dev/null @@ -1,90 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -idna==3.11 -pycparser==2.23 -triton==3.1.0 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -charset-normalizer==3.4.4 -wandb==0.25.0 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -accelerate==1.13.0 -torch==2.5.1 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -torchvision==0.20.1 -shellingham==1.5.4 -torchaudio==2.5.1 -sympy==1.13.1 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -click==8.3.1 -MarkupSafe==3.0.2 -urllib3==2.6.3 -propcache==0.4.1 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_040739-5x72h4h4/files/wandb-metadata.json b/wandb/run-20260305_040739-5x72h4h4/files/wandb-metadata.json deleted file mode 100644 index 17597cd53ecbef35d08a5dc1f9f160d86f6c4403..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040739-5x72h4h4/files/wandb-metadata.json +++ /dev/null @@ -1,134 +0,0 @@ -{ - "os": "Linux-5.15.0-72-generic-x86_64-with-glibc2.35", - "python": "CPython 3.10.19", - "startedAt": "2026-03-05T04:07:39.730040Z", - "args": [ - "--model_name_or_path", - "/home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000", - "--tokenizer_path", - "/home/n5huang/dna_token/tokenizer_evaluation/baseline_bpe/tokenizer.json", - "--trust_remote_code", - "True", - "--data_path", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/enhancers_types/split", - "--kmer", - "-1", - "--run_name", - "hg38_BPE_base__baseline_bpe_tokenizer_3e-5_enhancers_types_seed42", - "--model_max_length", - "100", - "--per_device_train_batch_size", - "128", - "--per_device_eval_batch_size", - "128", - "--gradient_accumulation_steps", - "1", - "--learning_rate", - "3e-5", - "--num_train_epochs", - "4", - "--fp16", - "--save_steps", - "200", - "--output_dir", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers_types", - "--evaluation_strategy", - "steps", - "--eval_steps", - "200", - "--warmup_steps", - "30", - "--logging_steps", - "100000", - "--log_level", - "info", - "--seed", - "42", - "--find_unused_parameters", - "False", - "--project_name", - "genomic_bench_tune_hg38_1024" - ], - "program": 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/home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 - - --tokenizer_path - - /home/n5huang/dna_token/tokenizer_evaluation/baseline_bpe/tokenizer.json - - --trust_remote_code - - "True" - - --data_path - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/promoter_all/split - - --kmer - - "-1" - - --run_name - - hg38_BPE_base__baseline_bpe_tokenizer_3e-5_promoter_all_seed42 - - --model_max_length - - "80" - - --per_device_train_batch_size - - "128" - - --per_device_eval_batch_size - - "128" - - --gradient_accumulation_steps - - "1" - - --learning_rate - - "3e-5" - - --num_train_epochs - - "2" - - --fp16 - - --save_steps - - "200" - - --output_dir - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/promoter_all - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "546917056512" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:07:52.586034Z" - writerId: r2gvx46n33bxaa5ct2yw2bkodco27r5v - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 41 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 41 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_040752-oaf56rxq/files/output.log b/wandb/run-20260305_040752-oaf56rxq/files/output.log deleted file mode 100644 index b5f9132702b494b30fe21ef3d5a9d9ed391eb551..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040752-oaf56rxq/files/output.log +++ /dev/null @@ -1,37 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 diff --git a/wandb/run-20260305_040752-oaf56rxq/files/requirements.txt b/wandb/run-20260305_040752-oaf56rxq/files/requirements.txt deleted file mode 100644 index e3d9629db6fa5f00aab96101b087d1d57a440fb4..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040752-oaf56rxq/files/requirements.txt +++ /dev/null @@ -1,90 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -idna==3.11 -pycparser==2.23 -triton==3.1.0 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -charset-normalizer==3.4.4 -wandb==0.25.0 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -accelerate==1.13.0 -torch==2.5.1 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -torchvision==0.20.1 -shellingham==1.5.4 -torchaudio==2.5.1 -sympy==1.13.1 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -click==8.3.1 -MarkupSafe==3.0.2 -urllib3==2.6.3 -propcache==0.4.1 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_040752-oaf56rxq/files/wandb-metadata.json b/wandb/run-20260305_040752-oaf56rxq/files/wandb-metadata.json deleted file mode 100644 index 064cf030891197e325fc622e94dc76a3399837bd..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040752-oaf56rxq/files/wandb-metadata.json +++ /dev/null @@ -1,134 +0,0 @@ -{ - "os": "Linux-5.15.0-72-generic-x86_64-with-glibc2.35", - "python": "CPython 3.10.19", - "startedAt": "2026-03-05T04:07:52.586034Z", - "args": [ - "--model_name_or_path", - "/home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000", - "--tokenizer_path", - "/home/n5huang/dna_token/tokenizer_evaluation/baseline_bpe/tokenizer.json", - "--trust_remote_code", - "True", - "--data_path", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/promoter_all/split", - "--kmer", - "-1", - "--run_name", - "hg38_BPE_base__baseline_bpe_tokenizer_3e-5_promoter_all_seed42", - "--model_max_length", - "80", - "--per_device_train_batch_size", - "128", - "--per_device_eval_batch_size", - "128", - "--gradient_accumulation_steps", - "1", - "--learning_rate", - "3e-5", - "--num_train_epochs", - "2", - "--fp16", - "--save_steps", - "200", - "--output_dir", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/promoter_all", - "--evaluation_strategy", - "steps", - "--eval_steps", - "200", - "--warmup_steps", - "30", - "--logging_steps", - "100000", - "--log_level", - "info", - "--seed", - "42", - "--find_unused_parameters", - "False", - "--project_name", - "genomic_bench_tune_hg38_1024" - ], - "program": 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/home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 - - --tokenizer_path - - /home/n5huang/dna_token/tokenizer_evaluation/baseline_bpe/tokenizer.json - - --trust_remote_code - - "True" - - --data_path - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/promoter_no_tata/split - - --kmer - - "-1" - - --run_name - - hg38_BPE_base__baseline_bpe_tokenizer_3e-5_promoter_no_tata_seed42 - - --model_max_length - - "80" - - --per_device_train_batch_size - - "128" - - --per_device_eval_batch_size - - "128" - - --gradient_accumulation_steps - - "1" - - --learning_rate - - "3e-5" - - --num_train_epochs - - "2" - - --fp16 - - --save_steps - - "200" - - --output_dir - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/promoter_no_tata - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "546917150720" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB 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/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:08:04.929558Z" - writerId: 17da3qmzxz64dpoziqvzifrlx6x86cr3 - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 41 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 41 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_040804-2w8kmapq/files/output.log b/wandb/run-20260305_040804-2w8kmapq/files/output.log deleted file mode 100644 index b5f9132702b494b30fe21ef3d5a9d9ed391eb551..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040804-2w8kmapq/files/output.log +++ /dev/null @@ -1,37 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 diff --git a/wandb/run-20260305_040804-2w8kmapq/files/requirements.txt b/wandb/run-20260305_040804-2w8kmapq/files/requirements.txt deleted file mode 100644 index e3d9629db6fa5f00aab96101b087d1d57a440fb4..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040804-2w8kmapq/files/requirements.txt +++ /dev/null @@ -1,90 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -idna==3.11 -pycparser==2.23 -triton==3.1.0 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -charset-normalizer==3.4.4 -wandb==0.25.0 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -accelerate==1.13.0 -torch==2.5.1 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -torchvision==0.20.1 -shellingham==1.5.4 -torchaudio==2.5.1 -sympy==1.13.1 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -click==8.3.1 -MarkupSafe==3.0.2 -urllib3==2.6.3 -propcache==0.4.1 -regex==2026.2.28 -xxhash==3.6.0 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"/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/promoter_no_tata/split", - "--kmer", - "-1", - "--run_name", - "hg38_BPE_base__baseline_bpe_tokenizer_3e-5_promoter_no_tata_seed42", - "--model_max_length", - "80", - "--per_device_train_batch_size", - "128", - "--per_device_eval_batch_size", - "128", - "--gradient_accumulation_steps", - "1", - "--learning_rate", - "3e-5", - "--num_train_epochs", - "2", - "--fp16", - "--save_steps", - "200", - "--output_dir", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/promoter_no_tata", - "--evaluation_strategy", - "steps", - "--eval_steps", - "200", - "--warmup_steps", - "30", - "--logging_steps", - "100000", - "--log_level", - "info", - "--seed", - "42", - "--find_unused_parameters", - "False", - "--project_name", - "genomic_bench_tune_hg38_1024" - ], - "program": 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/home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 - - --tokenizer_path - - /home/n5huang/dna_token/tokenizer_evaluation/baseline_bpe/tokenizer.json - - --trust_remote_code - - "True" - - --data_path - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/promoter_tata/split - - --kmer - - "-1" - - --run_name - - hg38_BPE_base__baseline_bpe_tokenizer_3e-5_promoter_tata_seed42 - - --model_max_length - - "80" - - --per_device_train_batch_size - - "128" - - --per_device_eval_batch_size - - "128" - - --gradient_accumulation_steps - - "1" - - --learning_rate - - "3e-5" - - --num_train_epochs - - "2" - - --fp16 - - --save_steps - - "200" - - --output_dir - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/promoter_tata - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "546917277696" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:08:17.447574Z" - writerId: qyvj17fgycf06f4fvd4f0bjxgef2xqlr - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 41 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 41 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_040817-y7tto91s/files/output.log b/wandb/run-20260305_040817-y7tto91s/files/output.log deleted file mode 100644 index b5f9132702b494b30fe21ef3d5a9d9ed391eb551..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040817-y7tto91s/files/output.log +++ /dev/null @@ -1,37 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 diff --git a/wandb/run-20260305_040817-y7tto91s/files/requirements.txt b/wandb/run-20260305_040817-y7tto91s/files/requirements.txt deleted file mode 100644 index e3d9629db6fa5f00aab96101b087d1d57a440fb4..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040817-y7tto91s/files/requirements.txt +++ /dev/null @@ -1,90 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -idna==3.11 -pycparser==2.23 -triton==3.1.0 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -charset-normalizer==3.4.4 -wandb==0.25.0 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -accelerate==1.13.0 -torch==2.5.1 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -torchvision==0.20.1 -shellingham==1.5.4 -torchaudio==2.5.1 -sympy==1.13.1 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -click==8.3.1 -MarkupSafe==3.0.2 -urllib3==2.6.3 -propcache==0.4.1 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_040817-y7tto91s/files/wandb-metadata.json b/wandb/run-20260305_040817-y7tto91s/files/wandb-metadata.json deleted file mode 100644 index 28b4daae39ee163a6442c10f5cc0de8f54c7d1c0..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040817-y7tto91s/files/wandb-metadata.json +++ /dev/null @@ -1,134 +0,0 @@ -{ - "os": "Linux-5.15.0-72-generic-x86_64-with-glibc2.35", - "python": "CPython 3.10.19", - "startedAt": "2026-03-05T04:08:17.447574Z", - "args": [ - "--model_name_or_path", - "/home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000", - "--tokenizer_path", - "/home/n5huang/dna_token/tokenizer_evaluation/baseline_bpe/tokenizer.json", - "--trust_remote_code", - "True", - "--data_path", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/promoter_tata/split", - "--kmer", - "-1", - "--run_name", - "hg38_BPE_base__baseline_bpe_tokenizer_3e-5_promoter_tata_seed42", - "--model_max_length", - "80", - "--per_device_train_batch_size", - "128", - "--per_device_eval_batch_size", - "128", - "--gradient_accumulation_steps", - "1", - "--learning_rate", - "3e-5", - "--num_train_epochs", - "2", - "--fp16", - "--save_steps", - "200", - "--output_dir", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/promoter_tata", - "--evaluation_strategy", - "steps", - "--eval_steps", - "200", - "--warmup_steps", - "30", - "--logging_steps", - "100000", - "--log_level", - "info", - "--seed", - "42", - "--find_unused_parameters", - "False", - "--project_name", - "genomic_bench_tune_hg38_1024" - ], - "program": 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/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:08:26.688678Z" - writerId: e58adco3bqdlfoz0knros8wahhfctpc7 - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 41 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 41 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_040826-g8xkqd5h/files/output.log b/wandb/run-20260305_040826-g8xkqd5h/files/output.log deleted file mode 100644 index b5f9132702b494b30fe21ef3d5a9d9ed391eb551..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040826-g8xkqd5h/files/output.log +++ /dev/null @@ -1,37 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 diff --git a/wandb/run-20260305_040826-g8xkqd5h/files/requirements.txt b/wandb/run-20260305_040826-g8xkqd5h/files/requirements.txt deleted file mode 100644 index e3d9629db6fa5f00aab96101b087d1d57a440fb4..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040826-g8xkqd5h/files/requirements.txt +++ /dev/null @@ -1,90 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -idna==3.11 -pycparser==2.23 -triton==3.1.0 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 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GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:08:40.845594Z" - writerId: d7l5piwj6haetlsyld0k7fd80zhg6zub - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 41 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 41 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_040840-hcdbmy9c/files/output.log b/wandb/run-20260305_040840-hcdbmy9c/files/output.log deleted file mode 100644 index b5f9132702b494b30fe21ef3d5a9d9ed391eb551..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040840-hcdbmy9c/files/output.log +++ /dev/null @@ -1,37 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 diff --git a/wandb/run-20260305_040840-hcdbmy9c/files/requirements.txt b/wandb/run-20260305_040840-hcdbmy9c/files/requirements.txt deleted file mode 100644 index e3d9629db6fa5f00aab96101b087d1d57a440fb4..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040840-hcdbmy9c/files/requirements.txt +++ /dev/null @@ -1,90 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -idna==3.11 -pycparser==2.23 -triton==3.1.0 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -charset-normalizer==3.4.4 -wandb==0.25.0 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -accelerate==1.13.0 -torch==2.5.1 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -torchvision==0.20.1 -shellingham==1.5.4 -torchaudio==2.5.1 -sympy==1.13.1 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -click==8.3.1 -MarkupSafe==3.0.2 -urllib3==2.6.3 -propcache==0.4.1 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_040840-hcdbmy9c/files/wandb-metadata.json b/wandb/run-20260305_040840-hcdbmy9c/files/wandb-metadata.json deleted file mode 100644 index 875f56e9b1b4a4eb23ae4ae1c121368443975bf2..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040840-hcdbmy9c/files/wandb-metadata.json +++ /dev/null @@ -1,134 +0,0 @@ -{ - "os": "Linux-5.15.0-72-generic-x86_64-with-glibc2.35", - "python": "CPython 3.10.19", - "startedAt": "2026-03-05T04:08:40.845594Z", - "args": [ - "--model_name_or_path", - "/home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000", - "--tokenizer_path", - "/home/n5huang/dna_token/tokenizer_evaluation/baseline_bpe/tokenizer.json", - "--trust_remote_code", - "True", - "--data_path", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/splice_sites_all/split", - "--kmer", - "-1", - "--run_name", - "hg38_BPE_base__baseline_bpe_tokenizer_3e-5_splice_sites_all_seed42", - "--model_max_length", - "140", - "--per_device_train_batch_size", - "128", - "--per_device_eval_batch_size", - "128", - "--gradient_accumulation_steps", - "1", - "--learning_rate", - "3e-5", - "--num_train_epochs", - "4", - "--fp16", - "--save_steps", - "200", - "--output_dir", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_all", - "--evaluation_strategy", - "steps", - "--eval_steps", - "200", - "--warmup_steps", - "30", - "--logging_steps", - "100000", - "--log_level", - "info", - "--seed", - "42", - "--find_unused_parameters", - "False", - "--project_name", - "genomic_bench_tune_hg38_1024" - ], - "program": 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a/wandb/run-20260305_040854-r6j3c2l1/files/config.yaml +++ /dev/null @@ -1,141 +0,0 @@ -_wandb: - value: - cli_version: 0.25.0 - e: - qzrqos5r32m4qj8h998xkedd3xop1oe8: - args: - - --model_name_or_path - - /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 - - --tokenizer_path - - /home/n5huang/dna_token/tokenizer_evaluation/baseline_bpe/tokenizer.json - - --trust_remote_code - - "True" - - --data_path - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/splice_sites_donors/split - - --kmer - - "-1" - - --run_name - - hg38_BPE_base__baseline_bpe_tokenizer_3e-5_splice_sites_donors_seed42 - - --model_max_length - - "140" - - --per_device_train_batch_size - - "128" - - --per_device_eval_batch_size - - "128" - - --gradient_accumulation_steps - - "1" - - --learning_rate - - "3e-5" - - --num_train_epochs - - "4" - - --fp16 - - --save_steps - - "200" - - --output_dir - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_donors - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "546919522304" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:08:54.655809Z" - writerId: qzrqos5r32m4qj8h998xkedd3xop1oe8 - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 41 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 41 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_040854-r6j3c2l1/files/output.log b/wandb/run-20260305_040854-r6j3c2l1/files/output.log deleted file mode 100644 index b5f9132702b494b30fe21ef3d5a9d9ed391eb551..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040854-r6j3c2l1/files/output.log +++ /dev/null @@ -1,37 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 diff --git a/wandb/run-20260305_040854-r6j3c2l1/files/requirements.txt b/wandb/run-20260305_040854-r6j3c2l1/files/requirements.txt deleted file mode 100644 index e3d9629db6fa5f00aab96101b087d1d57a440fb4..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040854-r6j3c2l1/files/requirements.txt +++ /dev/null @@ -1,90 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -idna==3.11 -pycparser==2.23 -triton==3.1.0 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -charset-normalizer==3.4.4 -wandb==0.25.0 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -accelerate==1.13.0 -torch==2.5.1 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -torchvision==0.20.1 -shellingham==1.5.4 -torchaudio==2.5.1 -sympy==1.13.1 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -click==8.3.1 -MarkupSafe==3.0.2 -urllib3==2.6.3 -propcache==0.4.1 -regex==2026.2.28 -xxhash==3.6.0 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"/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/splice_sites_donors/split", - "--kmer", - "-1", - "--run_name", - "hg38_BPE_base__baseline_bpe_tokenizer_3e-5_splice_sites_donors_seed42", - "--model_max_length", - "140", - "--per_device_train_batch_size", - "128", - "--per_device_eval_batch_size", - "128", - "--gradient_accumulation_steps", - "1", - "--learning_rate", - "3e-5", - "--num_train_epochs", - "4", - "--fp16", - "--save_steps", - "200", - "--output_dir", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_donors", - "--evaluation_strategy", - "steps", - "--eval_steps", - "200", - "--warmup_steps", - "30", - "--logging_steps", - "100000", - "--log_level", - "info", - "--seed", - "42", - "--find_unused_parameters", - "False", - "--project_name", - "genomic_bench_tune_hg38_1024" - ], - "program": 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/home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 - - --tokenizer_path - - /home/n5huang/dna_token/tokenizer_evaluation/baseline_bpe/tokenizer.json - - --trust_remote_code - - "True" - - --data_path - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/H2AFZ/split - - --kmer - - "-1" - - --run_name - - hg38_BPE_base__baseline_bpe_tokenizer_3e-5_H2AFZ_seed42 - - --model_max_length - - "220" - - --per_device_train_batch_size - - "128" - - --per_device_eval_batch_size - - "128" - - --gradient_accumulation_steps - - "1" - - --learning_rate - - "3e-5" - - --num_train_epochs - - "2" - - --fp16 - - --save_steps - - "200" - - --output_dir - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H2AFZ - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "546919632896" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:09:09.540604Z" - writerId: t0qzrpa2k68cckrzsbdrbglhsdim2ifv - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 41 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 41 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_040909-0ugt2xq3/files/output.log b/wandb/run-20260305_040909-0ugt2xq3/files/output.log deleted file mode 100644 index b5f9132702b494b30fe21ef3d5a9d9ed391eb551..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040909-0ugt2xq3/files/output.log +++ /dev/null @@ -1,37 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 diff --git a/wandb/run-20260305_040909-0ugt2xq3/files/requirements.txt b/wandb/run-20260305_040909-0ugt2xq3/files/requirements.txt deleted file mode 100644 index e3d9629db6fa5f00aab96101b087d1d57a440fb4..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040909-0ugt2xq3/files/requirements.txt +++ /dev/null @@ -1,90 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -idna==3.11 -pycparser==2.23 -triton==3.1.0 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -charset-normalizer==3.4.4 -wandb==0.25.0 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -accelerate==1.13.0 -torch==2.5.1 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -torchvision==0.20.1 -shellingham==1.5.4 -torchaudio==2.5.1 -sympy==1.13.1 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -click==8.3.1 -MarkupSafe==3.0.2 -urllib3==2.6.3 -propcache==0.4.1 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_040909-0ugt2xq3/files/wandb-metadata.json b/wandb/run-20260305_040909-0ugt2xq3/files/wandb-metadata.json deleted file mode 100644 index 0c3b67b8e3d514e11accf7035d8f3b1f87579bbb..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040909-0ugt2xq3/files/wandb-metadata.json +++ /dev/null @@ -1,134 +0,0 @@ -{ - "os": "Linux-5.15.0-72-generic-x86_64-with-glibc2.35", - "python": "CPython 3.10.19", - "startedAt": "2026-03-05T04:09:09.540604Z", - "args": [ - "--model_name_or_path", - "/home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000", - "--tokenizer_path", - "/home/n5huang/dna_token/tokenizer_evaluation/baseline_bpe/tokenizer.json", - "--trust_remote_code", - "True", - "--data_path", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/H2AFZ/split", - "--kmer", - "-1", - "--run_name", - "hg38_BPE_base__baseline_bpe_tokenizer_3e-5_H2AFZ_seed42", - "--model_max_length", - "220", - "--per_device_train_batch_size", - "128", - "--per_device_eval_batch_size", - "128", - "--gradient_accumulation_steps", - "1", - "--learning_rate", - "3e-5", - "--num_train_epochs", - "2", - "--fp16", - "--save_steps", - "200", - "--output_dir", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H2AFZ", - "--evaluation_strategy", - "steps", - "--eval_steps", - "200", - "--warmup_steps", - "30", - "--logging_steps", - "100000", - "--log_level", - "info", - "--seed", - "42", - "--find_unused_parameters", - "False", - "--project_name", - "genomic_bench_tune_hg38_1024" - ], - "program": 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/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K27ac - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "546919796736" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:09:26.149982Z" - writerId: fjnm2dmkaqkr6cvzyraex55ha9zg8is6 - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 41 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 41 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_040926-4hw0owou/files/output.log b/wandb/run-20260305_040926-4hw0owou/files/output.log deleted file mode 100644 index b5f9132702b494b30fe21ef3d5a9d9ed391eb551..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040926-4hw0owou/files/output.log +++ /dev/null @@ -1,37 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 diff --git a/wandb/run-20260305_040926-4hw0owou/files/requirements.txt b/wandb/run-20260305_040926-4hw0owou/files/requirements.txt deleted file mode 100644 index e3d9629db6fa5f00aab96101b087d1d57a440fb4..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040926-4hw0owou/files/requirements.txt +++ /dev/null @@ -1,90 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -idna==3.11 -pycparser==2.23 -triton==3.1.0 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -charset-normalizer==3.4.4 -wandb==0.25.0 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -accelerate==1.13.0 -torch==2.5.1 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -torchvision==0.20.1 -shellingham==1.5.4 -torchaudio==2.5.1 -sympy==1.13.1 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -click==8.3.1 -MarkupSafe==3.0.2 -urllib3==2.6.3 -propcache==0.4.1 -regex==2026.2.28 -xxhash==3.6.0 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-WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 diff --git a/wandb/run-20260305_040941-zyxml21c/files/requirements.txt b/wandb/run-20260305_040941-zyxml21c/files/requirements.txt deleted file mode 100644 index e3d9629db6fa5f00aab96101b087d1d57a440fb4..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040941-zyxml21c/files/requirements.txt +++ /dev/null @@ -1,90 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -idna==3.11 -pycparser==2.23 -triton==3.1.0 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -charset-normalizer==3.4.4 -wandb==0.25.0 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -accelerate==1.13.0 -torch==2.5.1 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -torchvision==0.20.1 -shellingham==1.5.4 -torchaudio==2.5.1 -sympy==1.13.1 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -click==8.3.1 -MarkupSafe==3.0.2 -urllib3==2.6.3 -propcache==0.4.1 -regex==2026.2.28 -xxhash==3.6.0 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"/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/H3K27me3/split", - "--kmer", - "-1", - "--run_name", - "hg38_BPE_base__baseline_bpe_tokenizer_3e-5_H3K27me3_seed42", - "--model_max_length", - "220", - "--per_device_train_batch_size", - "128", - "--per_device_eval_batch_size", - "128", - "--gradient_accumulation_steps", - "1", - "--learning_rate", - "3e-5", - "--num_train_epochs", - "2", - "--fp16", - "--save_steps", - "200", - "--output_dir", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K27me3", - "--evaluation_strategy", - "steps", - "--eval_steps", - "200", - "--warmup_steps", - "30", - "--logging_steps", - "100000", - "--log_level", - "info", - "--seed", - "42", - "--find_unused_parameters", - "False", - "--project_name", - "genomic_bench_tune_hg38_1024" - ], - "program": 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a/wandb/run-20260305_040957-45gtvsiq/files/config.yaml +++ /dev/null @@ -1,141 +0,0 @@ -_wandb: - value: - cli_version: 0.25.0 - e: - oshpc8ipsiyeqmxxvsn1sl4udb7za5us: - args: - - --model_name_or_path - - /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 - - --tokenizer_path - - /home/n5huang/dna_token/tokenizer_evaluation/baseline_bpe/tokenizer.json - - --trust_remote_code - - "True" - - --data_path - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/H3K36me3/split - - --kmer - - "-1" - - --run_name - - hg38_BPE_base__baseline_bpe_tokenizer_3e-5_H3K36me3_seed42 - - --model_max_length - - "220" - - --per_device_train_batch_size - - "128" - - --per_device_eval_batch_size - - "128" - - --gradient_accumulation_steps - - "1" - - --learning_rate - - "3e-5" - - --num_train_epochs - - "2" - - --fp16 - - --save_steps - - "200" - - --output_dir - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K36me3 - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "546921963520" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:09:57.879159Z" - writerId: oshpc8ipsiyeqmxxvsn1sl4udb7za5us - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 41 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 41 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_040957-45gtvsiq/files/output.log b/wandb/run-20260305_040957-45gtvsiq/files/output.log deleted file mode 100644 index b5f9132702b494b30fe21ef3d5a9d9ed391eb551..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040957-45gtvsiq/files/output.log +++ /dev/null @@ -1,37 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 diff --git a/wandb/run-20260305_040957-45gtvsiq/files/requirements.txt b/wandb/run-20260305_040957-45gtvsiq/files/requirements.txt deleted file mode 100644 index e3d9629db6fa5f00aab96101b087d1d57a440fb4..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040957-45gtvsiq/files/requirements.txt +++ /dev/null @@ -1,90 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -idna==3.11 -pycparser==2.23 -triton==3.1.0 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -charset-normalizer==3.4.4 -wandb==0.25.0 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -accelerate==1.13.0 -torch==2.5.1 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -torchvision==0.20.1 -shellingham==1.5.4 -torchaudio==2.5.1 -sympy==1.13.1 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -click==8.3.1 -MarkupSafe==3.0.2 -urllib3==2.6.3 -propcache==0.4.1 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_040957-45gtvsiq/files/wandb-metadata.json b/wandb/run-20260305_040957-45gtvsiq/files/wandb-metadata.json deleted file mode 100644 index 94d3aa4325e02ed19d71cdfed4da13aa5777fbaf..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_040957-45gtvsiq/files/wandb-metadata.json +++ /dev/null @@ -1,134 +0,0 @@ -{ - "os": "Linux-5.15.0-72-generic-x86_64-with-glibc2.35", - "python": "CPython 3.10.19", - "startedAt": "2026-03-05T04:09:57.879159Z", - "args": [ - "--model_name_or_path", - "/home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000", - "--tokenizer_path", - "/home/n5huang/dna_token/tokenizer_evaluation/baseline_bpe/tokenizer.json", - "--trust_remote_code", - "True", - "--data_path", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/H3K36me3/split", - "--kmer", - "-1", - "--run_name", - "hg38_BPE_base__baseline_bpe_tokenizer_3e-5_H3K36me3_seed42", - "--model_max_length", - "220", - "--per_device_train_batch_size", - "128", - "--per_device_eval_batch_size", - "128", - "--gradient_accumulation_steps", - "1", - "--learning_rate", - "3e-5", - "--num_train_epochs", - "2", - "--fp16", - "--save_steps", - "200", - "--output_dir", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K36me3", - "--evaluation_strategy", - "steps", - "--eval_steps", - "200", - "--warmup_steps", - "30", - "--logging_steps", - "100000", - "--log_level", - "info", - "--seed", - "42", - "--find_unused_parameters", - "False", - "--project_name", - "genomic_bench_tune_hg38_1024" - ], - "program": 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a/wandb/run-20260305_041014-zlpwnu24/files/config.yaml +++ /dev/null @@ -1,141 +0,0 @@ -_wandb: - value: - cli_version: 0.25.0 - e: - 863afy18fe63pbijjzl8sqphbgk1sbar: - args: - - --model_name_or_path - - /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 - - --tokenizer_path - - /home/n5huang/dna_token/tokenizer_evaluation/baseline_bpe/tokenizer.json - - --trust_remote_code - - "True" - - --data_path - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/H3K4me1/split - - --kmer - - "-1" - - --run_name - - hg38_BPE_base__baseline_bpe_tokenizer_3e-5_H3K4me1_seed42 - - --model_max_length - - "220" - - --per_device_train_batch_size - - "128" - - --per_device_eval_batch_size - - "128" - - --gradient_accumulation_steps - - "1" - - --learning_rate - - "3e-5" - - --num_train_epochs - - "2" - - --fp16 - - --save_steps - - "200" - - --output_dir - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K4me1 - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "546922119168" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:10:14.345734Z" - writerId: 863afy18fe63pbijjzl8sqphbgk1sbar - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 41 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 41 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_041014-zlpwnu24/files/output.log b/wandb/run-20260305_041014-zlpwnu24/files/output.log deleted file mode 100644 index b5f9132702b494b30fe21ef3d5a9d9ed391eb551..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_041014-zlpwnu24/files/output.log +++ /dev/null @@ -1,37 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 diff --git a/wandb/run-20260305_041014-zlpwnu24/files/requirements.txt b/wandb/run-20260305_041014-zlpwnu24/files/requirements.txt deleted file mode 100644 index e3d9629db6fa5f00aab96101b087d1d57a440fb4..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_041014-zlpwnu24/files/requirements.txt +++ /dev/null @@ -1,90 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -idna==3.11 -pycparser==2.23 -triton==3.1.0 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -charset-normalizer==3.4.4 -wandb==0.25.0 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -accelerate==1.13.0 -torch==2.5.1 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -torchvision==0.20.1 -shellingham==1.5.4 -torchaudio==2.5.1 -sympy==1.13.1 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -click==8.3.1 -MarkupSafe==3.0.2 -urllib3==2.6.3 -propcache==0.4.1 -regex==2026.2.28 -xxhash==3.6.0 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"/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/H3K4me1/split", - "--kmer", - "-1", - "--run_name", - "hg38_BPE_base__baseline_bpe_tokenizer_3e-5_H3K4me1_seed42", - "--model_max_length", - "220", - "--per_device_train_batch_size", - "128", - "--per_device_eval_batch_size", - "128", - "--gradient_accumulation_steps", - "1", - "--learning_rate", - "3e-5", - "--num_train_epochs", - "2", - "--fp16", - "--save_steps", - "200", - "--output_dir", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K4me1", - "--evaluation_strategy", - "steps", - "--eval_steps", - "200", - "--warmup_steps", - "30", - "--logging_steps", - "100000", - "--log_level", - "info", - "--seed", - "42", - "--find_unused_parameters", - "False", - "--project_name", - "genomic_bench_tune_hg38_1024" - ], - "program": 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a/wandb/run-20260305_041030-12rfvdrd/files/config.yaml +++ /dev/null @@ -1,141 +0,0 @@ -_wandb: - value: - cli_version: 0.25.0 - e: - thhty8xg7s92aaad10i46bokk8gb0rb0: - args: - - --model_name_or_path - - /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 - - --tokenizer_path - - /home/n5huang/dna_token/tokenizer_evaluation/baseline_bpe/tokenizer.json - - --trust_remote_code - - "True" - - --data_path - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/H3K4me2/split - - --kmer - - "-1" - - --run_name - - hg38_BPE_base__baseline_bpe_tokenizer_3e-5_H3K4me2_seed42 - - --model_max_length - - "220" - - --per_device_train_batch_size - - "128" - - --per_device_eval_batch_size - - "128" - - --gradient_accumulation_steps - - "1" - - --learning_rate - - "3e-5" - - --num_train_epochs - - "2" - - --fp16 - - --save_steps - - "200" - - --output_dir - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K4me2 - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "546922246144" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:10:30.374680Z" - writerId: thhty8xg7s92aaad10i46bokk8gb0rb0 - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 41 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 41 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_041030-12rfvdrd/files/output.log b/wandb/run-20260305_041030-12rfvdrd/files/output.log deleted file mode 100644 index b5f9132702b494b30fe21ef3d5a9d9ed391eb551..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_041030-12rfvdrd/files/output.log +++ /dev/null @@ -1,37 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 diff --git a/wandb/run-20260305_041030-12rfvdrd/files/requirements.txt b/wandb/run-20260305_041030-12rfvdrd/files/requirements.txt deleted file mode 100644 index e3d9629db6fa5f00aab96101b087d1d57a440fb4..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_041030-12rfvdrd/files/requirements.txt +++ /dev/null @@ -1,90 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -idna==3.11 -pycparser==2.23 -triton==3.1.0 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -charset-normalizer==3.4.4 -wandb==0.25.0 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -accelerate==1.13.0 -torch==2.5.1 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -torchvision==0.20.1 -shellingham==1.5.4 -torchaudio==2.5.1 -sympy==1.13.1 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -click==8.3.1 -MarkupSafe==3.0.2 -urllib3==2.6.3 -propcache==0.4.1 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_041030-12rfvdrd/files/wandb-metadata.json b/wandb/run-20260305_041030-12rfvdrd/files/wandb-metadata.json deleted file mode 100644 index bee98277841b25e71f494d2bd05e1615a1341f03..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_041030-12rfvdrd/files/wandb-metadata.json +++ /dev/null @@ -1,134 +0,0 @@ -{ - "os": "Linux-5.15.0-72-generic-x86_64-with-glibc2.35", - "python": "CPython 3.10.19", - "startedAt": "2026-03-05T04:10:30.374680Z", - "args": [ - "--model_name_or_path", - "/home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000", - "--tokenizer_path", - "/home/n5huang/dna_token/tokenizer_evaluation/baseline_bpe/tokenizer.json", - "--trust_remote_code", - "True", - "--data_path", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/H3K4me2/split", - "--kmer", - "-1", - "--run_name", - "hg38_BPE_base__baseline_bpe_tokenizer_3e-5_H3K4me2_seed42", - "--model_max_length", - "220", - "--per_device_train_batch_size", - "128", - "--per_device_eval_batch_size", - "128", - "--gradient_accumulation_steps", - "1", - "--learning_rate", - "3e-5", - "--num_train_epochs", - "2", - "--fp16", - "--save_steps", - "200", - "--output_dir", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K4me2", - "--evaluation_strategy", - "steps", - "--eval_steps", - "200", - "--warmup_steps", - "30", - "--logging_steps", - "100000", - "--log_level", - "info", - "--seed", - "42", - "--find_unused_parameters", - "False", - "--project_name", - "genomic_bench_tune_hg38_1024" - ], - "program": 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a/wandb/run-20260305_041045-zsanq5v8/files/config.yaml +++ /dev/null @@ -1,141 +0,0 @@ -_wandb: - value: - cli_version: 0.25.0 - e: - coaijrhi7h38xn9dtcb4gzw55poz3nr0: - args: - - --model_name_or_path - - /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 - - --tokenizer_path - - /home/n5huang/dna_token/tokenizer_evaluation/baseline_bpe/tokenizer.json - - --trust_remote_code - - "True" - - --data_path - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/H3K4me3/split - - --kmer - - "-1" - - --run_name - - hg38_BPE_base__baseline_bpe_tokenizer_3e-5_H3K4me3_seed42 - - --model_max_length - - "220" - - --per_device_train_batch_size - - "128" - - --per_device_eval_batch_size - - "128" - - --gradient_accumulation_steps - - "1" - - --learning_rate - - "3e-5" - - --num_train_epochs - - "2" - - --fp16 - - --save_steps - - "200" - - --output_dir - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K4me3 - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "546924294144" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:10:45.971421Z" - writerId: coaijrhi7h38xn9dtcb4gzw55poz3nr0 - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 41 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 41 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_041045-zsanq5v8/files/output.log b/wandb/run-20260305_041045-zsanq5v8/files/output.log deleted file mode 100644 index b5f9132702b494b30fe21ef3d5a9d9ed391eb551..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_041045-zsanq5v8/files/output.log +++ /dev/null @@ -1,37 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 diff --git a/wandb/run-20260305_041045-zsanq5v8/files/requirements.txt b/wandb/run-20260305_041045-zsanq5v8/files/requirements.txt deleted file mode 100644 index e3d9629db6fa5f00aab96101b087d1d57a440fb4..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_041045-zsanq5v8/files/requirements.txt +++ /dev/null @@ -1,90 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -idna==3.11 -pycparser==2.23 -triton==3.1.0 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -charset-normalizer==3.4.4 -wandb==0.25.0 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -accelerate==1.13.0 -torch==2.5.1 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -torchvision==0.20.1 -shellingham==1.5.4 -torchaudio==2.5.1 -sympy==1.13.1 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -click==8.3.1 -MarkupSafe==3.0.2 -urllib3==2.6.3 -propcache==0.4.1 -regex==2026.2.28 -xxhash==3.6.0 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"/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/H3K4me3/split", - "--kmer", - "-1", - "--run_name", - "hg38_BPE_base__baseline_bpe_tokenizer_3e-5_H3K4me3_seed42", - "--model_max_length", - "220", - "--per_device_train_batch_size", - "128", - "--per_device_eval_batch_size", - "128", - "--gradient_accumulation_steps", - "1", - "--learning_rate", - "3e-5", - "--num_train_epochs", - "2", - "--fp16", - "--save_steps", - "200", - "--output_dir", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K4me3", - "--evaluation_strategy", - "steps", - "--eval_steps", - "200", - "--warmup_steps", - "30", - "--logging_steps", - "100000", - "--log_level", - "info", - "--seed", - "42", - "--find_unused_parameters", - "False", - "--project_name", - "genomic_bench_tune_hg38_1024" - ], - "program": 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/home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 - - --tokenizer_path - - /home/n5huang/dna_token/tokenizer_evaluation/baseline_bpe/tokenizer.json - - --trust_remote_code - - "True" - - --data_path - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/H3K9ac/split - - --kmer - - "-1" - - --run_name - - hg38_BPE_base__baseline_bpe_tokenizer_3e-5_H3K9ac_seed42 - - --model_max_length - - "220" - - --per_device_train_batch_size - - "128" - - --per_device_eval_batch_size - - "128" - - --gradient_accumulation_steps - - "1" - - --learning_rate - - "3e-5" - - --num_train_epochs - - "2" - - --fp16 - - --save_steps - - "200" - - --output_dir - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K9ac - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "546924392448" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:10:58.474038Z" - writerId: afgp1py9foylgkevwe0s4qd59xur7724 - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 41 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 41 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_041058-03nauhi3/files/output.log b/wandb/run-20260305_041058-03nauhi3/files/output.log deleted file mode 100644 index b5f9132702b494b30fe21ef3d5a9d9ed391eb551..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_041058-03nauhi3/files/output.log +++ /dev/null @@ -1,37 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 diff --git a/wandb/run-20260305_041058-03nauhi3/files/requirements.txt b/wandb/run-20260305_041058-03nauhi3/files/requirements.txt deleted file mode 100644 index e3d9629db6fa5f00aab96101b087d1d57a440fb4..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_041058-03nauhi3/files/requirements.txt +++ /dev/null @@ -1,90 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -idna==3.11 -pycparser==2.23 -triton==3.1.0 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -charset-normalizer==3.4.4 -wandb==0.25.0 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -accelerate==1.13.0 -torch==2.5.1 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -torchvision==0.20.1 -shellingham==1.5.4 -torchaudio==2.5.1 -sympy==1.13.1 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -click==8.3.1 -MarkupSafe==3.0.2 -urllib3==2.6.3 -propcache==0.4.1 -regex==2026.2.28 -xxhash==3.6.0 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-WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train - model = transformers.AutoModelForSequenceClassification.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained - return model_class.from_pretrained( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained - loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model - merged_state_dict.update(load_state_dict(ckpt_file)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict - check_torch_load_is_safe() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe - raise ValueError( -ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors. -See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434 diff --git a/wandb/run-20260305_041112-9a2ihn8a/files/requirements.txt b/wandb/run-20260305_041112-9a2ihn8a/files/requirements.txt deleted file mode 100644 index e3d9629db6fa5f00aab96101b087d1d57a440fb4..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_041112-9a2ihn8a/files/requirements.txt +++ /dev/null @@ -1,90 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -idna==3.11 -pycparser==2.23 -triton==3.1.0 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -charset-normalizer==3.4.4 -wandb==0.25.0 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -accelerate==1.13.0 -torch==2.5.1 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -torchvision==0.20.1 -shellingham==1.5.4 -torchaudio==2.5.1 -sympy==1.13.1 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -click==8.3.1 -MarkupSafe==3.0.2 -urllib3==2.6.3 -propcache==0.4.1 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_041112-9a2ihn8a/files/wandb-metadata.json b/wandb/run-20260305_041112-9a2ihn8a/files/wandb-metadata.json deleted file mode 100644 index 0afd6dd0b47e28ead0119f114932b60906a01505..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_041112-9a2ihn8a/files/wandb-metadata.json +++ /dev/null @@ -1,134 +0,0 @@ -{ - "os": "Linux-5.15.0-72-generic-x86_64-with-glibc2.35", - "python": "CPython 3.10.19", - "startedAt": "2026-03-05T04:11:12.949356Z", - "args": [ - "--model_name_or_path", - "/home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000", - "--tokenizer_path", - "/home/n5huang/dna_token/tokenizer_evaluation/baseline_bpe/tokenizer.json", - "--trust_remote_code", - "True", - "--data_path", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/H3K9me3/split", - "--kmer", - "-1", - "--run_name", - "hg38_BPE_base__baseline_bpe_tokenizer_3e-5_H3K9me3_seed42", - "--model_max_length", - "220", - "--per_device_train_batch_size", - "128", - "--per_device_eval_batch_size", - "128", - "--gradient_accumulation_steps", - "1", - "--learning_rate", - "3e-5", - "--num_train_epochs", - "2", - "--fp16", - "--save_steps", - "200", - "--output_dir", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K9me3", - "--evaluation_strategy", - "steps", - "--eval_steps", - "200", - "--warmup_steps", - "30", - "--logging_steps", - "100000", - "--log_level", - "info", - "--seed", - "42", - "--find_unused_parameters", - "False", - "--project_name", - "genomic_bench_tune_hg38_1024" - ], - "program": 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/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_len/enhancers - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "546948657152" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: 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sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 23100.92it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -bert.pooler.dense.weight | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.weight | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 428, in train - trainer = transformers.Trainer(model=model, -TypeError: Trainer.__init__() got an unexpected keyword argument 'tokenizer' -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 428, in train - trainer = transformers.Trainer(model=model, -TypeError: Trainer.__init__() got an unexpected keyword argument 'tokenizer' diff --git a/wandb/run-20260305_041514-18nha9bz/files/requirements.txt b/wandb/run-20260305_041514-18nha9bz/files/requirements.txt deleted file mode 100644 index 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/home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 - - --tokenizer_path - - /home/n5huang/dna_token/tokenizer_evaluation/merge_bpe/merge_tokenizer_unigram_len.json - - --trust_remote_code - - "True" - - --data_path - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/enhancers_types/split - - --kmer - - "-1" - - --run_name - - hg38_BPE_base__merge_bpe_merge_tokenizer_unigram_len_3e-5_enhancers_types_seed42 - - --model_max_length - - "100" - - --per_device_train_batch_size - - "128" - - --per_device_eval_batch_size - - "128" - - --gradient_accumulation_steps - - "1" - - --learning_rate - - "3e-5" - - --num_train_epochs - - "4" - - --fp16 - - --save_steps - - "200" - - --output_dir - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_len/enhancers_types - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "546948755456" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: 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/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:15:28.908576Z" - writerId: ven7z8l0knhcr235a3idhpz7rzk9oj6d - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_041528-9i34q3gs/files/output.log b/wandb/run-20260305_041528-9i34q3gs/files/output.log deleted file mode 100644 index 9d88a05bd00cd1d3cf0fa30e14bc83f31bd6b207..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_041528-9i34q3gs/files/output.log +++ /dev/null @@ -1,35 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 21666.57it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -bert.pooler.dense.weight | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.bias | MISSING | -classifier.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 428, in train - trainer = transformers.Trainer(model=model, -TypeError: Trainer.__init__() got an unexpected keyword argument 'tokenizer' -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 428, in train - trainer = transformers.Trainer(model=model, -TypeError: Trainer.__init__() got an unexpected keyword argument 'tokenizer' diff --git a/wandb/run-20260305_041528-9i34q3gs/files/requirements.txt b/wandb/run-20260305_041528-9i34q3gs/files/requirements.txt deleted file mode 100644 index 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/home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 - - --tokenizer_path - - /home/n5huang/dna_token/tokenizer_evaluation/merge_bpe/merge_tokenizer_unigram_len.json - - --trust_remote_code - - "True" - - --data_path - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/promoter_all/split - - --kmer - - "-1" - - --run_name - - hg38_BPE_base__merge_bpe_merge_tokenizer_unigram_len_3e-5_promoter_all_seed42 - - --model_max_length - - "80" - - --per_device_train_batch_size - - "128" - - --per_device_eval_batch_size - - "128" - - --gradient_accumulation_steps - - "1" - - --learning_rate - - "3e-5" - - --num_train_epochs - - "2" - - --fp16 - - --save_steps - - "200" - - --output_dir - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_len/promoter_all - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "546950807552" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: 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/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:15:42.702038Z" - writerId: sjq1upqwiy8lu1tgys2i5tg5ebbtlwd8 - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_041542-1h6dh0q1/files/output.log b/wandb/run-20260305_041542-1h6dh0q1/files/output.log deleted file mode 100644 index aa8c397874d93421abbbb4c6e33d1e6442f5ad9a..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_041542-1h6dh0q1/files/output.log +++ /dev/null @@ -1,35 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 24496.89it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -bert.pooler.dense.weight | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.weight | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 428, in train - trainer = transformers.Trainer(model=model, -TypeError: Trainer.__init__() got an unexpected keyword argument 'tokenizer' -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 428, in train - trainer = transformers.Trainer(model=model, -TypeError: Trainer.__init__() got an unexpected keyword argument 'tokenizer' diff --git a/wandb/run-20260305_041542-1h6dh0q1/files/requirements.txt b/wandb/run-20260305_041542-1h6dh0q1/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_041542-1h6dh0q1/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 -accelerate==1.13.0 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -triton==3.6.0 -nvidia-nccl-cu12==2.27.5 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -cuda-pathfinder==1.4.0 -shellingham==1.5.4 -torchaudio==2.5.1 -nvidia-cufile-cu12==1.13.1.3 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -nvidia-nvjitlink-cu12==12.8.93 -click==8.3.1 -MarkupSafe==3.0.2 -nvidia-nvshmem-cu12==3.4.5 -urllib3==2.6.3 -cuda-bindings==12.9.4 -propcache==0.4.1 -nvidia-cusolver-cu12==11.7.3.90 -sympy==1.14.0 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -nvidia-cuda-runtime-cu12==12.8.90 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_041542-1h6dh0q1/files/wandb-metadata.json b/wandb/run-20260305_041542-1h6dh0q1/files/wandb-metadata.json deleted file mode 100644 index 09d5d6b3ed9cc282458c1c5d3d1757e88a99421c..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_041542-1h6dh0q1/files/wandb-metadata.json +++ /dev/null @@ -1,134 +0,0 @@ -{ - "os": "Linux-5.15.0-72-generic-x86_64-with-glibc2.35", - "python": "CPython 3.10.19", - "startedAt": "2026-03-05T04:15:42.702038Z", - "args": [ - "--model_name_or_path", - "/home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000", - "--tokenizer_path", - "/home/n5huang/dna_token/tokenizer_evaluation/merge_bpe/merge_tokenizer_unigram_len.json", - 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/home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 - - --tokenizer_path - - /home/n5huang/dna_token/tokenizer_evaluation/baseline_bpe/tokenizer.json - - --trust_remote_code - - "True" - - --data_path - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/enhancers/split - - --kmer - - "-1" - - --run_name - - hg38_BPE_base__baseline_bpe_tokenizer_3e-5_enhancers_seed42 - - --model_max_length - - "100" - - --per_device_train_batch_size - - "128" - - --per_device_eval_batch_size - - "128" - - --gradient_accumulation_steps - - "1" - - --learning_rate - - "3e-5" - - --num_train_epochs - - "4" - - --fp16 - - --save_steps - - "200" - - --output_dir - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "546950955008" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:16:01.085987Z" - writerId: piflqsy98f0otzvlx1xf2ahd5o7neenu - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_041601-g8salyem/files/output.log b/wandb/run-20260305_041601-g8salyem/files/output.log deleted file mode 100644 index 6ec87d0c23efc52f1b35cb9cfddc392085a8b822..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_041601-g8salyem/files/output.log +++ /dev/null @@ -1,35 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 24597.88it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -classifier.bias | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.bias | MISSING | -bert.pooler.dense.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 428, in train - trainer = transformers.Trainer(model=model, -TypeError: Trainer.__init__() got an unexpected keyword argument 'tokenizer' -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 428, in train - trainer = transformers.Trainer(model=model, -TypeError: Trainer.__init__() got an unexpected keyword argument 'tokenizer' diff --git a/wandb/run-20260305_041601-g8salyem/files/requirements.txt b/wandb/run-20260305_041601-g8salyem/files/requirements.txt deleted file mode 100644 index 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/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:16:15.049330Z" - writerId: dp1iricnt8aqgj6u8bpj47l61b4vi9j5 - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_041615-0gqhp6y2/files/output.log b/wandb/run-20260305_041615-0gqhp6y2/files/output.log deleted file mode 100644 index a2ad111366bd2d95f63802045d9c8460f07e7ffd..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_041615-0gqhp6y2/files/output.log +++ /dev/null @@ -1,35 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 23847.37it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -classifier.bias | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 428, in train - trainer = transformers.Trainer(model=model, -TypeError: Trainer.__init__() got an unexpected keyword argument 'tokenizer' -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 428, in train - trainer = transformers.Trainer(model=model, -TypeError: Trainer.__init__() got an unexpected keyword argument 'tokenizer' diff --git a/wandb/run-20260305_041615-0gqhp6y2/files/requirements.txt b/wandb/run-20260305_041615-0gqhp6y2/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_041615-0gqhp6y2/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 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/home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 - - --tokenizer_path - - /home/n5huang/dna_token/tokenizer_evaluation/baseline_bpe/tokenizer.json - - --trust_remote_code - - "True" - - --data_path - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/promoter_all/split - - --kmer - - "-1" - - --run_name - - hg38_BPE_base__baseline_bpe_tokenizer_3e-5_promoter_all_seed42 - - --model_max_length - - "80" - - --per_device_train_batch_size - - "128" - - --per_device_eval_batch_size - - "128" - - --gradient_accumulation_steps - - "1" - - --learning_rate - - "3e-5" - - --num_train_epochs - - "2" - - --fp16 - - --save_steps - - "200" - - --output_dir - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/promoter_all - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "546951180288" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:16:28.401009Z" - writerId: 4cqq6x9b0du8sleopm1y125w4ghkf7ie - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_041628-t8lsia5q/files/output.log b/wandb/run-20260305_041628-t8lsia5q/files/output.log deleted file mode 100644 index 27d40c49ceca861dcfad7a778f80b86e32a0607c..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_041628-t8lsia5q/files/output.log +++ /dev/null @@ -1,35 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 24004.12it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -classifier.bias | MISSING | -bert.pooler.dense.bias | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 428, in train - trainer = transformers.Trainer(model=model, -TypeError: Trainer.__init__() got an unexpected keyword argument 'tokenizer' -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 428, in train - trainer = transformers.Trainer(model=model, -TypeError: Trainer.__init__() got an unexpected keyword argument 'tokenizer' diff --git a/wandb/run-20260305_041628-t8lsia5q/files/requirements.txt b/wandb/run-20260305_041628-t8lsia5q/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_041628-t8lsia5q/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 -accelerate==1.13.0 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -triton==3.6.0 -nvidia-nccl-cu12==2.27.5 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -cuda-pathfinder==1.4.0 -shellingham==1.5.4 -torchaudio==2.5.1 -nvidia-cufile-cu12==1.13.1.3 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -nvidia-nvjitlink-cu12==12.8.93 -click==8.3.1 -MarkupSafe==3.0.2 -nvidia-nvshmem-cu12==3.4.5 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/home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 - - --tokenizer_path - - /home/n5huang/dna_token/tokenizer_evaluation/baseline_bpe/tokenizer.json - - --trust_remote_code - - "True" - - --data_path - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/promoter_no_tata/split - - --kmer - - "-1" - - --run_name - - hg38_BPE_base__baseline_bpe_tokenizer_3e-5_promoter_no_tata_seed42 - - --model_max_length - - "80" - - --per_device_train_batch_size - - "128" - - --per_device_eval_batch_size - - "128" - - --gradient_accumulation_steps - - "1" - - --learning_rate - - "3e-5" - - --num_train_epochs - - "2" - - --fp16 - - --save_steps - - "200" - - --output_dir - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/promoter_no_tata - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "546953203712" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:16:41.241573Z" - writerId: tii3id1ieju4e5vywo2wwtumo3715om2 - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_041641-z1l3g705/files/output.log b/wandb/run-20260305_041641-z1l3g705/files/output.log deleted file mode 100644 index 0a8bc6d87d740fc1dbf36dc5d51fc5e623644ce6..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_041641-z1l3g705/files/output.log +++ /dev/null @@ -1,35 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 14922.14it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -classifier.bias | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 428, in train - trainer = transformers.Trainer(model=model, -TypeError: Trainer.__init__() got an unexpected keyword argument 'tokenizer' -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 428, in train - trainer = transformers.Trainer(model=model, -TypeError: Trainer.__init__() got an unexpected keyword argument 'tokenizer' diff --git a/wandb/run-20260305_041641-z1l3g705/files/requirements.txt b/wandb/run-20260305_041641-z1l3g705/files/requirements.txt deleted file mode 100644 index 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-multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 -accelerate==1.13.0 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -triton==3.6.0 -nvidia-nccl-cu12==2.27.5 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -cuda-pathfinder==1.4.0 -shellingham==1.5.4 -torchaudio==2.5.1 -nvidia-cufile-cu12==1.13.1.3 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -nvidia-nvjitlink-cu12==12.8.93 -click==8.3.1 -MarkupSafe==3.0.2 -nvidia-nvshmem-cu12==3.4.5 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/home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 - - --tokenizer_path - - /home/n5huang/dna_token/tokenizer_evaluation/baseline_bpe/tokenizer.json - - --trust_remote_code - - "True" - - --data_path - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/promoter_tata/split - - --kmer - - "-1" - - --run_name - - hg38_BPE_base__baseline_bpe_tokenizer_3e-5_promoter_tata_seed42 - - --model_max_length - - "80" - - --per_device_train_batch_size - - "128" - - --per_device_eval_batch_size - - "128" - - --gradient_accumulation_steps - - "1" - - --learning_rate - - "3e-5" - - --num_train_epochs - - "2" - - --fp16 - - --save_steps - - "200" - - --output_dir - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/promoter_tata - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "546953314304" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: 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python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:16:54.178391Z" - writerId: r86o8jyj5o8812x9grc89iclsw0f2lrh - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_041654-airood7a/files/output.log b/wandb/run-20260305_041654-airood7a/files/output.log deleted file mode 100644 index 8e764b605f8f443087635e7a0b59da399227b9cb..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_041654-airood7a/files/output.log +++ /dev/null @@ -1,35 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 11882.88it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -classifier.bias | MISSING | -bert.pooler.dense.weight | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 428, in train - trainer = transformers.Trainer(model=model, -TypeError: Trainer.__init__() got an unexpected keyword argument 'tokenizer' -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 428, in train - trainer = transformers.Trainer(model=model, -TypeError: Trainer.__init__() got an unexpected keyword argument 'tokenizer' diff --git a/wandb/run-20260305_041654-airood7a/files/requirements.txt b/wandb/run-20260305_041654-airood7a/files/requirements.txt deleted file mode 100644 index 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/home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 - - --tokenizer_path - - /home/n5huang/dna_token/tokenizer_evaluation/baseline_bpe/tokenizer.json - - --trust_remote_code - - "True" - - --data_path - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/splice_sites_acceptors/split - - --kmer - - "-1" - - --run_name - - hg38_BPE_base__baseline_bpe_tokenizer_3e-5_splice_sites_acceptors_seed42 - - --model_max_length - - "140" - - --per_device_train_batch_size - - "128" - - --per_device_eval_batch_size - - "128" - - --gradient_accumulation_steps - - "1" - - --learning_rate - - "3e-5" - - --num_train_epochs - - "4" - - --fp16 - - --save_steps - - "200" - - --output_dir - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_acceptors - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "546953392128" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA 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/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:17:04.307598Z" - writerId: 19ao5fws66ugn38z5x5phxmoapcy2xjd - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_041704-ky8ncs80/files/output.log b/wandb/run-20260305_041704-ky8ncs80/files/output.log deleted file mode 100644 index 801b3b772a5a540745c6eeb314574d49d579d1a2..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_041704-ky8ncs80/files/output.log +++ /dev/null @@ -1,35 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 19831.69it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -classifier.bias | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 428, in train - trainer = transformers.Trainer(model=model, -TypeError: Trainer.__init__() got an unexpected keyword argument 'tokenizer' -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 428, in train - trainer = transformers.Trainer(model=model, -TypeError: Trainer.__init__() got an unexpected keyword argument 'tokenizer' diff --git a/wandb/run-20260305_041704-ky8ncs80/files/requirements.txt b/wandb/run-20260305_041704-ky8ncs80/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_041704-ky8ncs80/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 -accelerate==1.13.0 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -triton==3.6.0 -nvidia-nccl-cu12==2.27.5 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -cuda-pathfinder==1.4.0 -shellingham==1.5.4 -torchaudio==2.5.1 -nvidia-cufile-cu12==1.13.1.3 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -nvidia-nvjitlink-cu12==12.8.93 -click==8.3.1 -MarkupSafe==3.0.2 -nvidia-nvshmem-cu12==3.4.5 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/home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 - - --tokenizer_path - - /home/n5huang/dna_token/tokenizer_evaluation/baseline_bpe/tokenizer.json - - --trust_remote_code - - "True" - - --data_path - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/splice_sites_all/split - - --kmer - - "-1" - - --run_name - - hg38_BPE_base__baseline_bpe_tokenizer_3e-5_splice_sites_all_seed42 - - --model_max_length - - "140" - - --per_device_train_batch_size - - "128" - - --per_device_eval_batch_size - - "128" - - --gradient_accumulation_steps - - "1" - - --learning_rate - - "3e-5" - - --num_train_epochs - - "4" - - --fp16 - - --save_steps - - "200" - - --output_dir - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_all - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "546953535488" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB 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/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:17:19.713710Z" - writerId: rcg2bjwm6cd2jh2z2jb0k1k9d53s9xsh - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_041719-roa03rlv/files/output.log b/wandb/run-20260305_041719-roa03rlv/files/output.log deleted file mode 100644 index 4b3868f88691ee93224215e1e6bdf6b05980740c..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_041719-roa03rlv/files/output.log +++ /dev/null @@ -1,35 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 21353.13it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -bert.pooler.dense.weight | MISSING | -classifier.bias | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 428, in train - trainer = transformers.Trainer(model=model, -TypeError: Trainer.__init__() got an unexpected keyword argument 'tokenizer' -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 428, in train - trainer = transformers.Trainer(model=model, -TypeError: Trainer.__init__() got an unexpected keyword argument 'tokenizer' diff --git a/wandb/run-20260305_041719-roa03rlv/files/requirements.txt b/wandb/run-20260305_041719-roa03rlv/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_041719-roa03rlv/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 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sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 23765.76it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -classifier.weight | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.bias | MISSING | -bert.pooler.dense.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 428, in train - trainer = transformers.Trainer(model=model, -TypeError: Trainer.__init__() got an unexpected keyword argument 'tokenizer' -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 428, in train - trainer = transformers.Trainer(model=model, -TypeError: Trainer.__init__() got an unexpected keyword argument 'tokenizer' diff --git a/wandb/run-20260305_041734-ptojl55r/files/requirements.txt b/wandb/run-20260305_041734-ptojl55r/files/requirements.txt deleted file mode 100644 index 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- - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "546955759616" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: 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python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:17:49.955451Z" - writerId: b424w1d3xn8gdv227h71tg5t7aptf1cd - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_041749-rf6vky9t/files/output.log b/wandb/run-20260305_041749-rf6vky9t/files/output.log deleted file mode 100644 index 09588f007e81834f0438c15683ba072bc90e3568..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_041749-rf6vky9t/files/output.log +++ /dev/null @@ -1,35 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 21951.74it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -classifier.weight | MISSING | -classifier.bias | MISSING | -bert.pooler.dense.bias | MISSING | -bert.pooler.dense.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 428, in train - trainer = transformers.Trainer(model=model, -TypeError: Trainer.__init__() got an unexpected keyword argument 'tokenizer' -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 428, in train - trainer = transformers.Trainer(model=model, -TypeError: Trainer.__init__() got an unexpected keyword argument 'tokenizer' diff --git a/wandb/run-20260305_041749-rf6vky9t/files/requirements.txt b/wandb/run-20260305_041749-rf6vky9t/files/requirements.txt deleted file mode 100644 index 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/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K27ac - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "546955886592" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:18:06.975951Z" - writerId: aaooc2334nl1m3jko7jq2z8uhlz8xvlr - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_041806-kwa9qoe4/files/output.log b/wandb/run-20260305_041806-kwa9qoe4/files/output.log deleted file mode 100644 index ee1fd1ee60139210add7096d145823185a12430e..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_041806-kwa9qoe4/files/output.log +++ /dev/null @@ -1,35 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 17561.03it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -classifier.bias | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 428, in train - trainer = transformers.Trainer(model=model, -TypeError: Trainer.__init__() got an unexpected keyword argument 'tokenizer' -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 428, in train - trainer = transformers.Trainer(model=model, -TypeError: Trainer.__init__() got an unexpected keyword argument 'tokenizer' diff --git a/wandb/run-20260305_041806-kwa9qoe4/files/requirements.txt b/wandb/run-20260305_041806-kwa9qoe4/files/requirements.txt deleted file mode 100644 index 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-multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 -accelerate==1.13.0 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -triton==3.6.0 -nvidia-nccl-cu12==2.27.5 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -cuda-pathfinder==1.4.0 -shellingham==1.5.4 -torchaudio==2.5.1 -nvidia-cufile-cu12==1.13.1.3 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -nvidia-nvjitlink-cu12==12.8.93 -click==8.3.1 -MarkupSafe==3.0.2 -nvidia-nvshmem-cu12==3.4.5 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/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K27me3 - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "546956042240" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:18:24.094911Z" - writerId: 3rs30tonz0df94kpc5kdb45xa72caj4w - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_041824-98h72ha4/files/output.log b/wandb/run-20260305_041824-98h72ha4/files/output.log deleted file mode 100644 index b9f86fca9c5443eea142b1a4924dc6695396acac..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_041824-98h72ha4/files/output.log +++ /dev/null @@ -1,35 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 24805.29it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -bert.pooler.dense.bias | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.weight | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 428, in train - trainer = transformers.Trainer(model=model, -TypeError: Trainer.__init__() got an unexpected keyword argument 'tokenizer' -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 428, in train - trainer = transformers.Trainer(model=model, -TypeError: Trainer.__init__() got an unexpected keyword argument 'tokenizer' diff --git a/wandb/run-20260305_041824-98h72ha4/files/requirements.txt b/wandb/run-20260305_041824-98h72ha4/files/requirements.txt deleted file mode 100644 index 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-multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 -accelerate==1.13.0 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -triton==3.6.0 -nvidia-nccl-cu12==2.27.5 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -cuda-pathfinder==1.4.0 -shellingham==1.5.4 -torchaudio==2.5.1 -nvidia-cufile-cu12==1.13.1.3 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -nvidia-nvjitlink-cu12==12.8.93 -click==8.3.1 -MarkupSafe==3.0.2 -nvidia-nvshmem-cu12==3.4.5 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/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K36me3 - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "546958049280" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:18:40.875191Z" - writerId: 92l2t5ron1d7u16je6pi50co15ukgghp - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_041840-egr782z4/files/output.log b/wandb/run-20260305_041840-egr782z4/files/output.log deleted file mode 100644 index 94f5da3a9688d50169533fcdc9fd1e1a3c4fdee3..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_041840-egr782z4/files/output.log +++ /dev/null @@ -1,35 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 22475.84it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -bert.pooler.dense.bias | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.weight | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 428, in train - trainer = transformers.Trainer(model=model, -TypeError: Trainer.__init__() got an unexpected keyword argument 'tokenizer' -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 428, in train - trainer = transformers.Trainer(model=model, -TypeError: Trainer.__init__() got an unexpected keyword argument 'tokenizer' diff --git a/wandb/run-20260305_041840-egr782z4/files/requirements.txt b/wandb/run-20260305_041840-egr782z4/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_041840-egr782z4/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 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/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K4me1 - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "546958192640" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:18:58.248869Z" - writerId: evva2gp22ys8yntnjrctm510f0svygai - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_041858-y5ssytae/files/output.log b/wandb/run-20260305_041858-y5ssytae/files/output.log deleted file mode 100644 index fa70607b269607dde41be3da23da51863c8f66f0..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_041858-y5ssytae/files/output.log +++ /dev/null @@ -1,35 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 20478.81it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -bert.pooler.dense.bias | MISSING | -classifier.bias | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - os.makedirs(results_path, exist_ok=True) - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 428, in train - # define trainer -TypeError: Trainer.__init__() got an unexpected keyword argument 'tokenizer' -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in - os.makedirs(results_path, exist_ok=True) - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 428, in train - # define trainer -TypeError: Trainer.__init__() got an unexpected keyword argument 'tokenizer' diff --git a/wandb/run-20260305_041858-y5ssytae/files/requirements.txt b/wandb/run-20260305_041858-y5ssytae/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_041858-y5ssytae/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 -accelerate==1.13.0 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -triton==3.6.0 -nvidia-nccl-cu12==2.27.5 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -cuda-pathfinder==1.4.0 -shellingham==1.5.4 -torchaudio==2.5.1 -nvidia-cufile-cu12==1.13.1.3 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -nvidia-nvjitlink-cu12==12.8.93 -click==8.3.1 -MarkupSafe==3.0.2 -nvidia-nvshmem-cu12==3.4.5 -urllib3==2.6.3 -cuda-bindings==12.9.4 -propcache==0.4.1 -nvidia-cusolver-cu12==11.7.3.90 -sympy==1.14.0 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -nvidia-cuda-runtime-cu12==12.8.90 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_041858-y5ssytae/files/wandb-metadata.json b/wandb/run-20260305_041858-y5ssytae/files/wandb-metadata.json deleted file mode 100644 index 8ea33942bf561e18cc908f6122147ef5838a198e..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_041858-y5ssytae/files/wandb-metadata.json +++ /dev/null @@ -1,134 +0,0 @@ -{ - "os": "Linux-5.15.0-72-generic-x86_64-with-glibc2.35", - "python": "CPython 3.10.19", - "startedAt": "2026-03-05T04:18:58.248869Z", - "args": [ - "--model_name_or_path", - "/home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000", - "--tokenizer_path", - "/home/n5huang/dna_token/tokenizer_evaluation/baseline_bpe/tokenizer.json", - "--trust_remote_code", - "True", - "--data_path", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/H3K4me1/split", - "--kmer", - "-1", - "--run_name", - "hg38_BPE_base__baseline_bpe_tokenizer_3e-5_H3K4me1_seed42", - "--model_max_length", - "220", - "--per_device_train_batch_size", - "128", - "--per_device_eval_batch_size", - "128", - "--gradient_accumulation_steps", - "1", - "--learning_rate", - "3e-5", - "--num_train_epochs", - "2", - "--fp16", - "--save_steps", - "200", - "--output_dir", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K4me1", - "--evaluation_strategy", - "steps", - "--eval_steps", - "200", - "--warmup_steps", - "30", - "--logging_steps", - "100000", - "--log_level", - "info", - "--seed", - "42", - "--find_unused_parameters", - "False", - "--project_name", - "genomic_bench_tune_hg38_1024" - ], 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a/wandb/run-20260305_041915-3xgbjp2x/files/output.log +++ /dev/null @@ -1,37 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 22835.68it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -bert.pooler.dense.bias | MISSING | -classifier.bias | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 25,710 - Num Epochs = 2 - Num update steps per epoch = 201 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 402 - Number of trainable parameters = 44,302,082 - 50%|████▉ | 199/402 [00:17<00:17, 11.76it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K4me2/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K4me2/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.16it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K4me2/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K4me2/checkpoint-200/tokenizer_config.json diff --git a/wandb/run-20260305_041915-3xgbjp2x/files/requirements.txt b/wandb/run-20260305_041915-3xgbjp2x/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_041915-3xgbjp2x/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_042131-26uulbed/files/output.log b/wandb/run-20260305_042131-26uulbed/files/output.log deleted file mode 100644 index ee7b1746e22a255380131175b4374be747c903dd..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_042131-26uulbed/files/output.log +++ /dev/null @@ -1,69 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 16179.38it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -bert.pooler.dense.bias | MISSING | -classifier.weight | MISSING | -classifier.bias | MISSING | -bert.pooler.dense.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 4 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 828 - Number of trainable parameters = 44,302,082 - 24%|██▍ | 199/828 [00:08<00:26, 24.02it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.01it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers/checkpoint-200/tokenizer_config.json - 48%|████▊ | 400/828 [00:17<00:17, 24.68it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.61it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers/checkpoint-400/tokenizer_config.json - 72%|███████▏ | 598/828 [00:26<00:09, 24.64it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers/checkpoint-600 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers/checkpoint-600/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.64it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers/checkpoint-600/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers/checkpoint-600/tokenizer_config.json - 96%|█████████▋| 799/828 [00:35<00:01, 24.69it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers/checkpoint-800 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers/checkpoint-800/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.23it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers/checkpoint-800/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers/checkpoint-800/tokenizer_config.json -100%|█████████▉| 826/828 [00:37<00:00, 21.36it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers/checkpoint-828 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers/checkpoint-828/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.89it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers/checkpoint-828/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers/checkpoint-828/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 828/828 [00:38<00:00, 21.38it/s] -{'train_runtime': '38.73', 'train_samples_per_second': '2727', 'train_steps_per_second': '21.38', 'train_loss': '0.4996', 'epoch': '4'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 80.16it/s] diff --git a/wandb/run-20260305_042131-26uulbed/files/requirements.txt b/wandb/run-20260305_042131-26uulbed/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_042131-26uulbed/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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wandb-AsyncioManager-main:1601812 [mailbox.py:close():155] Closing mailbox, abandoning 1 handles. diff --git a/wandb/run-20260305_042131-26uulbed/run-26uulbed.wandb b/wandb/run-20260305_042131-26uulbed/run-26uulbed.wandb deleted file mode 100644 index c9c075bd398448eca3e3b0d7bb486dc583eb894e..0000000000000000000000000000000000000000 Binary files a/wandb/run-20260305_042131-26uulbed/run-26uulbed.wandb and /dev/null differ diff --git a/wandb/run-20260305_042226-hilhn7cj/files/config.yaml b/wandb/run-20260305_042226-hilhn7cj/files/config.yaml deleted file mode 100644 index 402eb8a9b818a29aaba60851e9bf8c307fc2ff69..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_042226-hilhn7cj/files/config.yaml +++ /dev/null @@ -1,139 +0,0 @@ -_wandb: - value: - cli_version: 0.25.0 - e: - hwbxcjahd567hsnve1s66v9ax8d3mjtc: - args: - - --model_name_or_path - - /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 - - --tokenizer_path - - 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--find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "551214071808" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:22:26.401032Z" - writerId: hwbxcjahd567hsnve1s66v9ax8d3mjtc - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_042226-hilhn7cj/files/output.log b/wandb/run-20260305_042226-hilhn7cj/files/output.log deleted file mode 100644 index 2907b70ebeac44a6c581711d9346744c65b21636..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_042226-hilhn7cj/files/output.log +++ /dev/null @@ -1,69 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 22574.05it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -bert.pooler.dense.weight | MISSING | -classifier.bias | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 4 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 828 - Number of trainable parameters = 44,302,851 - 24%|██▍ | 198/828 [00:09<00:25, 24.31it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers_types/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers_types/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.41it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers_types/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers_types/checkpoint-200/tokenizer_config.json - 48%|████▊ | 398/828 [00:18<00:17, 24.15it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers_types/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers_types/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.31it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers_types/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers_types/checkpoint-400/tokenizer_config.json - 72%|███████▏ | 599/828 [00:28<00:11, 20.76it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers_types/checkpoint-600 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers_types/checkpoint-600/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 2.93it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers_types/checkpoint-600/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers_types/checkpoint-600/tokenizer_config.json - 97%|█████████▋| 800/828 [00:37<00:01, 22.96it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers_types/checkpoint-800 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers_types/checkpoint-800/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.07it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers_types/checkpoint-800/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers_types/checkpoint-800/tokenizer_config.json -100%|█████████▉| 827/828 [00:40<00:00, 20.37it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers_types/checkpoint-828 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers_types/checkpoint-828/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.23it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers_types/checkpoint-828/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers_types/checkpoint-828/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 828/828 [00:41<00:00, 20.15it/s] -{'train_runtime': '41.09', 'train_samples_per_second': '2570', 'train_steps_per_second': '20.15', 'train_loss': '0.6279', 'epoch': '4'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 81.07it/s] diff --git a/wandb/run-20260305_042226-hilhn7cj/files/requirements.txt b/wandb/run-20260305_042226-hilhn7cj/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_042226-hilhn7cj/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 -accelerate==1.13.0 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -triton==3.6.0 -nvidia-nccl-cu12==2.27.5 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -cuda-pathfinder==1.4.0 -shellingham==1.5.4 -torchaudio==2.5.1 -nvidia-cufile-cu12==1.13.1.3 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -nvidia-nvjitlink-cu12==12.8.93 -click==8.3.1 -MarkupSafe==3.0.2 -nvidia-nvshmem-cu12==3.4.5 -urllib3==2.6.3 -cuda-bindings==12.9.4 -propcache==0.4.1 -nvidia-cusolver-cu12==11.7.3.90 -sympy==1.14.0 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -nvidia-cuda-runtime-cu12==12.8.90 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_042226-hilhn7cj/files/wandb-metadata.json b/wandb/run-20260305_042226-hilhn7cj/files/wandb-metadata.json deleted file mode 100644 index 66eec2147e562301717b17bf88d4491adf002b5b..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_042226-hilhn7cj/files/wandb-metadata.json +++ /dev/null @@ -1,134 +0,0 @@ -{ - "os": "Linux-5.15.0-72-generic-x86_64-with-glibc2.35", - "python": "CPython 3.10.19", - "startedAt": "2026-03-05T04:22:26.401032Z", - "args": [ - "--model_name_or_path", - "/home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000", - "--tokenizer_path", - "/home/n5huang/dna_token/tokenizer_evaluation/baseline_bpe/tokenizer.json", - "--trust_remote_code", - "True", - "--data_path", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/enhancers_types/split", - "--kmer", - "-1", - "--run_name", - "hg38_BPE_base__baseline_bpe_tokenizer_3e-5_enhancers_types_seed42", - "--model_max_length", - "100", - "--per_device_train_batch_size", - "128", - "--per_device_eval_batch_size", - "128", - 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--find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "551216431104" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:23:22.238334Z" - writerId: izekvolzytb2qin9lun1xg2xcdfbzvpc - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_042322-ca70udyh/files/output.log b/wandb/run-20260305_042322-ca70udyh/files/output.log deleted file mode 100644 index 468ff81323c4897e4224e24b7bea656dd57c8452..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_042322-ca70udyh/files/output.log +++ /dev/null @@ -1,54 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 21871.27it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -bert.pooler.dense.weight | MISSING | -classifier.weight | MISSING | -classifier.bias | MISSING | -bert.pooler.dense.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 25,267 - Num Epochs = 2 - Num update steps per epoch = 198 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 396 - Number of trainable parameters = 44,302,082 - 51%|█████ | 200/396 [00:07<00:06, 29.78it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/promoter_all/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/promoter_all/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.36it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/promoter_all/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/promoter_all/checkpoint-200/tokenizer_config.json -100%|█████████▉| 395/396 [00:15<00:00, 26.70it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/promoter_all/checkpoint-396 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/promoter_all/checkpoint-396/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.23it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/promoter_all/checkpoint-396/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/promoter_all/checkpoint-396/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 396/396 [00:15<00:00, 24.85it/s] -{'train_runtime': '15.94', 'train_samples_per_second': '3171', 'train_steps_per_second': '24.85', 'train_loss': '0.3276', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3159 - Batch size = 128 -100%|██████████| 25/25 [00:00<00:00, 97.61it/s] diff --git a/wandb/run-20260305_042322-ca70udyh/files/requirements.txt b/wandb/run-20260305_042322-ca70udyh/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_042322-ca70udyh/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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/home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -bert.pooler.dense.weight | MISSING | -classifier.bias | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 25,097 - Num Epochs = 2 - Num update steps per epoch = 197 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 394 - Number of trainable parameters = 44,302,082 - 51%|█████ | 199/394 [00:07<00:07, 27.52it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/promoter_no_tata/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/promoter_no_tata/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.89it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/promoter_no_tata/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/promoter_no_tata/checkpoint-200/tokenizer_config.json - 99%|█████████▉| 391/394 [00:15<00:00, 28.63it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/promoter_no_tata/checkpoint-394 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/promoter_no_tata/checkpoint-394/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.03it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/promoter_no_tata/checkpoint-394/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/promoter_no_tata/checkpoint-394/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 394/394 [00:16<00:00, 24.55it/s] -{'train_runtime': '16.04', 'train_samples_per_second': '3129', 'train_steps_per_second': '24.56', 'train_loss': '0.3115', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3138 - Batch size = 128 -100%|██████████| 25/25 [00:00<00:00, 93.55it/s] diff --git a/wandb/run-20260305_042351-jf5f6mav/files/requirements.txt b/wandb/run-20260305_042351-jf5f6mav/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_042351-jf5f6mav/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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--find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "546970484736" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:24:21.108868Z" - writerId: bpfnbsm0qud3ywvwfb8yrtg7kfz0oi6z - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_042421-xiqkd5oe/files/output.log b/wandb/run-20260305_042421-xiqkd5oe/files/output.log deleted file mode 100644 index b9ff26563ab9eac0d8779870d520765625fcced3..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_042421-xiqkd5oe/files/output.log +++ /dev/null @@ -1,49 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 18934.64it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -classifier.weight | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.bias | MISSING | -bert.pooler.dense.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 4,219 - Num Epochs = 2 - Num update steps per epoch = 33 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 66 - Number of trainable parameters = 44,302,082 - 97%|█████████▋| 64/66 [00:02<00:00, 27.14it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/promoter_tata/checkpoint-66 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/promoter_tata/checkpoint-66/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.94it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/promoter_tata/checkpoint-66/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/promoter_tata/checkpoint-66/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 66/66 [00:03<00:00, 17.82it/s] -{'train_runtime': '3.704', 'train_samples_per_second': '2278', 'train_steps_per_second': '17.82', 'train_loss': '0.4528', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 528 - Batch size = 128 -100%|██████████| 5/5 [00:00<00:00, 93.06it/s] diff --git a/wandb/run-20260305_042421-xiqkd5oe/files/requirements.txt b/wandb/run-20260305_042421-xiqkd5oe/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_042421-xiqkd5oe/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 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- - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "546972508160" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:24:35.768267Z" - writerId: 9o6fmxnql3xudnec0xxuhi5cyz9szzci - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_042435-drr0w3s3/files/output.log b/wandb/run-20260305_042435-drr0w3s3/files/output.log deleted file mode 100644 index 2f4971ec868cdca4c9519840a65694610b938727..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_042435-drr0w3s3/files/output.log +++ /dev/null @@ -1,69 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 12423.01it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -classifier.bias | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.weight | MISSING | -bert.pooler.dense.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 4 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 828 - Number of trainable parameters = 44,302,082 - 24%|██▍ | 200/828 [00:12<00:35, 17.69it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.14it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-200/tokenizer_config.json - 48%|████▊ | 399/828 [00:24<00:24, 17.60it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.13it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-400/tokenizer_config.json - 72%|███████▏ | 600/828 [00:36<00:13, 17.16it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-600 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-600/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.10it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-600/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-600/tokenizer_config.json - 96%|█████████▋| 799/828 [00:48<00:01, 16.92it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-800 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-800/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.72it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-800/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-800/tokenizer_config.json -100%|█████████▉| 827/828 [00:51<00:00, 17.15it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-828 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-828/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.97it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-828/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-828/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 828/828 [00:51<00:00, 15.96it/s] -{'train_runtime': '51.88', 'train_samples_per_second': '2035', 'train_steps_per_second': '15.96', 'train_loss': '0.403', 'epoch': '4'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 59.38it/s] diff --git a/wandb/run-20260305_042435-drr0w3s3/files/requirements.txt b/wandb/run-20260305_042435-drr0w3s3/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_042435-drr0w3s3/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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/data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:25:43.576218Z" - writerId: 5gwszw91p20hbtskwdcl8iveqshq3u2l - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_042543-4d90jy5b/files/output.log b/wandb/run-20260305_042543-4d90jy5b/files/output.log deleted file mode 100644 index 8fc366b85d496bf15f0b05e4ac0606217d9c9a2d..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_042543-4d90jy5b/files/output.log +++ /dev/null @@ -1,69 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 21456.96it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -classifier.weight | MISSING | -bert.pooler.dense.weight | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 4 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 828 - Number of trainable parameters = 44,302,851 - 24%|██▍ | 199/828 [00:11<00:35, 17.62it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_all/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_all/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.92it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_all/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_all/checkpoint-200/tokenizer_config.json - 48%|████▊ | 400/828 [00:24<00:25, 17.01it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_all/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_all/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.16it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_all/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_all/checkpoint-400/tokenizer_config.json - 72%|███████▏ | 599/828 [00:36<00:13, 17.27it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_all/checkpoint-600 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_all/checkpoint-600/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.27it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_all/checkpoint-600/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_all/checkpoint-600/tokenizer_config.json - 97%|█████████▋| 800/828 [00:48<00:01, 17.53it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_all/checkpoint-800 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_all/checkpoint-800/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.29it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_all/checkpoint-800/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_all/checkpoint-800/tokenizer_config.json -100%|█████████▉| 826/828 [00:50<00:00, 16.95it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_all/checkpoint-828 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_all/checkpoint-828/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.90it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_all/checkpoint-828/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_all/checkpoint-828/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 828/828 [00:51<00:00, 15.94it/s] -{'train_runtime': '51.95', 'train_samples_per_second': '2033', 'train_steps_per_second': '15.94', 'train_loss': '0.6719', 'epoch': '4'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 60.59it/s] diff --git a/wandb/run-20260305_042543-4d90jy5b/files/requirements.txt b/wandb/run-20260305_042543-4d90jy5b/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_042543-4d90jy5b/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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- - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "546977206272" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:26:50.822015Z" - writerId: btckqm67d5sy6h4stu68ddsfba35f4g0 - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_042650-ftko818u/files/output.log b/wandb/run-20260305_042650-ftko818u/files/output.log deleted file mode 100644 index 1cc95c6bb6092ff99c90c1f467fa7aed89327c55..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_042650-ftko818u/files/output.log +++ /dev/null @@ -1,69 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 18357.80it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -classifier.weight | MISSING | -bert.pooler.dense.bias | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 4 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 828 - Number of trainable parameters = 44,302,082 - 24%|██▍ | 199/828 [00:12<00:35, 17.63it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.22it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-200/tokenizer_config.json - 48%|████▊ | 400/828 [00:24<00:25, 17.12it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.35it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-400/tokenizer_config.json - 72%|███████▏ | 599/828 [00:36<00:13, 17.60it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-600 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-600/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.45it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-600/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-600/tokenizer_config.json - 97%|█████████▋| 800/828 [00:48<00:01, 17.05it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-800 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-800/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.84it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-800/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-800/tokenizer_config.json -100%|█████████▉| 826/828 [00:51<00:00, 16.63it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-828 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-828/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.20it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-828/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-828/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 828/828 [00:52<00:00, 15.86it/s] -{'train_runtime': '52.2', 'train_samples_per_second': '2023', 'train_steps_per_second': '15.86', 'train_loss': '0.3911', 'epoch': '4'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 60.99it/s] diff --git a/wandb/run-20260305_042650-ftko818u/files/requirements.txt b/wandb/run-20260305_042650-ftko818u/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_042650-ftko818u/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 -accelerate==1.13.0 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -triton==3.6.0 -nvidia-nccl-cu12==2.27.5 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -cuda-pathfinder==1.4.0 -shellingham==1.5.4 -torchaudio==2.5.1 -nvidia-cufile-cu12==1.13.1.3 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -nvidia-nvjitlink-cu12==12.8.93 -click==8.3.1 -MarkupSafe==3.0.2 -nvidia-nvshmem-cu12==3.4.5 -urllib3==2.6.3 -cuda-bindings==12.9.4 -propcache==0.4.1 -nvidia-cusolver-cu12==11.7.3.90 -sympy==1.14.0 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -nvidia-cuda-runtime-cu12==12.8.90 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_042650-ftko818u/files/wandb-metadata.json b/wandb/run-20260305_042650-ftko818u/files/wandb-metadata.json deleted file mode 100644 index 90fcdae5727b592a457b3ba7a77baddf568c7a86..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_042650-ftko818u/files/wandb-metadata.json +++ /dev/null @@ -1,134 +0,0 @@ -{ - "os": "Linux-5.15.0-72-generic-x86_64-with-glibc2.35", - "python": "CPython 3.10.19", - "startedAt": "2026-03-05T04:26:50.822015Z", - "args": [ - "--model_name_or_path", - "/home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000", - "--tokenizer_path", - "/home/n5huang/dna_token/tokenizer_evaluation/baseline_bpe/tokenizer.json", - "--trust_remote_code", - "True", - "--data_path", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/splice_sites_donors/split", - "--kmer", - "-1", - "--run_name", - "hg38_BPE_base__baseline_bpe_tokenizer_3e-5_splice_sites_donors_seed42", - "--model_max_length", - "140", - "--per_device_train_batch_size", - "128", - "--per_device_eval_batch_size", - "128", - 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- - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "546979676160" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA 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"2026-03-05T04:27:58.594026Z" - writerId: bdaybjhkeeoz9c121dllsqa0esqyq2zn - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_042758-ye0fbjxh/files/output.log b/wandb/run-20260305_042758-ye0fbjxh/files/output.log deleted file mode 100644 index 86a765a7f4311016dd237c53f642d81f6061aad4..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_042758-ye0fbjxh/files/output.log +++ /dev/null @@ -1,59 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 23697.96it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -classifier.bias | MISSING | -bert.pooler.dense.bias | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 2 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 414 - Number of trainable parameters = 44,302,082 - 48%|████▊ | 199/414 [00:18<00:18, 11.46it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H2AFZ/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H2AFZ/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.91it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H2AFZ/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H2AFZ/checkpoint-200/tokenizer_config.json - 96%|█████████▋| 399/414 [00:36<00:01, 11.55it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H2AFZ/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H2AFZ/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.66it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H2AFZ/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H2AFZ/checkpoint-400/tokenizer_config.json -100%|█████████▉| 413/414 [00:38<00:00, 9.94it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H2AFZ/checkpoint-414 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H2AFZ/checkpoint-414/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.25it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H2AFZ/checkpoint-414/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H2AFZ/checkpoint-414/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 414/414 [00:39<00:00, 10.57it/s] -{'train_runtime': '39.18', 'train_samples_per_second': '1348', 'train_steps_per_second': '10.57', 'train_loss': '0.5192', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 40.12it/s] diff --git a/wandb/run-20260305_042758-ye0fbjxh/files/requirements.txt b/wandb/run-20260305_042758-ye0fbjxh/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_042758-ye0fbjxh/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:28:55.066672Z" - writerId: im4vg7k33qak83mur2qjf6hnfc79e3z5 - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_042855-8gkb9dwq/files/output.log b/wandb/run-20260305_042855-8gkb9dwq/files/output.log deleted file mode 100644 index 7cb006450f3aae459ffd9635f795170cc58707cb..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_042855-8gkb9dwq/files/output.log +++ /dev/null @@ -1,54 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 21374.68it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -classifier.bias | MISSING | -bert.pooler.dense.weight | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 25,292 - Num Epochs = 2 - Num update steps per epoch = 198 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 396 - Number of trainable parameters = 44,302,082 - 50%|█████ | 199/396 [00:17<00:16, 12.18it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K27ac/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K27ac/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.71it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K27ac/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K27ac/checkpoint-200/tokenizer_config.json -100%|█████████▉| 395/396 [00:35<00:00, 11.38it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K27ac/checkpoint-396 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K27ac/checkpoint-396/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.28it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K27ac/checkpoint-396/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K27ac/checkpoint-396/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 396/396 [00:35<00:00, 11.01it/s] -{'train_runtime': '35.98', 'train_samples_per_second': '1406', 'train_steps_per_second': '11.01', 'train_loss': '0.5385', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3163 - Batch size = 128 -100%|██████████| 25/25 [00:00<00:00, 39.84it/s] diff --git a/wandb/run-20260305_042855-8gkb9dwq/files/requirements.txt b/wandb/run-20260305_042855-8gkb9dwq/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_042855-8gkb9dwq/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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"2026-03-05T04:29:48.332193Z" - writerId: cudj8zhl4bfn54e4h6hlx71ylvtk57yu - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_042948-99ysdo6o/files/output.log b/wandb/run-20260305_042948-99ysdo6o/files/output.log deleted file mode 100644 index 36633f799c62b475e428e20ad68aaf6fd634e725..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_042948-99ysdo6o/files/output.log +++ /dev/null @@ -1,59 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 20634.42it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.decoder.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -classifier.weight | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.bias | MISSING | -bert.pooler.dense.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 2 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 414 - Number of trainable parameters = 44,302,082 - 48%|████▊ | 199/414 [00:17<00:18, 11.43it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K27me3/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K27me3/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.86it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K27me3/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K27me3/checkpoint-200/tokenizer_config.json - 96%|█████████▋| 399/414 [00:35<00:01, 11.51it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K27me3/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K27me3/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.86it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K27me3/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K27me3/checkpoint-400/tokenizer_config.json -100%|█████████▉| 413/414 [00:37<00:00, 10.05it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K27me3/checkpoint-414 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K27me3/checkpoint-414/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.04it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K27me3/checkpoint-414/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K27me3/checkpoint-414/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 414/414 [00:38<00:00, 10.86it/s] -{'train_runtime': '38.12', 'train_samples_per_second': '1385', 'train_steps_per_second': '10.86', 'train_loss': '0.4646', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 40.34it/s] diff --git a/wandb/run-20260305_042948-99ysdo6o/files/requirements.txt b/wandb/run-20260305_042948-99ysdo6o/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_042948-99ysdo6o/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 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"2026-03-05T04:30:44.587727Z" - writerId: yg2mb635g1wdmvf3p6jrrxey93f1i36r - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_043044-go5jjb3e/files/output.log b/wandb/run-20260305_043044-go5jjb3e/files/output.log deleted file mode 100644 index 9344b1f86ca788029393967d47260c37fc323b5c..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_043044-go5jjb3e/files/output.log +++ /dev/null @@ -1,59 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 22466.31it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -classifier.weight | MISSING | -bert.pooler.dense.weight | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 2 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 414 - Number of trainable parameters = 44,302,082 - 48%|████▊ | 199/414 [00:17<00:18, 11.65it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K36me3/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K36me3/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.91it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K36me3/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K36me3/checkpoint-200/tokenizer_config.json - 96%|█████████▋| 399/414 [00:35<00:01, 11.57it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K36me3/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K36me3/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.71it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K36me3/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K36me3/checkpoint-400/tokenizer_config.json -100%|█████████▉| 413/414 [00:37<00:00, 10.08it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K36me3/checkpoint-414 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K36me3/checkpoint-414/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 5.15it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K36me3/checkpoint-414/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K36me3/checkpoint-414/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 414/414 [00:38<00:00, 10.81it/s] -{'train_runtime': '38.3', 'train_samples_per_second': '1378', 'train_steps_per_second': '10.81', 'train_loss': '0.463', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 39.28it/s] diff --git a/wandb/run-20260305_043044-go5jjb3e/files/requirements.txt b/wandb/run-20260305_043044-go5jjb3e/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_043044-go5jjb3e/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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"2026-03-05T04:31:40.816065Z" - writerId: oz5elqq21iz7wjj6z8onkf6erlpgbp0c - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_043140-550ullwi/files/output.log b/wandb/run-20260305_043140-550ullwi/files/output.log deleted file mode 100644 index bfeab29ade18b97171ebfde622c04aa1e168180f..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_043140-550ullwi/files/output.log +++ /dev/null @@ -1,59 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 22389.13it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -classifier.bias | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 2 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 414 - Number of trainable parameters = 44,302,082 - 48%|████▊ | 199/414 [00:17<00:18, 11.59it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K4me1/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K4me1/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 5.06it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K4me1/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K4me1/checkpoint-200/tokenizer_config.json - 96%|█████████▋| 399/414 [00:35<00:01, 11.54it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K4me1/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K4me1/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 5.18it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K4me1/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K4me1/checkpoint-400/tokenizer_config.json -100%|█████████▉| 413/414 [00:37<00:00, 10.35it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K4me1/checkpoint-414 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K4me1/checkpoint-414/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 5.01it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K4me1/checkpoint-414/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K4me1/checkpoint-414/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 414/414 [00:38<00:00, 10.89it/s] -{'train_runtime': '38.02', 'train_samples_per_second': '1389', 'train_steps_per_second': '10.89', 'train_loss': '0.5469', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 40.34it/s] diff --git a/wandb/run-20260305_043140-550ullwi/files/requirements.txt b/wandb/run-20260305_043140-550ullwi/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_043140-550ullwi/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 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"2026-03-05T04:32:37.792529Z" - writerId: 75veo6oyb8eadoahdmdecpdap6ijcg2h - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_043237-2g2sgwq2/files/output.log b/wandb/run-20260305_043237-2g2sgwq2/files/output.log deleted file mode 100644 index 3c8ce67c7e43831cdbb31e4ea6aa822cfb2c0cd2..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_043237-2g2sgwq2/files/output.log +++ /dev/null @@ -1,59 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 16706.42it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.dense.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -classifier.weight | MISSING | -bert.pooler.dense.weight | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 25,710 - Num Epochs = 2 - Num update steps per epoch = 201 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 402 - Number of trainable parameters = 44,302,082 - 50%|████▉ | 199/402 [00:17<00:17, 11.63it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K4me2/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K4me2/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 1.40it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K4me2/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K4me2/checkpoint-200/tokenizer_config.json - 99%|█████████▉| 399/402 [00:37<00:00, 11.49it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K4me2/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K4me2/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.33it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K4me2/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K4me2/checkpoint-400/tokenizer_config.json -100%|█████████▉| 401/402 [00:38<00:00, 4.98it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K4me2/checkpoint-402 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K4me2/checkpoint-402/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.64it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K4me2/checkpoint-402/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K4me2/checkpoint-402/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 402/402 [00:39<00:00, 10.31it/s] -{'train_runtime': '39.01', 'train_samples_per_second': '1318', 'train_steps_per_second': '10.31', 'train_loss': '0.4897', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3215 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 40.84it/s] diff --git a/wandb/run-20260305_043237-2g2sgwq2/files/requirements.txt b/wandb/run-20260305_043237-2g2sgwq2/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_043237-2g2sgwq2/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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"2026-03-05T04:33:35.053547Z" - writerId: e6cdsost84g7p4mj2e3qi62tnnw1hhct - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_043335-mxv8yomj/files/output.log b/wandb/run-20260305_043335-mxv8yomj/files/output.log deleted file mode 100644 index 1a1941da15a0d364461d13b1980d0643b29ca05d..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_043335-mxv8yomj/files/output.log +++ /dev/null @@ -1,54 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 21181.24it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -classifier.weight | MISSING | -bert.pooler.dense.bias | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 14,595 - Num Epochs = 2 - Num update steps per epoch = 115 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 230 - Number of trainable parameters = 44,302,082 - 87%|████████▋ | 199/230 [00:17<00:02, 11.57it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K4me3/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K4me3/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.92it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K4me3/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K4me3/checkpoint-200/tokenizer_config.json -100%|█████████▉| 229/230 [00:20<00:00, 11.58it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K4me3/checkpoint-230 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K4me3/checkpoint-230/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.43it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K4me3/checkpoint-230/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K4me3/checkpoint-230/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 230/230 [00:21<00:00, 10.56it/s] -{'train_runtime': '21.78', 'train_samples_per_second': '1340', 'train_steps_per_second': '10.56', 'train_loss': '0.4087', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 1825 - Batch size = 128 -100%|██████████| 15/15 [00:00<00:00, 42.74it/s] diff --git a/wandb/run-20260305_043335-mxv8yomj/files/requirements.txt b/wandb/run-20260305_043335-mxv8yomj/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_043335-mxv8yomj/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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-cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -classifier.bias | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.weight | MISSING | -bert.pooler.dense.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 19,422 - Num Epochs = 2 - Num update steps per epoch = 152 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 304 - Number of trainable parameters = 44,302,082 - 65%|██████▌ | 199/304 [00:17<00:09, 11.24it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K9ac/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K9ac/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 2.88it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K9ac/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K9ac/checkpoint-200/tokenizer_config.json -100%|█████████▉| 303/304 [00:27<00:00, 11.47it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K9ac/checkpoint-304 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K9ac/checkpoint-304/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 2.95it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K9ac/checkpoint-304/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K9ac/checkpoint-304/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 304/304 [00:28<00:00, 10.51it/s] -{'train_runtime': '28.94', 'train_samples_per_second': '1342', 'train_steps_per_second': '10.51', 'train_loss': '0.516', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 2429 - Batch size = 128 -100%|██████████| 19/19 [00:00<00:00, 40.76it/s] diff --git a/wandb/run-20260305_043411-prfxsy0h/files/requirements.txt b/wandb/run-20260305_043411-prfxsy0h/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_043411-prfxsy0h/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:34:56.591261Z" - writerId: jc6fhtvti1hnrezdzeacacrthgzutuja - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_043456-0ys1kfha/files/output.log b/wandb/run-20260305_043456-0ys1kfha/files/output.log deleted file mode 100644 index 2a859fd34fad143641cf4a185938a79596c3ef8d..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_043456-0ys1kfha/files/output.log +++ /dev/null @@ -1,54 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 20788.34it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -bert.pooler.dense.weight | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.bias | MISSING | -classifier.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 22,630 - Num Epochs = 2 - Num update steps per epoch = 177 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 354 - Number of trainable parameters = 44,302,082 - 56%|█████▌ | 199/354 [00:17<00:13, 11.67it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K9me3/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K9me3/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 5.08it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K9me3/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K9me3/checkpoint-200/tokenizer_config.json -100%|█████████▉| 353/354 [00:31<00:00, 11.53it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K9me3/checkpoint-354 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K9me3/checkpoint-354/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.61it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K9me3/checkpoint-354/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K9me3/checkpoint-354/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 354/354 [00:32<00:00, 10.87it/s] -{'train_runtime': '32.57', 'train_samples_per_second': '1389', 'train_steps_per_second': '10.87', 'train_loss': '0.59', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 2830 - Batch size = 128 -100%|██████████| 23/23 [00:00<00:00, 40.75it/s] diff --git a/wandb/run-20260305_043456-0ys1kfha/files/requirements.txt b/wandb/run-20260305_043456-0ys1kfha/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_043456-0ys1kfha/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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"2026-03-05T04:35:46.046789Z" - writerId: nwhetuiglp2aekvc6y9f793a3j0m66jf - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_043546-375z7c4q/files/output.log b/wandb/run-20260305_043546-375z7c4q/files/output.log deleted file mode 100644 index 7635a49590088c744d681d025af669df6fe24047..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_043546-375z7c4q/files/output.log +++ /dev/null @@ -1,59 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 20516.50it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -classifier.bias | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 25,816 - Num Epochs = 2 - Num update steps per epoch = 202 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 404 - Number of trainable parameters = 44,302,082 - 49%|████▉ | 199/404 [00:17<00:17, 11.59it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H4K20me1/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H4K20me1/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.74it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H4K20me1/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H4K20me1/checkpoint-200/tokenizer_config.json - 99%|█████████▉| 399/404 [00:35<00:00, 11.58it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H4K20me1/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H4K20me1/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 5.01it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H4K20me1/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H4K20me1/checkpoint-400/tokenizer_config.json -100%|█████████▉| 403/404 [00:36<00:00, 6.86it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H4K20me1/checkpoint-404 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H4K20me1/checkpoint-404/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.20it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H4K20me1/checkpoint-404/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H4K20me1/checkpoint-404/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 404/404 [00:37<00:00, 10.78it/s] -{'train_runtime': '37.47', 'train_samples_per_second': '1378', 'train_steps_per_second': '10.78', 'train_loss': '0.4417', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3227 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 41.09it/s] diff --git a/wandb/run-20260305_043546-375z7c4q/files/requirements.txt b/wandb/run-20260305_043546-375z7c4q/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_043546-375z7c4q/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 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/data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:36:41.788203Z" - writerId: 8yww3kt5os2d4vsvdq93bgesnkft5zhr - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_043641-6pbv11qc/files/output.log b/wandb/run-20260305_043641-6pbv11qc/files/output.log deleted file mode 100644 index c9316199f3e4ef82f0aa526750db0fc73cd44038..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_043641-6pbv11qc/files/output.log +++ /dev/null @@ -1,150 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 22390.31it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -bert.pooler.dense.weight | MISSING | -classifier.weight | MISSING | -classifier.bias | MISSING | -bert.pooler.dense.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 4 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 828 - Number of trainable parameters = 44,302,082 - 0%| | 0/828 [00:00 - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 445, in train - trainer.train() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1424, in train - return inner_training_loop( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1506, in _inner_training_loop - self._run_epoch( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1734, in _run_epoch - tr_loss_step = self.training_step(model, inputs, num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1906, in training_step - loss = self.compute_loss(model, inputs, num_items_in_batch=num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1978, in compute_loss - outputs = model(**inputs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 823, in forward - return model_forward(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 811, in __call__ - return convert_to_fp32(self.model_forward(*args, **kwargs)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/amp/autocast_mode.py", line 44, in decorate_autocast - return func(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 843, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 1139, in forward - outputs = self.bert( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 917, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/output_capturing.py", line 253, in wrapper - outputs = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 680, in forward - embedding_output = self.embeddings( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 110, in forward - embeddings = self.LayerNorm(embeddings) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/normalization.py", line 229, in forward - return F.layer_norm( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/functional.py", line 2935, in layer_norm - return torch.layer_norm( -torch.AcceleratorError: CUDA error: device-side assert triggered -Search for `cudaErrorAssert' in https://docs.nvidia.com/cuda/cuda-runtime-api/group__CUDART__TYPES.html for more information. -CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect. -For debugging consider passing CUDA_LAUNCH_BLOCKING=1 -Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions. - -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 464, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 445, in train - trainer.train() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1424, in train - return inner_training_loop( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1506, in _inner_training_loop - self._run_epoch( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1734, in _run_epoch - tr_loss_step = self.training_step(model, inputs, num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1906, in training_step - loss = self.compute_loss(model, inputs, num_items_in_batch=num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1978, in compute_loss - outputs = model(**inputs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 823, in forward - return model_forward(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 811, in __call__ - return convert_to_fp32(self.model_forward(*args, **kwargs)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/amp/autocast_mode.py", line 44, in decorate_autocast - return func(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 843, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 1139, in forward - outputs = self.bert( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 917, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/output_capturing.py", line 253, in wrapper - outputs = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 680, in forward - embedding_output = self.embeddings( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 110, in forward - embeddings = self.LayerNorm(embeddings) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/normalization.py", line 229, in forward - return F.layer_norm( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/functional.py", line 2935, in layer_norm - return torch.layer_norm( -torch.AcceleratorError: CUDA error: device-side assert triggered -Search for `cudaErrorAssert' in https://docs.nvidia.com/cuda/cuda-runtime-api/group__CUDART__TYPES.html for more information. -CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect. -For debugging consider passing CUDA_LAUNCH_BLOCKING=1 -Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions. diff --git a/wandb/run-20260305_043641-6pbv11qc/files/requirements.txt b/wandb/run-20260305_043641-6pbv11qc/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_043641-6pbv11qc/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 -accelerate==1.13.0 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -triton==3.6.0 -nvidia-nccl-cu12==2.27.5 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -cuda-pathfinder==1.4.0 -shellingham==1.5.4 -torchaudio==2.5.1 -nvidia-cufile-cu12==1.13.1.3 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -nvidia-nvjitlink-cu12==12.8.93 -click==8.3.1 -MarkupSafe==3.0.2 -nvidia-nvshmem-cu12==3.4.5 -urllib3==2.6.3 -cuda-bindings==12.9.4 -propcache==0.4.1 -nvidia-cusolver-cu12==11.7.3.90 -sympy==1.14.0 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -nvidia-cuda-runtime-cu12==12.8.90 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_043641-6pbv11qc/files/wandb-metadata.json b/wandb/run-20260305_043641-6pbv11qc/files/wandb-metadata.json deleted file mode 100644 index 0bbdf1febf05f143bf50ae6d59e758cd6d968b41..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_043641-6pbv11qc/files/wandb-metadata.json +++ /dev/null @@ -1,134 +0,0 @@ -{ - "os": "Linux-5.15.0-72-generic-x86_64-with-glibc2.35", - "python": "CPython 3.10.19", - "startedAt": "2026-03-05T04:36:41.788203Z", - "args": [ - "--model_name_or_path", - "/home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000", - "--tokenizer_path", - "/home/n5huang/dna_token/tokenizer_evaluation/merge_bpe/merge_tokenizer_unigram_len.json", - "--trust_remote_code", - "True", - "--data_path", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/enhancers/split", - "--kmer", - "-1", - "--run_name", - "hg38_BPE_base__merge_bpe_merge_tokenizer_unigram_len_3e-5_enhancers_seed42", - "--model_max_length", - "100", - "--per_device_train_batch_size", - "128", - "--per_device_eval_batch_size", - "128", - "--gradient_accumulation_steps", - "1", - "--learning_rate", - "3e-5", - 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handles. diff --git a/wandb/run-20260305_043641-6pbv11qc/run-6pbv11qc.wandb b/wandb/run-20260305_043641-6pbv11qc/run-6pbv11qc.wandb deleted file mode 100644 index 21f963cf50e51bed4b88109318174a1a889bc7b4..0000000000000000000000000000000000000000 Binary files a/wandb/run-20260305_043641-6pbv11qc/run-6pbv11qc.wandb and /dev/null differ diff --git a/wandb/run-20260305_043656-c9sfdtwh/files/config.yaml b/wandb/run-20260305_043656-c9sfdtwh/files/config.yaml deleted file mode 100644 index b3785b2c2a6aa55a739e39056850e6f84744a355..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_043656-c9sfdtwh/files/config.yaml +++ /dev/null @@ -1,139 +0,0 @@ -_wandb: - value: - cli_version: 0.25.0 - e: - 5sjeeis9hbt33g1kg1v1hi28p5t96vfg: - args: - - --model_name_or_path - - /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 - - --tokenizer_path - - /home/n5huang/dna_token/tokenizer_evaluation/merge_bpe/merge_tokenizer_unigram_len.json - - --trust_remote_code - - "True" - - --data_path - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/enhancers_types/split - - --kmer - - "-1" - - --run_name - - hg38_BPE_base__merge_bpe_merge_tokenizer_unigram_len_3e-5_enhancers_types_seed42 - - --model_max_length - - "100" - - --per_device_train_batch_size - - "128" - - --per_device_eval_batch_size - - "128" - - --gradient_accumulation_steps - - "1" - - --learning_rate - - "3e-5" - - --num_train_epochs - - "4" - - --fp16 - - --save_steps - - "200" - - --output_dir - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_len/enhancers_types - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "547001417728" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:36:56.153518Z" - writerId: 5sjeeis9hbt33g1kg1v1hi28p5t96vfg - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_043656-c9sfdtwh/files/output.log b/wandb/run-20260305_043656-c9sfdtwh/files/output.log deleted file mode 100644 index 1fd6972a980da132197cfc6d991f8f73304346ae..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_043656-c9sfdtwh/files/output.log +++ /dev/null @@ -1,150 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 19026.49it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -bert.pooler.dense.weight | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 4 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 828 - Number of trainable parameters = 44,302,851 - 0%| | 0/828 [00:00 - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 445, in train - trainer.train() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1424, in train - return inner_training_loop( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1506, in _inner_training_loop - self._run_epoch( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1734, in _run_epoch - tr_loss_step = self.training_step(model, inputs, num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1906, in training_step - loss = self.compute_loss(model, inputs, num_items_in_batch=num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1978, in compute_loss - outputs = model(**inputs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 823, in forward - return model_forward(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 811, in __call__ - return convert_to_fp32(self.model_forward(*args, **kwargs)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/amp/autocast_mode.py", line 44, in decorate_autocast - return func(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 843, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 1139, in forward - outputs = self.bert( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 917, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/output_capturing.py", line 253, in wrapper - outputs = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 680, in forward - embedding_output = self.embeddings( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 110, in forward - embeddings = self.LayerNorm(embeddings) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/normalization.py", line 229, in forward - return F.layer_norm( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/functional.py", line 2935, in layer_norm - return torch.layer_norm( -torch.AcceleratorError: CUDA error: device-side assert triggered -Search for `cudaErrorAssert' in https://docs.nvidia.com/cuda/cuda-runtime-api/group__CUDART__TYPES.html for more information. -CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect. -For debugging consider passing CUDA_LAUNCH_BLOCKING=1 -Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions. - -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 464, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 445, in train - trainer.train() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1424, in train - return inner_training_loop( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1506, in _inner_training_loop - self._run_epoch( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1734, in _run_epoch - tr_loss_step = self.training_step(model, inputs, num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1906, in training_step - loss = self.compute_loss(model, inputs, num_items_in_batch=num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1978, in compute_loss - outputs = model(**inputs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 823, in forward - return model_forward(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 811, in __call__ - return convert_to_fp32(self.model_forward(*args, **kwargs)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/amp/autocast_mode.py", line 44, in decorate_autocast - return func(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 843, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 1139, in forward - outputs = self.bert( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 917, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/output_capturing.py", line 253, in wrapper - outputs = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 680, in forward - embedding_output = self.embeddings( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 110, in forward - embeddings = self.LayerNorm(embeddings) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/normalization.py", line 229, in forward - return F.layer_norm( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/functional.py", line 2935, in layer_norm - return torch.layer_norm( -torch.AcceleratorError: CUDA error: device-side assert triggered -Search for `cudaErrorAssert' in https://docs.nvidia.com/cuda/cuda-runtime-api/group__CUDART__TYPES.html for more information. -CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect. -For debugging consider passing CUDA_LAUNCH_BLOCKING=1 -Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions. diff --git a/wandb/run-20260305_043656-c9sfdtwh/files/requirements.txt b/wandb/run-20260305_043656-c9sfdtwh/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_043656-c9sfdtwh/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 -accelerate==1.13.0 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -triton==3.6.0 -nvidia-nccl-cu12==2.27.5 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -cuda-pathfinder==1.4.0 -shellingham==1.5.4 -torchaudio==2.5.1 -nvidia-cufile-cu12==1.13.1.3 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -nvidia-nvjitlink-cu12==12.8.93 -click==8.3.1 -MarkupSafe==3.0.2 -nvidia-nvshmem-cu12==3.4.5 -urllib3==2.6.3 -cuda-bindings==12.9.4 -propcache==0.4.1 -nvidia-cusolver-cu12==11.7.3.90 -sympy==1.14.0 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -nvidia-cuda-runtime-cu12==12.8.90 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_043656-c9sfdtwh/files/wandb-metadata.json b/wandb/run-20260305_043656-c9sfdtwh/files/wandb-metadata.json deleted file mode 100644 index 2924d1a97602325d8d4e02583886cc9d0ffa7151..0000000000000000000000000000000000000000 --- 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"True" - - --data_path - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/promoter_all/split - - --kmer - - "-1" - - --run_name - - hg38_BPE_base__merge_bpe_merge_tokenizer_unigram_len_3e-5_promoter_all_seed42 - - --model_max_length - - "80" - - --per_device_train_batch_size - - "128" - - --per_device_eval_batch_size - - "128" - - --gradient_accumulation_steps - - "1" - - --learning_rate - - "3e-5" - - --num_train_epochs - - "2" - - --fp16 - - --save_steps - - "200" - - --output_dir - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_len/promoter_all - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "547001495552" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:37:11.755754Z" - writerId: pssbzmyd2xehwxrecba4ewqioimxvae7 - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_043711-0ccsm6vx/files/output.log b/wandb/run-20260305_043711-0ccsm6vx/files/output.log deleted file mode 100644 index 991f56d314b1da511c4b415dc97420b47d709a7c..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_043711-0ccsm6vx/files/output.log +++ /dev/null @@ -1,150 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 23249.26it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -classifier.bias | MISSING | -bert.pooler.dense.bias | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 25,267 - Num Epochs = 2 - Num update steps per epoch = 198 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 396 - Number of trainable parameters = 44,302,082 - 0%| | 0/396 [00:00 - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 445, in train - trainer.train() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1424, in train - return inner_training_loop( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1506, in _inner_training_loop - self._run_epoch( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1734, in _run_epoch - tr_loss_step = self.training_step(model, inputs, num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1906, in training_step - loss = self.compute_loss(model, inputs, num_items_in_batch=num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1978, in compute_loss - outputs = model(**inputs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 823, in forward - return model_forward(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 811, in __call__ - return convert_to_fp32(self.model_forward(*args, **kwargs)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/amp/autocast_mode.py", line 44, in decorate_autocast - return func(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 843, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 1139, in forward - outputs = self.bert( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 917, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/output_capturing.py", line 253, in wrapper - outputs = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 680, in forward - embedding_output = self.embeddings( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 110, in forward - embeddings = self.LayerNorm(embeddings) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/normalization.py", line 229, in forward - return F.layer_norm( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/functional.py", line 2935, in layer_norm - return torch.layer_norm( -torch.AcceleratorError: CUDA error: device-side assert triggered -Search for `cudaErrorAssert' in https://docs.nvidia.com/cuda/cuda-runtime-api/group__CUDART__TYPES.html for more information. -CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect. -For debugging consider passing CUDA_LAUNCH_BLOCKING=1 -Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions. - -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 464, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 445, in train - trainer.train() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1424, in train - return inner_training_loop( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1506, in _inner_training_loop - self._run_epoch( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1734, in _run_epoch - tr_loss_step = self.training_step(model, inputs, num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1906, in training_step - loss = self.compute_loss(model, inputs, num_items_in_batch=num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1978, in compute_loss - outputs = model(**inputs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 823, in forward - return model_forward(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 811, in __call__ - return convert_to_fp32(self.model_forward(*args, **kwargs)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/amp/autocast_mode.py", line 44, in decorate_autocast - return func(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 843, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 1139, in forward - outputs = self.bert( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 917, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/output_capturing.py", line 253, in wrapper - outputs = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 680, in forward - embedding_output = self.embeddings( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 110, in forward - embeddings = self.LayerNorm(embeddings) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/normalization.py", line 229, in forward - return F.layer_norm( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/functional.py", line 2935, in layer_norm - return torch.layer_norm( -torch.AcceleratorError: CUDA error: device-side assert triggered -Search for `cudaErrorAssert' in https://docs.nvidia.com/cuda/cuda-runtime-api/group__CUDART__TYPES.html for more information. -CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect. -For debugging consider passing CUDA_LAUNCH_BLOCKING=1 -Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions. diff --git a/wandb/run-20260305_043711-0ccsm6vx/files/requirements.txt b/wandb/run-20260305_043711-0ccsm6vx/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_043711-0ccsm6vx/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 -accelerate==1.13.0 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -triton==3.6.0 -nvidia-nccl-cu12==2.27.5 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -cuda-pathfinder==1.4.0 -shellingham==1.5.4 -torchaudio==2.5.1 -nvidia-cufile-cu12==1.13.1.3 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -nvidia-nvjitlink-cu12==12.8.93 -click==8.3.1 -MarkupSafe==3.0.2 -nvidia-nvshmem-cu12==3.4.5 -urllib3==2.6.3 -cuda-bindings==12.9.4 -propcache==0.4.1 -nvidia-cusolver-cu12==11.7.3.90 -sympy==1.14.0 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -nvidia-cuda-runtime-cu12==12.8.90 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_043711-0ccsm6vx/files/wandb-metadata.json b/wandb/run-20260305_043711-0ccsm6vx/files/wandb-metadata.json deleted file mode 100644 index eacaac9ab01d8ab34345f2ff238eb196900c9597..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_043711-0ccsm6vx/files/wandb-metadata.json +++ /dev/null @@ -1,134 +0,0 @@ -{ - "os": "Linux-5.15.0-72-generic-x86_64-with-glibc2.35", - "python": "CPython 3.10.19", - "startedAt": "2026-03-05T04:37:11.755754Z", - "args": [ - "--model_name_or_path", - "/home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000", - "--tokenizer_path", - "/home/n5huang/dna_token/tokenizer_evaluation/merge_bpe/merge_tokenizer_unigram_len.json", - "--trust_remote_code", - "True", - "--data_path", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/promoter_all/split", - "--kmer", - "-1", - "--run_name", - "hg38_BPE_base__merge_bpe_merge_tokenizer_unigram_len_3e-5_promoter_all_seed42", - "--model_max_length", - "80", - "--per_device_train_batch_size", - "128", - "--per_device_eval_batch_size", - "128", - "--gradient_accumulation_steps", - "1", - "--learning_rate", - "3e-5", - 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/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/promoter_no_tata/split - - --kmer - - "-1" - - --run_name - - hg38_BPE_base__merge_bpe_merge_tokenizer_unigram_len_3e-5_promoter_no_tata_seed42 - - --model_max_length - - "80" - - --per_device_train_batch_size - - "128" - - --per_device_eval_batch_size - - "128" - - --gradient_accumulation_steps - - "1" - - --learning_rate - - "3e-5" - - --num_train_epochs - - "2" - - --fp16 - - --save_steps - - "200" - - --output_dir - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_len/promoter_no_tata - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "547001634816" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:37:26.331015Z" - writerId: n5qay1zj7w5d8g5rmxignw0bd1fh5rg7 - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_043726-yb4ub915/files/output.log b/wandb/run-20260305_043726-yb4ub915/files/output.log deleted file mode 100644 index 36197162e9a1e63282c9207f02832159bb094da5..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_043726-yb4ub915/files/output.log +++ /dev/null @@ -1,150 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 21935.83it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -classifier.weight | MISSING | -bert.pooler.dense.bias | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 25,097 - Num Epochs = 2 - Num update steps per epoch = 197 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 394 - Number of trainable parameters = 44,302,082 - 0%| | 0/394 [00:00 - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 445, in train - trainer.train() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1424, in train - return inner_training_loop( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1506, in _inner_training_loop - self._run_epoch( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1734, in _run_epoch - tr_loss_step = self.training_step(model, inputs, num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1906, in training_step - loss = self.compute_loss(model, inputs, num_items_in_batch=num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1978, in compute_loss - outputs = model(**inputs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 823, in forward - return model_forward(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 811, in __call__ - return convert_to_fp32(self.model_forward(*args, **kwargs)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/amp/autocast_mode.py", line 44, in decorate_autocast - return func(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 843, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 1139, in forward - outputs = self.bert( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 917, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/output_capturing.py", line 253, in wrapper - outputs = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 680, in forward - embedding_output = self.embeddings( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 110, in forward - embeddings = self.LayerNorm(embeddings) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/normalization.py", line 229, in forward - return F.layer_norm( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/functional.py", line 2935, in layer_norm - return torch.layer_norm( -torch.AcceleratorError: CUDA error: device-side assert triggered -Search for `cudaErrorAssert' in https://docs.nvidia.com/cuda/cuda-runtime-api/group__CUDART__TYPES.html for more information. -CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect. -For debugging consider passing CUDA_LAUNCH_BLOCKING=1 -Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions. - -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 464, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 445, in train - trainer.train() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1424, in train - return inner_training_loop( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1506, in _inner_training_loop - self._run_epoch( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1734, in _run_epoch - tr_loss_step = self.training_step(model, inputs, num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1906, in training_step - loss = self.compute_loss(model, inputs, num_items_in_batch=num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1978, in compute_loss - outputs = model(**inputs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 823, in forward - return model_forward(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 811, in __call__ - return convert_to_fp32(self.model_forward(*args, **kwargs)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/amp/autocast_mode.py", line 44, in decorate_autocast - return func(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 843, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 1139, in forward - outputs = self.bert( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 917, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/output_capturing.py", line 253, in wrapper - outputs = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 680, in forward - embedding_output = self.embeddings( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 110, in forward - embeddings = self.LayerNorm(embeddings) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/normalization.py", line 229, in forward - return F.layer_norm( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/functional.py", line 2935, in layer_norm - return torch.layer_norm( -torch.AcceleratorError: CUDA error: device-side assert triggered -Search for `cudaErrorAssert' in https://docs.nvidia.com/cuda/cuda-runtime-api/group__CUDART__TYPES.html for more information. -CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect. -For debugging consider passing CUDA_LAUNCH_BLOCKING=1 -Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions. diff --git a/wandb/run-20260305_043726-yb4ub915/files/requirements.txt b/wandb/run-20260305_043726-yb4ub915/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_043726-yb4ub915/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 -accelerate==1.13.0 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -triton==3.6.0 -nvidia-nccl-cu12==2.27.5 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -cuda-pathfinder==1.4.0 -shellingham==1.5.4 -torchaudio==2.5.1 -nvidia-cufile-cu12==1.13.1.3 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -nvidia-nvjitlink-cu12==12.8.93 -click==8.3.1 -MarkupSafe==3.0.2 -nvidia-nvshmem-cu12==3.4.5 -urllib3==2.6.3 -cuda-bindings==12.9.4 -propcache==0.4.1 -nvidia-cusolver-cu12==11.7.3.90 -sympy==1.14.0 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -nvidia-cuda-runtime-cu12==12.8.90 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_043726-yb4ub915/files/wandb-metadata.json b/wandb/run-20260305_043726-yb4ub915/files/wandb-metadata.json deleted file mode 100644 index 643c509afeb1ca3049d24519090a40079e255c54..0000000000000000000000000000000000000000 --- 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deleted file mode 100644 index 44bf2ad3748aded0d4cf39688caaeaa02145f3eb..0000000000000000000000000000000000000000 Binary files a/wandb/run-20260305_043726-yb4ub915/run-yb4ub915.wandb and /dev/null differ diff --git a/wandb/run-20260305_043741-60r3ynsi/files/config.yaml b/wandb/run-20260305_043741-60r3ynsi/files/config.yaml deleted file mode 100644 index 4d87c4b66c3f34d3aab74199a3437a582e09a4f4..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_043741-60r3ynsi/files/config.yaml +++ /dev/null @@ -1,139 +0,0 @@ -_wandb: - value: - cli_version: 0.25.0 - e: - p8u04mlu8uw6i1c0gigc1b9ya1q4074y: - args: - - --model_name_or_path - - /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 - - --tokenizer_path - - /home/n5huang/dna_token/tokenizer_evaluation/merge_bpe/merge_tokenizer_unigram_len.json - - --trust_remote_code - - "True" - - --data_path - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/promoter_tata/split - - --kmer - - "-1" - - --run_name - - hg38_BPE_base__merge_bpe_merge_tokenizer_unigram_len_3e-5_promoter_tata_seed42 - - --model_max_length - - "80" - - --per_device_train_batch_size - - "128" - - --per_device_eval_batch_size - - "128" - - --gradient_accumulation_steps - - "1" - - --learning_rate - - "3e-5" - - --num_train_epochs - - "2" - - --fp16 - - --save_steps - - "200" - - --output_dir - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_len/promoter_tata - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "547003691008" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:37:41.349007Z" - writerId: p8u04mlu8uw6i1c0gigc1b9ya1q4074y - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_043741-60r3ynsi/files/output.log b/wandb/run-20260305_043741-60r3ynsi/files/output.log deleted file mode 100644 index f958ae300705c336f8d292575a74517079eeaa3e..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_043741-60r3ynsi/files/output.log +++ /dev/null @@ -1,150 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 22604.17it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -bert.pooler.dense.bias | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.weight | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 4,219 - Num Epochs = 2 - Num update steps per epoch = 33 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 66 - Number of trainable parameters = 44,302,082 - 0%| | 0/66 [00:00 - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 445, in train - trainer.train() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1424, in train - return inner_training_loop( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1506, in _inner_training_loop - self._run_epoch( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1734, in _run_epoch - tr_loss_step = self.training_step(model, inputs, num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1906, in training_step - loss = self.compute_loss(model, inputs, num_items_in_batch=num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1978, in compute_loss - outputs = model(**inputs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 823, in forward - return model_forward(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 811, in __call__ - return convert_to_fp32(self.model_forward(*args, **kwargs)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/amp/autocast_mode.py", line 44, in decorate_autocast - return func(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 843, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 1139, in forward - outputs = self.bert( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 917, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/output_capturing.py", line 253, in wrapper - outputs = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 680, in forward - embedding_output = self.embeddings( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 110, in forward - embeddings = self.LayerNorm(embeddings) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/normalization.py", line 229, in forward - return F.layer_norm( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/functional.py", line 2935, in layer_norm - return torch.layer_norm( -torch.AcceleratorError: CUDA error: device-side assert triggered -Search for `cudaErrorAssert' in https://docs.nvidia.com/cuda/cuda-runtime-api/group__CUDART__TYPES.html for more information. -CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect. -For debugging consider passing CUDA_LAUNCH_BLOCKING=1 -Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions. - -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 464, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 445, in train - trainer.train() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1424, in train - return inner_training_loop( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1506, in _inner_training_loop - self._run_epoch( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1734, in _run_epoch - tr_loss_step = self.training_step(model, inputs, num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1906, in training_step - loss = self.compute_loss(model, inputs, num_items_in_batch=num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1978, in compute_loss - outputs = model(**inputs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 823, in forward - return model_forward(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 811, in __call__ - return convert_to_fp32(self.model_forward(*args, **kwargs)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/amp/autocast_mode.py", line 44, in decorate_autocast - return func(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 843, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 1139, in forward - outputs = self.bert( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 917, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/output_capturing.py", line 253, in wrapper - outputs = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 680, in forward - embedding_output = self.embeddings( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 110, in forward - embeddings = self.LayerNorm(embeddings) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/normalization.py", line 229, in forward - return F.layer_norm( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/functional.py", line 2935, in layer_norm - return torch.layer_norm( -torch.AcceleratorError: CUDA error: device-side assert triggered -Search for `cudaErrorAssert' in https://docs.nvidia.com/cuda/cuda-runtime-api/group__CUDART__TYPES.html for more information. -CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect. -For debugging consider passing CUDA_LAUNCH_BLOCKING=1 -Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions. diff --git a/wandb/run-20260305_043741-60r3ynsi/files/requirements.txt b/wandb/run-20260305_043741-60r3ynsi/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_043741-60r3ynsi/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 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aae5s73jpzxiqzv88a1v2rccd2ji1and - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_043753-4upvyid8/files/output.log b/wandb/run-20260305_043753-4upvyid8/files/output.log deleted file mode 100644 index bb9fae2dfc433e3b95f4f346735b9fa5bbd879e5..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_043753-4upvyid8/files/output.log +++ /dev/null @@ -1,150 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 8038.88it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -classifier.bias | MISSING | -bert.pooler.dense.bias | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 4 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 828 - Number of trainable parameters = 44,302,082 - 0%| | 0/828 [00:00 - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 445, in train - trainer.train() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1424, in train - return inner_training_loop( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1506, in _inner_training_loop - self._run_epoch( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1734, in _run_epoch - tr_loss_step = self.training_step(model, inputs, num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1906, in training_step - loss = self.compute_loss(model, inputs, num_items_in_batch=num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1978, in compute_loss - outputs = model(**inputs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 823, in forward - return model_forward(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 811, in __call__ - return convert_to_fp32(self.model_forward(*args, **kwargs)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/amp/autocast_mode.py", line 44, in decorate_autocast - return func(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 843, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 1139, in forward - outputs = self.bert( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 917, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/output_capturing.py", line 253, in wrapper - outputs = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 680, in forward - embedding_output = self.embeddings( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 110, in forward - embeddings = self.LayerNorm(embeddings) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/normalization.py", line 229, in forward - return F.layer_norm( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/functional.py", line 2935, in layer_norm - return torch.layer_norm( -torch.AcceleratorError: CUDA error: device-side assert triggered -Search for `cudaErrorAssert' in https://docs.nvidia.com/cuda/cuda-runtime-api/group__CUDART__TYPES.html for more information. -CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect. -For debugging consider passing CUDA_LAUNCH_BLOCKING=1 -Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions. - -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 464, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 445, in train - trainer.train() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1424, in train - return inner_training_loop( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1506, in _inner_training_loop - self._run_epoch( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1734, in _run_epoch - tr_loss_step = self.training_step(model, inputs, num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1906, in training_step - loss = self.compute_loss(model, inputs, num_items_in_batch=num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1978, in compute_loss - outputs = model(**inputs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 823, in forward - return model_forward(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 811, in __call__ - return convert_to_fp32(self.model_forward(*args, **kwargs)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/amp/autocast_mode.py", line 44, in decorate_autocast - return func(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 843, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 1139, in forward - outputs = self.bert( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 917, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/output_capturing.py", line 253, in wrapper - outputs = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 680, in forward - embedding_output = self.embeddings( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 110, in forward - embeddings = self.LayerNorm(embeddings) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/normalization.py", line 229, in forward - return F.layer_norm( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/functional.py", line 2935, in layer_norm - return torch.layer_norm( -torch.AcceleratorError: CUDA error: device-side assert triggered -Search for `cudaErrorAssert' in https://docs.nvidia.com/cuda/cuda-runtime-api/group__CUDART__TYPES.html for more information. -CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect. -For debugging consider passing CUDA_LAUNCH_BLOCKING=1 -Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions. diff --git a/wandb/run-20260305_043753-4upvyid8/files/requirements.txt b/wandb/run-20260305_043753-4upvyid8/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_043753-4upvyid8/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 -accelerate==1.13.0 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -triton==3.6.0 -nvidia-nccl-cu12==2.27.5 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -cuda-pathfinder==1.4.0 -shellingham==1.5.4 -torchaudio==2.5.1 -nvidia-cufile-cu12==1.13.1.3 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -nvidia-nvjitlink-cu12==12.8.93 -click==8.3.1 -MarkupSafe==3.0.2 -nvidia-nvshmem-cu12==3.4.5 -urllib3==2.6.3 -cuda-bindings==12.9.4 -propcache==0.4.1 -nvidia-cusolver-cu12==11.7.3.90 -sympy==1.14.0 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -nvidia-cuda-runtime-cu12==12.8.90 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_043753-4upvyid8/files/wandb-metadata.json b/wandb/run-20260305_043753-4upvyid8/files/wandb-metadata.json deleted file mode 100644 index 20ff6adb868946a4c6e8c1df50eb31f2d463a68d..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_043753-4upvyid8/files/wandb-metadata.json +++ /dev/null @@ -1,134 +0,0 @@ -{ - "os": "Linux-5.15.0-72-generic-x86_64-with-glibc2.35", - "python": "CPython 3.10.19", - "startedAt": "2026-03-05T04:37:53.345771Z", - "args": [ - "--model_name_or_path", - "/home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000", - "--tokenizer_path", - "/home/n5huang/dna_token/tokenizer_evaluation/merge_bpe/merge_tokenizer_unigram_len.json", - "--trust_remote_code", - "True", - "--data_path", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/splice_sites_acceptors/split", - "--kmer", - "-1", - "--run_name", - "hg38_BPE_base__merge_bpe_merge_tokenizer_unigram_len_3e-5_splice_sites_acceptors_seed42", - "--model_max_length", - "140", - "--per_device_train_batch_size", - "128", - "--per_device_eval_batch_size", - "128", - "--gradient_accumulation_steps", - "1", - "--learning_rate", - 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handles. diff --git a/wandb/run-20260305_043753-4upvyid8/run-4upvyid8.wandb b/wandb/run-20260305_043753-4upvyid8/run-4upvyid8.wandb deleted file mode 100644 index c2f8427539cc52a2d9741061567ef9ceaa0186c3..0000000000000000000000000000000000000000 Binary files a/wandb/run-20260305_043753-4upvyid8/run-4upvyid8.wandb and /dev/null differ diff --git a/wandb/run-20260305_043809-0yl618v5/files/config.yaml b/wandb/run-20260305_043809-0yl618v5/files/config.yaml deleted file mode 100644 index e54b3378135ddbcd5bb5ed4a07d8296834236a9b..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_043809-0yl618v5/files/config.yaml +++ /dev/null @@ -1,139 +0,0 @@ -_wandb: - value: - cli_version: 0.25.0 - e: - x2i8eafm9pi8eulioc87kc4um0jtauow: - args: - - --model_name_or_path - - /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 - - --tokenizer_path - - /home/n5huang/dna_token/tokenizer_evaluation/merge_bpe/merge_tokenizer_unigram_len.json - - --trust_remote_code - - "True" - - --data_path - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/splice_sites_all/split - - --kmer - - "-1" - - --run_name - - hg38_BPE_base__merge_bpe_merge_tokenizer_unigram_len_3e-5_splice_sites_all_seed42 - - --model_max_length - - "140" - - --per_device_train_batch_size - - "128" - - --per_device_eval_batch_size - - "128" - - --gradient_accumulation_steps - - "1" - - --learning_rate - - "3e-5" - - --num_train_epochs - - "4" - - --fp16 - - --save_steps - - "200" - - --output_dir - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_len/splice_sites_all - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "547003908096" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:38:09.457044Z" - writerId: x2i8eafm9pi8eulioc87kc4um0jtauow - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_043809-0yl618v5/files/output.log b/wandb/run-20260305_043809-0yl618v5/files/output.log deleted file mode 100644 index 0c72fb66d377ace9832407b09e71e736d963ec6a..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_043809-0yl618v5/files/output.log +++ /dev/null @@ -1,150 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 25283.48it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -classifier.weight | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.bias | MISSING | -bert.pooler.dense.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 4 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 828 - Number of trainable parameters = 44,302,851 - 0%| | 0/828 [00:00 - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 445, in train - trainer.train() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1424, in train - return inner_training_loop( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1506, in _inner_training_loop - self._run_epoch( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1734, in _run_epoch - tr_loss_step = self.training_step(model, inputs, num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1906, in training_step - loss = self.compute_loss(model, inputs, num_items_in_batch=num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1978, in compute_loss - outputs = model(**inputs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 823, in forward - return model_forward(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 811, in __call__ - return convert_to_fp32(self.model_forward(*args, **kwargs)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/amp/autocast_mode.py", line 44, in decorate_autocast - return func(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 843, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 1139, in forward - outputs = self.bert( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 917, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/output_capturing.py", line 253, in wrapper - outputs = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 680, in forward - embedding_output = self.embeddings( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 110, in forward - embeddings = self.LayerNorm(embeddings) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/normalization.py", line 229, in forward - return F.layer_norm( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/functional.py", line 2935, in layer_norm - return torch.layer_norm( -torch.AcceleratorError: CUDA error: device-side assert triggered -Search for `cudaErrorAssert' in https://docs.nvidia.com/cuda/cuda-runtime-api/group__CUDART__TYPES.html for more information. -CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect. -For debugging consider passing CUDA_LAUNCH_BLOCKING=1 -Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions. - -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 464, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 445, in train - trainer.train() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1424, in train - return inner_training_loop( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1506, in _inner_training_loop - self._run_epoch( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1734, in _run_epoch - tr_loss_step = self.training_step(model, inputs, num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1906, in training_step - loss = self.compute_loss(model, inputs, num_items_in_batch=num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1978, in compute_loss - outputs = model(**inputs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 823, in forward - return model_forward(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 811, in __call__ - return convert_to_fp32(self.model_forward(*args, **kwargs)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/amp/autocast_mode.py", line 44, in decorate_autocast - return func(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 843, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 1139, in forward - outputs = self.bert( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 917, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/output_capturing.py", line 253, in wrapper - outputs = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 680, in forward - embedding_output = self.embeddings( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 110, in forward - embeddings = self.LayerNorm(embeddings) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/normalization.py", line 229, in forward - return F.layer_norm( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/functional.py", line 2935, in layer_norm - return torch.layer_norm( -torch.AcceleratorError: CUDA error: device-side assert triggered -Search for `cudaErrorAssert' in https://docs.nvidia.com/cuda/cuda-runtime-api/group__CUDART__TYPES.html for more information. -CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect. -For debugging consider passing CUDA_LAUNCH_BLOCKING=1 -Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions. diff --git a/wandb/run-20260305_043809-0yl618v5/files/requirements.txt b/wandb/run-20260305_043809-0yl618v5/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_043809-0yl618v5/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 -accelerate==1.13.0 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -triton==3.6.0 -nvidia-nccl-cu12==2.27.5 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -cuda-pathfinder==1.4.0 -shellingham==1.5.4 -torchaudio==2.5.1 -nvidia-cufile-cu12==1.13.1.3 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -nvidia-nvjitlink-cu12==12.8.93 -click==8.3.1 -MarkupSafe==3.0.2 -nvidia-nvshmem-cu12==3.4.5 -urllib3==2.6.3 -cuda-bindings==12.9.4 -propcache==0.4.1 -nvidia-cusolver-cu12==11.7.3.90 -sympy==1.14.0 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -nvidia-cuda-runtime-cu12==12.8.90 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_043809-0yl618v5/files/wandb-metadata.json b/wandb/run-20260305_043809-0yl618v5/files/wandb-metadata.json deleted file mode 100644 index 112ba599015bc623d18605fbd2c7e0aadba15940..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_043809-0yl618v5/files/wandb-metadata.json +++ /dev/null @@ -1,134 +0,0 @@ -{ - "os": "Linux-5.15.0-72-generic-x86_64-with-glibc2.35", - "python": "CPython 3.10.19", - "startedAt": "2026-03-05T04:38:09.457044Z", - "args": [ - "--model_name_or_path", - "/home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000", - "--tokenizer_path", - "/home/n5huang/dna_token/tokenizer_evaluation/merge_bpe/merge_tokenizer_unigram_len.json", - "--trust_remote_code", - "True", - "--data_path", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/splice_sites_all/split", - "--kmer", - "-1", - "--run_name", - "hg38_BPE_base__merge_bpe_merge_tokenizer_unigram_len_3e-5_splice_sites_all_seed42", - "--model_max_length", - "140", - "--per_device_train_batch_size", - "128", - "--per_device_eval_batch_size", - "128", - "--gradient_accumulation_steps", - "1", - "--learning_rate", - "3e-5", - 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"True" - - --data_path - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/splice_sites_donors/split - - --kmer - - "-1" - - --run_name - - hg38_BPE_base__merge_bpe_merge_tokenizer_unigram_len_3e-5_splice_sites_donors_seed42 - - --model_max_length - - "140" - - --per_device_train_batch_size - - "128" - - --per_device_eval_batch_size - - "128" - - --gradient_accumulation_steps - - "1" - - --learning_rate - - "3e-5" - - --num_train_epochs - - "4" - - --fp16 - - --save_steps - - "200" - - --output_dir - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_len/splice_sites_donors - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "547004047360" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:38:25.372717Z" - writerId: ytzd9q4rrqoxui17s3z5aoee30wy8i2s - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_043825-k5wumtls/files/output.log b/wandb/run-20260305_043825-k5wumtls/files/output.log deleted file mode 100644 index 97aad928bbb21c3639a69f79779bf22abccf9fc7..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_043825-k5wumtls/files/output.log +++ /dev/null @@ -1,150 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 21172.77it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -bert.pooler.dense.bias | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 4 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 828 - Number of trainable parameters = 44,302,082 - 0%| | 0/828 [00:00 - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 445, in train - trainer.train() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1424, in train - return inner_training_loop( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1506, in _inner_training_loop - self._run_epoch( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1734, in _run_epoch - tr_loss_step = self.training_step(model, inputs, num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1906, in training_step - loss = self.compute_loss(model, inputs, num_items_in_batch=num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1978, in compute_loss - outputs = model(**inputs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 823, in forward - return model_forward(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 811, in __call__ - return convert_to_fp32(self.model_forward(*args, **kwargs)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/amp/autocast_mode.py", line 44, in decorate_autocast - return func(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 843, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 1139, in forward - outputs = self.bert( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 917, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/output_capturing.py", line 253, in wrapper - outputs = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 680, in forward - embedding_output = self.embeddings( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 110, in forward - embeddings = self.LayerNorm(embeddings) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/normalization.py", line 229, in forward - return F.layer_norm( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/functional.py", line 2935, in layer_norm - return torch.layer_norm( -torch.AcceleratorError: CUDA error: device-side assert triggered -Search for `cudaErrorAssert' in https://docs.nvidia.com/cuda/cuda-runtime-api/group__CUDART__TYPES.html for more information. -CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect. -For debugging consider passing CUDA_LAUNCH_BLOCKING=1 -Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions. - -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 464, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 445, in train - trainer.train() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1424, in train - return inner_training_loop( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1506, in _inner_training_loop - self._run_epoch( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1734, in _run_epoch - tr_loss_step = self.training_step(model, inputs, num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1906, in training_step - loss = self.compute_loss(model, inputs, num_items_in_batch=num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1978, in compute_loss - outputs = model(**inputs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 823, in forward - return model_forward(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 811, in __call__ - return convert_to_fp32(self.model_forward(*args, **kwargs)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/amp/autocast_mode.py", line 44, in decorate_autocast - return func(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 843, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 1139, in forward - outputs = self.bert( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 917, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/output_capturing.py", line 253, in wrapper - outputs = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 680, in forward - embedding_output = self.embeddings( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 110, in forward - embeddings = self.LayerNorm(embeddings) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/normalization.py", line 229, in forward - return F.layer_norm( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/functional.py", line 2935, in layer_norm - return torch.layer_norm( -torch.AcceleratorError: CUDA error: device-side assert triggered -Search for `cudaErrorAssert' in https://docs.nvidia.com/cuda/cuda-runtime-api/group__CUDART__TYPES.html for more information. -CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect. -For debugging consider passing CUDA_LAUNCH_BLOCKING=1 -Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions. diff --git a/wandb/run-20260305_043825-k5wumtls/files/requirements.txt b/wandb/run-20260305_043825-k5wumtls/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_043825-k5wumtls/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 -accelerate==1.13.0 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -triton==3.6.0 -nvidia-nccl-cu12==2.27.5 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -cuda-pathfinder==1.4.0 -shellingham==1.5.4 -torchaudio==2.5.1 -nvidia-cufile-cu12==1.13.1.3 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -nvidia-nvjitlink-cu12==12.8.93 -click==8.3.1 -MarkupSafe==3.0.2 -nvidia-nvshmem-cu12==3.4.5 -urllib3==2.6.3 -cuda-bindings==12.9.4 -propcache==0.4.1 -nvidia-cusolver-cu12==11.7.3.90 -sympy==1.14.0 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -nvidia-cuda-runtime-cu12==12.8.90 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_043825-k5wumtls/files/wandb-metadata.json b/wandb/run-20260305_043825-k5wumtls/files/wandb-metadata.json deleted file mode 100644 index 3f96bd48066a12cc959e47a196af1c8433323411..0000000000000000000000000000000000000000 --- 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python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_043841-tqhhfrfi/files/output.log b/wandb/run-20260305_043841-tqhhfrfi/files/output.log deleted file mode 100644 index 35b9098a5fcf4663f3983bf5047e3bfed48cf33d..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_043841-tqhhfrfi/files/output.log +++ /dev/null @@ -1,150 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 22814.77it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -classifier.bias | MISSING | -bert.pooler.dense.bias | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 2 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 414 - Number of trainable parameters = 44,302,082 - 0%| | 0/414 [00:00 - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 445, in train - trainer.train() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1424, in train - return inner_training_loop( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1506, in _inner_training_loop - self._run_epoch( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1734, in _run_epoch - tr_loss_step = self.training_step(model, inputs, num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1906, in training_step - loss = self.compute_loss(model, inputs, num_items_in_batch=num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1978, in compute_loss - outputs = model(**inputs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 823, in forward - return model_forward(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 811, in __call__ - return convert_to_fp32(self.model_forward(*args, **kwargs)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/amp/autocast_mode.py", line 44, in decorate_autocast - return func(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 843, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 1139, in forward - outputs = self.bert( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 917, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/output_capturing.py", line 253, in wrapper - outputs = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 680, in forward - embedding_output = self.embeddings( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 110, in forward - embeddings = self.LayerNorm(embeddings) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/normalization.py", line 229, in forward - return F.layer_norm( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/functional.py", line 2935, in layer_norm - return torch.layer_norm( -torch.AcceleratorError: CUDA error: device-side assert triggered -Search for `cudaErrorAssert' in https://docs.nvidia.com/cuda/cuda-runtime-api/group__CUDART__TYPES.html for more information. -CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect. -For debugging consider passing CUDA_LAUNCH_BLOCKING=1 -Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions. - -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 464, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 445, in train - trainer.train() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1424, in train - return inner_training_loop( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1506, in _inner_training_loop - self._run_epoch( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1734, in _run_epoch - tr_loss_step = self.training_step(model, inputs, num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1906, in training_step - loss = self.compute_loss(model, inputs, num_items_in_batch=num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1978, in compute_loss - outputs = model(**inputs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 823, in forward - return model_forward(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 811, in __call__ - return convert_to_fp32(self.model_forward(*args, **kwargs)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/amp/autocast_mode.py", line 44, in decorate_autocast - return func(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 843, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 1139, in forward - outputs = self.bert( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 917, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/output_capturing.py", line 253, in wrapper - outputs = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 680, in forward - embedding_output = self.embeddings( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 110, in forward - embeddings = self.LayerNorm(embeddings) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/normalization.py", line 229, in forward - return F.layer_norm( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/functional.py", line 2935, in layer_norm - return torch.layer_norm( -torch.AcceleratorError: CUDA error: device-side assert triggered -Search for `cudaErrorAssert' in https://docs.nvidia.com/cuda/cuda-runtime-api/group__CUDART__TYPES.html for more information. -CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect. -For debugging consider passing CUDA_LAUNCH_BLOCKING=1 -Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions. diff --git a/wandb/run-20260305_043841-tqhhfrfi/files/requirements.txt b/wandb/run-20260305_043841-tqhhfrfi/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_043841-tqhhfrfi/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 -accelerate==1.13.0 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -triton==3.6.0 -nvidia-nccl-cu12==2.27.5 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -cuda-pathfinder==1.4.0 -shellingham==1.5.4 -torchaudio==2.5.1 -nvidia-cufile-cu12==1.13.1.3 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -nvidia-nvjitlink-cu12==12.8.93 -click==8.3.1 -MarkupSafe==3.0.2 -nvidia-nvshmem-cu12==3.4.5 -urllib3==2.6.3 -cuda-bindings==12.9.4 -propcache==0.4.1 -nvidia-cusolver-cu12==11.7.3.90 -sympy==1.14.0 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -nvidia-cuda-runtime-cu12==12.8.90 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_043841-tqhhfrfi/files/wandb-metadata.json b/wandb/run-20260305_043841-tqhhfrfi/files/wandb-metadata.json deleted file mode 100644 index 89f8932c20f29f34fa1a9998b25a712358c24035..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_043841-tqhhfrfi/files/wandb-metadata.json +++ /dev/null @@ -1,134 +0,0 @@ -{ - "os": "Linux-5.15.0-72-generic-x86_64-with-glibc2.35", - "python": "CPython 3.10.19", - "startedAt": "2026-03-05T04:38:41.010686Z", - "args": [ - "--model_name_or_path", - "/home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000", - "--tokenizer_path", - "/home/n5huang/dna_token/tokenizer_evaluation/merge_bpe/merge_tokenizer_unigram_len.json", - "--trust_remote_code", - "True", - "--data_path", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/H2AFZ/split", - "--kmer", - "-1", - "--run_name", - "hg38_BPE_base__merge_bpe_merge_tokenizer_unigram_len_3e-5_H2AFZ_seed42", - "--model_max_length", - "220", - "--per_device_train_batch_size", - "128", - "--per_device_eval_batch_size", - "128", - "--gradient_accumulation_steps", - "1", - "--learning_rate", - "3e-5", - "--num_train_epochs", - 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handles. diff --git a/wandb/run-20260305_043841-tqhhfrfi/run-tqhhfrfi.wandb b/wandb/run-20260305_043841-tqhhfrfi/run-tqhhfrfi.wandb deleted file mode 100644 index 56e6cc0767f337be50e51e6cf20039e62946cd99..0000000000000000000000000000000000000000 Binary files a/wandb/run-20260305_043841-tqhhfrfi/run-tqhhfrfi.wandb and /dev/null differ diff --git a/wandb/run-20260305_043859-75ycbhw1/files/config.yaml b/wandb/run-20260305_043859-75ycbhw1/files/config.yaml deleted file mode 100644 index 8243c202d6061986c6171420f4d9b6b2cc393962..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_043859-75ycbhw1/files/config.yaml +++ /dev/null @@ -1,139 +0,0 @@ -_wandb: - value: - cli_version: 0.25.0 - e: - wfa37ljuofd5tzcgmvvn7s74emvl4j0b: - args: - - --model_name_or_path - - /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 - - --tokenizer_path - - /home/n5huang/dna_token/tokenizer_evaluation/merge_bpe/merge_tokenizer_unigram_len.json - - --trust_remote_code - - "True" - - --data_path - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/H3K27ac/split - - --kmer - - "-1" - - --run_name - - hg38_BPE_base__merge_bpe_merge_tokenizer_unigram_len_3e-5_H3K27ac_seed42 - - --model_max_length - - "220" - - --per_device_train_batch_size - - "128" - - --per_device_eval_batch_size - - "128" - - --gradient_accumulation_steps - - "1" - - --learning_rate - - "3e-5" - - --num_train_epochs - - "2" - - --fp16 - - --save_steps - - "200" - - --output_dir - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_len/H3K27ac - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "547006242816" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:38:59.191487Z" - writerId: wfa37ljuofd5tzcgmvvn7s74emvl4j0b - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_043859-75ycbhw1/files/output.log b/wandb/run-20260305_043859-75ycbhw1/files/output.log deleted file mode 100644 index f1237c1c2f36981a0d3ecf5fd0b2a021f3381fcd..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_043859-75ycbhw1/files/output.log +++ /dev/null @@ -1,150 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 21713.21it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -classifier.weight | MISSING | -classifier.bias | MISSING | -bert.pooler.dense.bias | MISSING | -bert.pooler.dense.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 25,292 - Num Epochs = 2 - Num update steps per epoch = 198 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 396 - Number of trainable parameters = 44,302,082 - 0%| | 0/396 [00:00 - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 445, in train - trainer.train() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1424, in train - return inner_training_loop( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1506, in _inner_training_loop - self._run_epoch( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1734, in _run_epoch - tr_loss_step = self.training_step(model, inputs, num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1906, in training_step - loss = self.compute_loss(model, inputs, num_items_in_batch=num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1978, in compute_loss - outputs = model(**inputs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 823, in forward - return model_forward(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 811, in __call__ - return convert_to_fp32(self.model_forward(*args, **kwargs)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/amp/autocast_mode.py", line 44, in decorate_autocast - return func(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 843, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 1139, in forward - outputs = self.bert( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 917, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/output_capturing.py", line 253, in wrapper - outputs = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 680, in forward - embedding_output = self.embeddings( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 110, in forward - embeddings = self.LayerNorm(embeddings) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/normalization.py", line 229, in forward - return F.layer_norm( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/functional.py", line 2935, in layer_norm - return torch.layer_norm( -torch.AcceleratorError: CUDA error: device-side assert triggered -Search for `cudaErrorAssert' in https://docs.nvidia.com/cuda/cuda-runtime-api/group__CUDART__TYPES.html for more information. -CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect. -For debugging consider passing CUDA_LAUNCH_BLOCKING=1 -Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions. - -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 464, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 445, in train - trainer.train() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1424, in train - return inner_training_loop( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1506, in _inner_training_loop - self._run_epoch( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1734, in _run_epoch - tr_loss_step = self.training_step(model, inputs, num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1906, in training_step - loss = self.compute_loss(model, inputs, num_items_in_batch=num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1978, in compute_loss - outputs = model(**inputs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 823, in forward - return model_forward(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 811, in __call__ - return convert_to_fp32(self.model_forward(*args, **kwargs)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/amp/autocast_mode.py", line 44, in decorate_autocast - return func(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 843, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 1139, in forward - outputs = self.bert( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 917, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/output_capturing.py", line 253, in wrapper - outputs = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 680, in forward - embedding_output = self.embeddings( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 110, in forward - embeddings = self.LayerNorm(embeddings) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/normalization.py", line 229, in forward - return F.layer_norm( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/functional.py", line 2935, in layer_norm - return torch.layer_norm( -torch.AcceleratorError: CUDA error: device-side assert triggered -Search for `cudaErrorAssert' in https://docs.nvidia.com/cuda/cuda-runtime-api/group__CUDART__TYPES.html for more information. -CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect. -For debugging consider passing CUDA_LAUNCH_BLOCKING=1 -Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions. diff --git a/wandb/run-20260305_043859-75ycbhw1/files/requirements.txt b/wandb/run-20260305_043859-75ycbhw1/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_043859-75ycbhw1/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 -accelerate==1.13.0 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -triton==3.6.0 -nvidia-nccl-cu12==2.27.5 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -cuda-pathfinder==1.4.0 -shellingham==1.5.4 -torchaudio==2.5.1 -nvidia-cufile-cu12==1.13.1.3 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -nvidia-nvjitlink-cu12==12.8.93 -click==8.3.1 -MarkupSafe==3.0.2 -nvidia-nvshmem-cu12==3.4.5 -urllib3==2.6.3 -cuda-bindings==12.9.4 -propcache==0.4.1 -nvidia-cusolver-cu12==11.7.3.90 -sympy==1.14.0 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -nvidia-cuda-runtime-cu12==12.8.90 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_043859-75ycbhw1/files/wandb-metadata.json b/wandb/run-20260305_043859-75ycbhw1/files/wandb-metadata.json deleted file mode 100644 index 7bc3ad8a4844c6924e274d7d71f68d5de1d10a17..0000000000000000000000000000000000000000 --- 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"True" - - --data_path - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/H3K27me3/split - - --kmer - - "-1" - - --run_name - - hg38_BPE_base__merge_bpe_merge_tokenizer_unigram_len_3e-5_H3K27me3_seed42 - - --model_max_length - - "220" - - --per_device_train_batch_size - - "128" - - --per_device_eval_batch_size - - "128" - - --gradient_accumulation_steps - - "1" - - --learning_rate - - "3e-5" - - --num_train_epochs - - "2" - - --fp16 - - --save_steps - - "200" - - --output_dir - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_len/H3K27me3 - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "547006410752" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:39:16.624287Z" - writerId: h2y96xucbooqndoo6nr6y8nkatm3jtii - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_043916-58t57dy9/files/output.log b/wandb/run-20260305_043916-58t57dy9/files/output.log deleted file mode 100644 index 9da43df9a16f14b1553eb24bade9f5403bc0a59d..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_043916-58t57dy9/files/output.log +++ /dev/null @@ -1,150 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 11889.55it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.decoder.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -bert.pooler.dense.weight | MISSING | -classifier.weight | MISSING | -classifier.bias | MISSING | -bert.pooler.dense.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 2 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 414 - Number of trainable parameters = 44,302,082 - 0%| | 0/414 [00:00 - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 445, in train - trainer.train() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1424, in train - return inner_training_loop( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1506, in _inner_training_loop - self._run_epoch( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1734, in _run_epoch - tr_loss_step = self.training_step(model, inputs, num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1906, in training_step - loss = self.compute_loss(model, inputs, num_items_in_batch=num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1978, in compute_loss - outputs = model(**inputs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 823, in forward - return model_forward(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 811, in __call__ - return convert_to_fp32(self.model_forward(*args, **kwargs)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/amp/autocast_mode.py", line 44, in decorate_autocast - return func(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 843, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 1139, in forward - outputs = self.bert( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 917, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/output_capturing.py", line 253, in wrapper - outputs = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 680, in forward - embedding_output = self.embeddings( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 110, in forward - embeddings = self.LayerNorm(embeddings) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/normalization.py", line 229, in forward - return F.layer_norm( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/functional.py", line 2935, in layer_norm - return torch.layer_norm( -torch.AcceleratorError: CUDA error: device-side assert triggered -Search for `cudaErrorAssert' in https://docs.nvidia.com/cuda/cuda-runtime-api/group__CUDART__TYPES.html for more information. -CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect. -For debugging consider passing CUDA_LAUNCH_BLOCKING=1 -Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions. - -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 464, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 445, in train - trainer.train() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1424, in train - return inner_training_loop( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1506, in _inner_training_loop - self._run_epoch( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1734, in _run_epoch - tr_loss_step = self.training_step(model, inputs, num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1906, in training_step - loss = self.compute_loss(model, inputs, num_items_in_batch=num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1978, in compute_loss - outputs = model(**inputs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 823, in forward - return model_forward(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 811, in __call__ - return convert_to_fp32(self.model_forward(*args, **kwargs)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/amp/autocast_mode.py", line 44, in decorate_autocast - return func(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 843, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 1139, in forward - outputs = self.bert( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 917, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/output_capturing.py", line 253, in wrapper - outputs = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 680, in forward - embedding_output = self.embeddings( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 110, in forward - embeddings = self.LayerNorm(embeddings) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/normalization.py", line 229, in forward - return F.layer_norm( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/functional.py", line 2935, in layer_norm - return torch.layer_norm( -torch.AcceleratorError: CUDA error: device-side assert triggered -Search for `cudaErrorAssert' in https://docs.nvidia.com/cuda/cuda-runtime-api/group__CUDART__TYPES.html for more information. -CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect. -For debugging consider passing CUDA_LAUNCH_BLOCKING=1 -Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions. diff --git a/wandb/run-20260305_043916-58t57dy9/files/requirements.txt b/wandb/run-20260305_043916-58t57dy9/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_043916-58t57dy9/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 -accelerate==1.13.0 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -triton==3.6.0 -nvidia-nccl-cu12==2.27.5 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -cuda-pathfinder==1.4.0 -shellingham==1.5.4 -torchaudio==2.5.1 -nvidia-cufile-cu12==1.13.1.3 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -nvidia-nvjitlink-cu12==12.8.93 -click==8.3.1 -MarkupSafe==3.0.2 -nvidia-nvshmem-cu12==3.4.5 -urllib3==2.6.3 -cuda-bindings==12.9.4 -propcache==0.4.1 -nvidia-cusolver-cu12==11.7.3.90 -sympy==1.14.0 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -nvidia-cuda-runtime-cu12==12.8.90 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_043916-58t57dy9/files/wandb-metadata.json b/wandb/run-20260305_043916-58t57dy9/files/wandb-metadata.json deleted file mode 100644 index a4059cdc54c66051973f1199c8899dcc577a0a46..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_043916-58t57dy9/files/wandb-metadata.json +++ /dev/null @@ -1,134 +0,0 @@ -{ - "os": "Linux-5.15.0-72-generic-x86_64-with-glibc2.35", - "python": "CPython 3.10.19", - "startedAt": "2026-03-05T04:39:16.624287Z", - "args": [ - "--model_name_or_path", - "/home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000", - "--tokenizer_path", - "/home/n5huang/dna_token/tokenizer_evaluation/merge_bpe/merge_tokenizer_unigram_len.json", - "--trust_remote_code", - "True", - "--data_path", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/H3K27me3/split", - "--kmer", - "-1", - "--run_name", - "hg38_BPE_base__merge_bpe_merge_tokenizer_unigram_len_3e-5_H3K27me3_seed42", - "--model_max_length", - "220", - "--per_device_train_batch_size", - "128", - "--per_device_eval_batch_size", - "128", - "--gradient_accumulation_steps", - "1", - "--learning_rate", - "3e-5", - 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cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "547008471040" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:39:34.853449Z" - writerId: z4xoehk05cv7p6lptgfrn8wqx6bsnxl0 - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_043934-q0bm5sy9/files/output.log b/wandb/run-20260305_043934-q0bm5sy9/files/output.log deleted file mode 100644 index 48e1ba54c429d9967e23fcaa885fe46c68d1f595..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_043934-q0bm5sy9/files/output.log +++ /dev/null @@ -1,150 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 18400.07it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -classifier.weight | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.bias | MISSING | -bert.pooler.dense.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 2 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 414 - Number of trainable parameters = 44,302,082 - 0%| | 0/414 [00:00 - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 445, in train - trainer.train() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1424, in train - return inner_training_loop( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1506, in _inner_training_loop - self._run_epoch( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1734, in _run_epoch - tr_loss_step = self.training_step(model, inputs, num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1906, in training_step - loss = self.compute_loss(model, inputs, num_items_in_batch=num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1978, in compute_loss - outputs = model(**inputs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 823, in forward - return model_forward(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 811, in __call__ - return convert_to_fp32(self.model_forward(*args, **kwargs)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/amp/autocast_mode.py", line 44, in decorate_autocast - return func(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 843, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 1139, in forward - outputs = self.bert( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 917, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/output_capturing.py", line 253, in wrapper - outputs = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 680, in forward - embedding_output = self.embeddings( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 110, in forward - embeddings = self.LayerNorm(embeddings) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/normalization.py", line 229, in forward - return F.layer_norm( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/functional.py", line 2935, in layer_norm - return torch.layer_norm( -torch.AcceleratorError: CUDA error: device-side assert triggered -Search for `cudaErrorAssert' in https://docs.nvidia.com/cuda/cuda-runtime-api/group__CUDART__TYPES.html for more information. -CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect. -For debugging consider passing CUDA_LAUNCH_BLOCKING=1 -Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions. - -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 464, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 445, in train - trainer.train() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1424, in train - return inner_training_loop( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1506, in _inner_training_loop - self._run_epoch( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1734, in _run_epoch - tr_loss_step = self.training_step(model, inputs, num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1906, in training_step - loss = self.compute_loss(model, inputs, num_items_in_batch=num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1978, in compute_loss - outputs = model(**inputs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 823, in forward - return model_forward(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 811, in __call__ - return convert_to_fp32(self.model_forward(*args, **kwargs)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/amp/autocast_mode.py", line 44, in decorate_autocast - return func(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 843, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 1139, in forward - outputs = self.bert( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 917, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/output_capturing.py", line 253, in wrapper - outputs = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 680, in forward - embedding_output = self.embeddings( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 110, in forward - embeddings = self.LayerNorm(embeddings) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/normalization.py", line 229, in forward - return F.layer_norm( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/functional.py", line 2935, in layer_norm - return torch.layer_norm( -torch.AcceleratorError: CUDA error: device-side assert triggered -Search for `cudaErrorAssert' in https://docs.nvidia.com/cuda/cuda-runtime-api/group__CUDART__TYPES.html for more information. -CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect. -For debugging consider passing CUDA_LAUNCH_BLOCKING=1 -Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions. diff --git a/wandb/run-20260305_043934-q0bm5sy9/files/requirements.txt b/wandb/run-20260305_043934-q0bm5sy9/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_043934-q0bm5sy9/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 -accelerate==1.13.0 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -triton==3.6.0 -nvidia-nccl-cu12==2.27.5 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -cuda-pathfinder==1.4.0 -shellingham==1.5.4 -torchaudio==2.5.1 -nvidia-cufile-cu12==1.13.1.3 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -nvidia-nvjitlink-cu12==12.8.93 -click==8.3.1 -MarkupSafe==3.0.2 -nvidia-nvshmem-cu12==3.4.5 -urllib3==2.6.3 -cuda-bindings==12.9.4 -propcache==0.4.1 -nvidia-cusolver-cu12==11.7.3.90 -sympy==1.14.0 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -nvidia-cuda-runtime-cu12==12.8.90 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_043934-q0bm5sy9/files/wandb-metadata.json b/wandb/run-20260305_043934-q0bm5sy9/files/wandb-metadata.json deleted file mode 100644 index a4941c92e27744b70ff53cb8f4f1d85ebe13ccfd..0000000000000000000000000000000000000000 --- 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handles. diff --git a/wandb/run-20260305_043934-q0bm5sy9/run-q0bm5sy9.wandb b/wandb/run-20260305_043934-q0bm5sy9/run-q0bm5sy9.wandb deleted file mode 100644 index 45a088a62a2f0970df5f8d8b3ccbf7e68556fd8e..0000000000000000000000000000000000000000 Binary files a/wandb/run-20260305_043934-q0bm5sy9/run-q0bm5sy9.wandb and /dev/null differ diff --git a/wandb/run-20260305_043953-duwq6pva/files/config.yaml b/wandb/run-20260305_043953-duwq6pva/files/config.yaml deleted file mode 100644 index 3f3f4e3e8abb0e75d02590337336f8e743c2fb5e..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_043953-duwq6pva/files/config.yaml +++ /dev/null @@ -1,139 +0,0 @@ -_wandb: - value: - cli_version: 0.25.0 - e: - q9ogs7m73n6wuw7dcnw11lcd2fjz38xw: - args: - - --model_name_or_path - - /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 - - --tokenizer_path - - /home/n5huang/dna_token/tokenizer_evaluation/merge_bpe/merge_tokenizer_unigram_len.json - - --trust_remote_code - - "True" - - --data_path - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/H3K4me1/split - - --kmer - - "-1" - - --run_name - - hg38_BPE_base__merge_bpe_merge_tokenizer_unigram_len_3e-5_H3K4me1_seed42 - - --model_max_length - - "220" - - --per_device_train_batch_size - - "128" - - --per_device_eval_batch_size - - "128" - - --gradient_accumulation_steps - - "1" - - --learning_rate - - "3e-5" - - --num_train_epochs - - "2" - - --fp16 - - --save_steps - - "200" - - --output_dir - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_len/H3K4me1 - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "547008655360" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:39:53.858201Z" - writerId: q9ogs7m73n6wuw7dcnw11lcd2fjz38xw - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_043953-duwq6pva/files/output.log b/wandb/run-20260305_043953-duwq6pva/files/output.log deleted file mode 100644 index d22d29c787c8c1e9246f9a6a4afc8464db5baf82..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_043953-duwq6pva/files/output.log +++ /dev/null @@ -1,150 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 24444.59it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -classifier.weight | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.bias | MISSING | -bert.pooler.dense.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 2 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 414 - Number of trainable parameters = 44,302,082 - 0%| | 0/414 [00:00 - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 445, in train - trainer.train() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1424, in train - return inner_training_loop( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1506, in _inner_training_loop - self._run_epoch( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1734, in _run_epoch - tr_loss_step = self.training_step(model, inputs, num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1906, in training_step - loss = self.compute_loss(model, inputs, num_items_in_batch=num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1978, in compute_loss - outputs = model(**inputs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 823, in forward - return model_forward(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 811, in __call__ - return convert_to_fp32(self.model_forward(*args, **kwargs)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/amp/autocast_mode.py", line 44, in decorate_autocast - return func(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 843, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 1139, in forward - outputs = self.bert( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 917, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/output_capturing.py", line 253, in wrapper - outputs = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 680, in forward - embedding_output = self.embeddings( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 110, in forward - embeddings = self.LayerNorm(embeddings) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/normalization.py", line 229, in forward - return F.layer_norm( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/functional.py", line 2935, in layer_norm - return torch.layer_norm( -torch.AcceleratorError: CUDA error: device-side assert triggered -Search for `cudaErrorAssert' in https://docs.nvidia.com/cuda/cuda-runtime-api/group__CUDART__TYPES.html for more information. -CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect. -For debugging consider passing CUDA_LAUNCH_BLOCKING=1 -Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions. - -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 464, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 445, in train - trainer.train() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1424, in train - return inner_training_loop( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1506, in _inner_training_loop - self._run_epoch( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1734, in _run_epoch - tr_loss_step = self.training_step(model, inputs, num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1906, in training_step - loss = self.compute_loss(model, inputs, num_items_in_batch=num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1978, in compute_loss - outputs = model(**inputs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 823, in forward - return model_forward(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 811, in __call__ - return convert_to_fp32(self.model_forward(*args, **kwargs)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/amp/autocast_mode.py", line 44, in decorate_autocast - return func(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 843, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 1139, in forward - outputs = self.bert( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 917, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/output_capturing.py", line 253, in wrapper - outputs = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 680, in forward - embedding_output = self.embeddings( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 110, in forward - embeddings = self.LayerNorm(embeddings) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/normalization.py", line 229, in forward - return F.layer_norm( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/functional.py", line 2935, in layer_norm - return torch.layer_norm( -torch.AcceleratorError: CUDA error: device-side assert triggered -Search for `cudaErrorAssert' in https://docs.nvidia.com/cuda/cuda-runtime-api/group__CUDART__TYPES.html for more information. -CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect. -For debugging consider passing CUDA_LAUNCH_BLOCKING=1 -Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions. diff --git a/wandb/run-20260305_043953-duwq6pva/files/requirements.txt b/wandb/run-20260305_043953-duwq6pva/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_043953-duwq6pva/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 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- architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:40:12.643298Z" - writerId: ioaf7u9zs4y3zht0kit7eawgrwfsqudo - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_044012-9iza1660/files/output.log b/wandb/run-20260305_044012-9iza1660/files/output.log deleted file mode 100644 index e328518cd3bf352b8787dcbb06895391b8c2269d..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_044012-9iza1660/files/output.log +++ /dev/null @@ -1,150 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 18177.42it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -classifier.bias | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.weight | MISSING | -bert.pooler.dense.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 25,710 - Num Epochs = 2 - Num update steps per epoch = 201 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 402 - Number of trainable parameters = 44,302,082 - 0%| | 0/402 [00:00 - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 445, in train - trainer.train() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1424, in train - return inner_training_loop( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1506, in _inner_training_loop - self._run_epoch( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1734, in _run_epoch - tr_loss_step = self.training_step(model, inputs, num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1906, in training_step - loss = self.compute_loss(model, inputs, num_items_in_batch=num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1978, in compute_loss - outputs = model(**inputs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 823, in forward - return model_forward(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 811, in __call__ - return convert_to_fp32(self.model_forward(*args, **kwargs)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/amp/autocast_mode.py", line 44, in decorate_autocast - return func(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 843, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 1139, in forward - outputs = self.bert( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 917, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/output_capturing.py", line 253, in wrapper - outputs = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 680, in forward - embedding_output = self.embeddings( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 110, in forward - embeddings = self.LayerNorm(embeddings) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/normalization.py", line 229, in forward - return F.layer_norm( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/functional.py", line 2935, in layer_norm - return torch.layer_norm( -torch.AcceleratorError: CUDA error: device-side assert triggered -Search for `cudaErrorAssert' in https://docs.nvidia.com/cuda/cuda-runtime-api/group__CUDART__TYPES.html for more information. -CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect. -For debugging consider passing CUDA_LAUNCH_BLOCKING=1 -Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions. - -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 464, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 445, in train - trainer.train() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1424, in train - return inner_training_loop( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1506, in _inner_training_loop - self._run_epoch( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1734, in _run_epoch - tr_loss_step = self.training_step(model, inputs, num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1906, in training_step - loss = self.compute_loss(model, inputs, num_items_in_batch=num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1978, in compute_loss - outputs = model(**inputs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 823, in forward - return model_forward(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 811, in __call__ - return convert_to_fp32(self.model_forward(*args, **kwargs)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/amp/autocast_mode.py", line 44, in decorate_autocast - return func(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 843, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 1139, in forward - outputs = self.bert( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 917, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/output_capturing.py", line 253, in wrapper - outputs = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 680, in forward - embedding_output = self.embeddings( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 110, in forward - embeddings = self.LayerNorm(embeddings) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/normalization.py", line 229, in forward - return F.layer_norm( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/functional.py", line 2935, in layer_norm - return torch.layer_norm( -torch.AcceleratorError: CUDA error: device-side assert triggered -Search for `cudaErrorAssert' in https://docs.nvidia.com/cuda/cuda-runtime-api/group__CUDART__TYPES.html for more information. -CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect. -For debugging consider passing CUDA_LAUNCH_BLOCKING=1 -Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions. diff --git a/wandb/run-20260305_044012-9iza1660/files/requirements.txt b/wandb/run-20260305_044012-9iza1660/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_044012-9iza1660/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 -accelerate==1.13.0 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -triton==3.6.0 -nvidia-nccl-cu12==2.27.5 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -cuda-pathfinder==1.4.0 -shellingham==1.5.4 -torchaudio==2.5.1 -nvidia-cufile-cu12==1.13.1.3 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -nvidia-nvjitlink-cu12==12.8.93 -click==8.3.1 -MarkupSafe==3.0.2 -nvidia-nvshmem-cu12==3.4.5 -urllib3==2.6.3 -cuda-bindings==12.9.4 -propcache==0.4.1 -nvidia-cusolver-cu12==11.7.3.90 -sympy==1.14.0 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -nvidia-cuda-runtime-cu12==12.8.90 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_044012-9iza1660/files/wandb-metadata.json b/wandb/run-20260305_044012-9iza1660/files/wandb-metadata.json deleted file mode 100644 index e55ba4980d5a97282fefeccf53a04859a5416fbd..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_044012-9iza1660/files/wandb-metadata.json +++ /dev/null @@ -1,134 +0,0 @@ -{ - "os": "Linux-5.15.0-72-generic-x86_64-with-glibc2.35", - "python": "CPython 3.10.19", - "startedAt": "2026-03-05T04:40:12.643298Z", - "args": [ - "--model_name_or_path", - "/home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000", - "--tokenizer_path", - "/home/n5huang/dna_token/tokenizer_evaluation/merge_bpe/merge_tokenizer_unigram_len.json", - "--trust_remote_code", - "True", - "--data_path", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/H3K4me2/split", - "--kmer", - "-1", - "--run_name", - "hg38_BPE_base__merge_bpe_merge_tokenizer_unigram_len_3e-5_H3K4me2_seed42", - "--model_max_length", - "220", - "--per_device_train_batch_size", - "128", - "--per_device_eval_batch_size", - "128", - "--gradient_accumulation_steps", - "1", - "--learning_rate", - "3e-5", - "--num_train_epochs", - "2", - "--fp16", - "--save_steps", - "200", - "--output_dir", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_len/H3K4me2", - "--evaluation_strategy", - "steps", - "--eval_steps", - "200", - "--warmup_steps", - "30", - "--logging_steps", - "100000", - "--log_level", - "info", - "--seed", - "42", - "--find_unused_parameters", - "False", - "--project_name", - "genomic_bench_tune_hg38_1024" - ], - "program": "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", - "git": { - "remote": "https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks", - "commit": "5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6" - }, - "email": "mtapiapacheco@ucsd.edu", - "root": "/data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data", - "host": "sn4622116170", - "executable": "/home/n5huang/miniconda3/envs/nt_ft/bin/python", - "cpu_count": 128, - "cpu_count_logical": 255, - "gpu": 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handles. diff --git a/wandb/run-20260305_044012-9iza1660/run-9iza1660.wandb b/wandb/run-20260305_044012-9iza1660/run-9iza1660.wandb deleted file mode 100644 index 21f93522255bd53da5386da2073bbf85706ae23d..0000000000000000000000000000000000000000 Binary files a/wandb/run-20260305_044012-9iza1660/run-9iza1660.wandb and /dev/null differ diff --git a/wandb/run-20260305_044029-3uv2b1v0/files/config.yaml b/wandb/run-20260305_044029-3uv2b1v0/files/config.yaml deleted file mode 100644 index fc91104d60b4e4b375de8bb53feccfff9d080bd3..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_044029-3uv2b1v0/files/config.yaml +++ /dev/null @@ -1,139 +0,0 @@ -_wandb: - value: - cli_version: 0.25.0 - e: - ofyg1amdtdivuny3qf8ilrf6a8gvj6l8: - args: - - --model_name_or_path - - /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 - - --tokenizer_path - - /home/n5huang/dna_token/tokenizer_evaluation/merge_bpe/merge_tokenizer_unigram_len.json - - --trust_remote_code - - "True" - - --data_path - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/H3K4me3/split - - --kmer - - "-1" - - --run_name - - hg38_BPE_base__merge_bpe_merge_tokenizer_unigram_len_3e-5_H3K4me3_seed42 - - --model_max_length - - "220" - - --per_device_train_batch_size - - "128" - - --per_device_eval_batch_size - - "128" - - --gradient_accumulation_steps - - "1" - - --learning_rate - - "3e-5" - - --num_train_epochs - - "2" - - --fp16 - - --save_steps - - "200" - - --output_dir - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_len/H3K4me3 - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "547008950272" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:40:29.787286Z" - writerId: ofyg1amdtdivuny3qf8ilrf6a8gvj6l8 - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_044029-3uv2b1v0/files/output.log b/wandb/run-20260305_044029-3uv2b1v0/files/output.log deleted file mode 100644 index eb7fcabe64ed4468f6f61926bc5539900b2ee562..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_044029-3uv2b1v0/files/output.log +++ /dev/null @@ -1,150 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 22083.34it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -classifier.weight | MISSING | -classifier.bias | MISSING | -bert.pooler.dense.bias | MISSING | -bert.pooler.dense.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 14,595 - Num Epochs = 2 - Num update steps per epoch = 115 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 230 - Number of trainable parameters = 44,302,082 - 0%| | 0/230 [00:00 - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 445, in train - trainer.train() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1424, in train - return inner_training_loop( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1506, in _inner_training_loop - self._run_epoch( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1734, in _run_epoch - tr_loss_step = self.training_step(model, inputs, num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1906, in training_step - loss = self.compute_loss(model, inputs, num_items_in_batch=num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1978, in compute_loss - outputs = model(**inputs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 823, in forward - return model_forward(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 811, in __call__ - return convert_to_fp32(self.model_forward(*args, **kwargs)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/amp/autocast_mode.py", line 44, in decorate_autocast - return func(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 843, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 1139, in forward - outputs = self.bert( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 917, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/output_capturing.py", line 253, in wrapper - outputs = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 680, in forward - embedding_output = self.embeddings( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 110, in forward - embeddings = self.LayerNorm(embeddings) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/normalization.py", line 229, in forward - return F.layer_norm( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/functional.py", line 2935, in layer_norm - return torch.layer_norm( -torch.AcceleratorError: CUDA error: device-side assert triggered -Search for `cudaErrorAssert' in https://docs.nvidia.com/cuda/cuda-runtime-api/group__CUDART__TYPES.html for more information. -CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect. -For debugging consider passing CUDA_LAUNCH_BLOCKING=1 -Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions. - -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 464, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 445, in train - trainer.train() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1424, in train - return inner_training_loop( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1506, in _inner_training_loop - self._run_epoch( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1734, in _run_epoch - tr_loss_step = self.training_step(model, inputs, num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1906, in training_step - loss = self.compute_loss(model, inputs, num_items_in_batch=num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1978, in compute_loss - outputs = model(**inputs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 823, in forward - return model_forward(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 811, in __call__ - return convert_to_fp32(self.model_forward(*args, **kwargs)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/amp/autocast_mode.py", line 44, in decorate_autocast - return func(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 843, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 1139, in forward - outputs = self.bert( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 917, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/output_capturing.py", line 253, in wrapper - outputs = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 680, in forward - embedding_output = self.embeddings( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 110, in forward - embeddings = self.LayerNorm(embeddings) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/normalization.py", line 229, in forward - return F.layer_norm( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/functional.py", line 2935, in layer_norm - return torch.layer_norm( -torch.AcceleratorError: CUDA error: device-side assert triggered -Search for `cudaErrorAssert' in https://docs.nvidia.com/cuda/cuda-runtime-api/group__CUDART__TYPES.html for more information. -CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect. -For debugging consider passing CUDA_LAUNCH_BLOCKING=1 -Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions. diff --git a/wandb/run-20260305_044029-3uv2b1v0/files/requirements.txt b/wandb/run-20260305_044029-3uv2b1v0/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_044029-3uv2b1v0/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 -accelerate==1.13.0 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -triton==3.6.0 -nvidia-nccl-cu12==2.27.5 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -cuda-pathfinder==1.4.0 -shellingham==1.5.4 -torchaudio==2.5.1 -nvidia-cufile-cu12==1.13.1.3 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -nvidia-nvjitlink-cu12==12.8.93 -click==8.3.1 -MarkupSafe==3.0.2 -nvidia-nvshmem-cu12==3.4.5 -urllib3==2.6.3 -cuda-bindings==12.9.4 -propcache==0.4.1 -nvidia-cusolver-cu12==11.7.3.90 -sympy==1.14.0 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -nvidia-cuda-runtime-cu12==12.8.90 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_044029-3uv2b1v0/files/wandb-metadata.json b/wandb/run-20260305_044029-3uv2b1v0/files/wandb-metadata.json deleted file mode 100644 index 5e91629c9d8ac719e8fb2c3ea03b4dc89b292c81..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_044029-3uv2b1v0/files/wandb-metadata.json +++ /dev/null @@ -1,134 +0,0 @@ -{ - "os": "Linux-5.15.0-72-generic-x86_64-with-glibc2.35", - "python": "CPython 3.10.19", - "startedAt": "2026-03-05T04:40:29.787286Z", - "args": [ - "--model_name_or_path", - "/home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000", - "--tokenizer_path", - "/home/n5huang/dna_token/tokenizer_evaluation/merge_bpe/merge_tokenizer_unigram_len.json", - "--trust_remote_code", - "True", - "--data_path", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/H3K4me3/split", - "--kmer", - "-1", - "--run_name", - "hg38_BPE_base__merge_bpe_merge_tokenizer_unigram_len_3e-5_H3K4me3_seed42", - "--model_max_length", - "220", - "--per_device_train_batch_size", - "128", - "--per_device_eval_batch_size", - "128", - "--gradient_accumulation_steps", - "1", - "--learning_rate", - "3e-5", - "--num_train_epochs", 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handles. diff --git a/wandb/run-20260305_044029-3uv2b1v0/run-3uv2b1v0.wandb b/wandb/run-20260305_044029-3uv2b1v0/run-3uv2b1v0.wandb deleted file mode 100644 index f1b3887ce08d9520f2681806dd46108fef770cc3..0000000000000000000000000000000000000000 Binary files a/wandb/run-20260305_044029-3uv2b1v0/run-3uv2b1v0.wandb and /dev/null differ diff --git a/wandb/run-20260305_044045-ruafmolu/files/config.yaml b/wandb/run-20260305_044045-ruafmolu/files/config.yaml deleted file mode 100644 index 7d23f6e40cdacb1fa1720aee4cc4753e384fd4c6..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_044045-ruafmolu/files/config.yaml +++ /dev/null @@ -1,139 +0,0 @@ -_wandb: - value: - cli_version: 0.25.0 - e: - 9pxnbptdasa8spthj0a28qrr2vhjr7s4: - args: - - --model_name_or_path - - /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 - - --tokenizer_path - - /home/n5huang/dna_token/tokenizer_evaluation/merge_bpe/merge_tokenizer_unigram_len.json - - --trust_remote_code - - "True" - - --data_path - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/H3K9ac/split - - --kmer - - "-1" - - --run_name - - hg38_BPE_base__merge_bpe_merge_tokenizer_unigram_len_3e-5_H3K9ac_seed42 - - --model_max_length - - "220" - - --per_device_train_batch_size - - "128" - - --per_device_eval_batch_size - - "128" - - --gradient_accumulation_steps - - "1" - - --learning_rate - - "3e-5" - - --num_train_epochs - - "2" - - --fp16 - - --save_steps - - "200" - - --output_dir - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_len/H3K9ac - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "547010981888" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:40:45.347334Z" - writerId: 9pxnbptdasa8spthj0a28qrr2vhjr7s4 - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_044045-ruafmolu/files/output.log b/wandb/run-20260305_044045-ruafmolu/files/output.log deleted file mode 100644 index 43b05d280df551a6a94e246512c6c8997ca1d519..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_044045-ruafmolu/files/output.log +++ /dev/null @@ -1,150 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 20543.36it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -bert.pooler.dense.bias | MISSING | -classifier.bias | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 19,422 - Num Epochs = 2 - Num update steps per epoch = 152 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 304 - Number of trainable parameters = 44,302,082 - 0%| | 0/304 [00:00 - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 445, in train - trainer.train() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1424, in train - return inner_training_loop( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1506, in _inner_training_loop - self._run_epoch( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1734, in _run_epoch - tr_loss_step = self.training_step(model, inputs, num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1906, in training_step - loss = self.compute_loss(model, inputs, num_items_in_batch=num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1978, in compute_loss - outputs = model(**inputs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 823, in forward - return model_forward(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 811, in __call__ - return convert_to_fp32(self.model_forward(*args, **kwargs)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/amp/autocast_mode.py", line 44, in decorate_autocast - return func(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 843, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 1139, in forward - outputs = self.bert( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 917, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/output_capturing.py", line 253, in wrapper - outputs = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 680, in forward - embedding_output = self.embeddings( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 110, in forward - embeddings = self.LayerNorm(embeddings) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/normalization.py", line 229, in forward - return F.layer_norm( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/functional.py", line 2935, in layer_norm - return torch.layer_norm( -torch.AcceleratorError: CUDA error: device-side assert triggered -Search for `cudaErrorAssert' in https://docs.nvidia.com/cuda/cuda-runtime-api/group__CUDART__TYPES.html for more information. -CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect. -For debugging consider passing CUDA_LAUNCH_BLOCKING=1 -Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions. - -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 464, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 445, in train - trainer.train() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1424, in train - return inner_training_loop( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1506, in _inner_training_loop - self._run_epoch( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1734, in _run_epoch - tr_loss_step = self.training_step(model, inputs, num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1906, in training_step - loss = self.compute_loss(model, inputs, num_items_in_batch=num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1978, in compute_loss - outputs = model(**inputs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 823, in forward - return model_forward(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 811, in __call__ - return convert_to_fp32(self.model_forward(*args, **kwargs)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/amp/autocast_mode.py", line 44, in decorate_autocast - return func(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 843, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 1139, in forward - outputs = self.bert( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 917, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/output_capturing.py", line 253, in wrapper - outputs = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 680, in forward - embedding_output = self.embeddings( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 110, in forward - embeddings = self.LayerNorm(embeddings) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/normalization.py", line 229, in forward - return F.layer_norm( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/functional.py", line 2935, in layer_norm - return torch.layer_norm( -torch.AcceleratorError: CUDA error: device-side assert triggered -Search for `cudaErrorAssert' in https://docs.nvidia.com/cuda/cuda-runtime-api/group__CUDART__TYPES.html for more information. -CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect. -For debugging consider passing CUDA_LAUNCH_BLOCKING=1 -Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions. diff --git a/wandb/run-20260305_044045-ruafmolu/files/requirements.txt b/wandb/run-20260305_044045-ruafmolu/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_044045-ruafmolu/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 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python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_044102-vzc9cjuz/files/output.log b/wandb/run-20260305_044102-vzc9cjuz/files/output.log deleted file mode 100644 index de6b5fad0d4741e0b81e39ab762c5b21bf0fda03..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_044102-vzc9cjuz/files/output.log +++ /dev/null @@ -1,150 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 12247.74it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -bert.pooler.dense.weight | MISSING | -classifier.weight | MISSING | -classifier.bias | MISSING | -bert.pooler.dense.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 22,630 - Num Epochs = 2 - Num update steps per epoch = 177 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 354 - Number of trainable parameters = 44,302,082 - 0%| | 0/354 [00:00 - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 445, in train - trainer.train() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1424, in train - return inner_training_loop( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1506, in _inner_training_loop - self._run_epoch( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1734, in _run_epoch - tr_loss_step = self.training_step(model, inputs, num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1906, in training_step - loss = self.compute_loss(model, inputs, num_items_in_batch=num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1978, in compute_loss - outputs = model(**inputs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 823, in forward - return model_forward(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 811, in __call__ - return convert_to_fp32(self.model_forward(*args, **kwargs)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/amp/autocast_mode.py", line 44, in decorate_autocast - return func(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 843, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 1139, in forward - outputs = self.bert( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 917, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/output_capturing.py", line 253, in wrapper - outputs = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 680, in forward - embedding_output = self.embeddings( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 110, in forward - embeddings = self.LayerNorm(embeddings) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/normalization.py", line 229, in forward - return F.layer_norm( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/functional.py", line 2935, in layer_norm - return torch.layer_norm( -torch.AcceleratorError: CUDA error: device-side assert triggered -Search for `cudaErrorAssert' in https://docs.nvidia.com/cuda/cuda-runtime-api/group__CUDART__TYPES.html for more information. -CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect. -For debugging consider passing CUDA_LAUNCH_BLOCKING=1 -Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions. - -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 464, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 445, in train - trainer.train() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1424, in train - return inner_training_loop( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1506, in _inner_training_loop - self._run_epoch( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1734, in _run_epoch - tr_loss_step = self.training_step(model, inputs, num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1906, in training_step - loss = self.compute_loss(model, inputs, num_items_in_batch=num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1978, in compute_loss - outputs = model(**inputs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 823, in forward - return model_forward(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 811, in __call__ - return convert_to_fp32(self.model_forward(*args, **kwargs)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/amp/autocast_mode.py", line 44, in decorate_autocast - return func(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 843, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 1139, in forward - outputs = self.bert( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 917, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/output_capturing.py", line 253, in wrapper - outputs = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 680, in forward - embedding_output = self.embeddings( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 110, in forward - embeddings = self.LayerNorm(embeddings) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/normalization.py", line 229, in forward - return F.layer_norm( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/functional.py", line 2935, in layer_norm - return torch.layer_norm( -torch.AcceleratorError: CUDA error: device-side assert triggered -Search for `cudaErrorAssert' in https://docs.nvidia.com/cuda/cuda-runtime-api/group__CUDART__TYPES.html for more information. -CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect. -For debugging consider passing CUDA_LAUNCH_BLOCKING=1 -Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions. diff --git a/wandb/run-20260305_044102-vzc9cjuz/files/requirements.txt b/wandb/run-20260305_044102-vzc9cjuz/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_044102-vzc9cjuz/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 -accelerate==1.13.0 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -triton==3.6.0 -nvidia-nccl-cu12==2.27.5 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -cuda-pathfinder==1.4.0 -shellingham==1.5.4 -torchaudio==2.5.1 -nvidia-cufile-cu12==1.13.1.3 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -nvidia-nvjitlink-cu12==12.8.93 -click==8.3.1 -MarkupSafe==3.0.2 -nvidia-nvshmem-cu12==3.4.5 -urllib3==2.6.3 -cuda-bindings==12.9.4 -propcache==0.4.1 -nvidia-cusolver-cu12==11.7.3.90 -sympy==1.14.0 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -nvidia-cuda-runtime-cu12==12.8.90 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_044102-vzc9cjuz/files/wandb-metadata.json b/wandb/run-20260305_044102-vzc9cjuz/files/wandb-metadata.json deleted file mode 100644 index 030d689aac28c55d4e263fb1d5f198830d575d7a..0000000000000000000000000000000000000000 --- 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handles. diff --git a/wandb/run-20260305_044102-vzc9cjuz/run-vzc9cjuz.wandb b/wandb/run-20260305_044102-vzc9cjuz/run-vzc9cjuz.wandb deleted file mode 100644 index 1cd018cd5ad4d7c94cde3a79f208109d617c6c43..0000000000000000000000000000000000000000 Binary files a/wandb/run-20260305_044102-vzc9cjuz/run-vzc9cjuz.wandb and /dev/null differ diff --git a/wandb/run-20260305_044119-dvqho4ti/files/config.yaml b/wandb/run-20260305_044119-dvqho4ti/files/config.yaml deleted file mode 100644 index 078ef4793237557c459abec482ee483ed00d0a14..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_044119-dvqho4ti/files/config.yaml +++ /dev/null @@ -1,139 +0,0 @@ -_wandb: - value: - cli_version: 0.25.0 - e: - dvnstbhfoh3eei2ppaocfhhhnstgniud: - args: - - --model_name_or_path - - /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 - - --tokenizer_path - - /home/n5huang/dna_token/tokenizer_evaluation/merge_bpe/merge_tokenizer_unigram_len.json - - --trust_remote_code - - "True" - - --data_path - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/H4K20me1/split - - --kmer - - "-1" - - --run_name - - hg38_BPE_base__merge_bpe_merge_tokenizer_unigram_len_3e-5_H4K20me1_seed42 - - --model_max_length - - "220" - - --per_device_train_batch_size - - "128" - - --per_device_eval_batch_size - - "128" - - --gradient_accumulation_steps - - "1" - - --learning_rate - - "3e-5" - - --num_train_epochs - - "2" - - --fp16 - - --save_steps - - "200" - - --output_dir - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_len/H4K20me1 - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "547011256320" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:41:19.332474Z" - writerId: dvnstbhfoh3eei2ppaocfhhhnstgniud - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_044119-dvqho4ti/files/output.log b/wandb/run-20260305_044119-dvqho4ti/files/output.log deleted file mode 100644 index 46ee7f970804e0f9db35adbc744e4d1b985bd7f0..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_044119-dvqho4ti/files/output.log +++ /dev/null @@ -1,150 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 22875.14it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -bert.pooler.dense.bias | MISSING | -classifier.bias | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 25,816 - Num Epochs = 2 - Num update steps per epoch = 202 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 404 - Number of trainable parameters = 44,302,082 - 0%| | 0/404 [00:00 - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 445, in train - trainer.train() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1424, in train - return inner_training_loop( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1506, in _inner_training_loop - self._run_epoch( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1734, in _run_epoch - tr_loss_step = self.training_step(model, inputs, num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1906, in training_step - loss = self.compute_loss(model, inputs, num_items_in_batch=num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1978, in compute_loss - outputs = model(**inputs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 823, in forward - return model_forward(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 811, in __call__ - return convert_to_fp32(self.model_forward(*args, **kwargs)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/amp/autocast_mode.py", line 44, in decorate_autocast - return func(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 843, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 1139, in forward - outputs = self.bert( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 917, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/output_capturing.py", line 253, in wrapper - outputs = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 680, in forward - embedding_output = self.embeddings( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 110, in forward - embeddings = self.LayerNorm(embeddings) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/normalization.py", line 229, in forward - return F.layer_norm( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/functional.py", line 2935, in layer_norm - return torch.layer_norm( -torch.AcceleratorError: CUDA error: device-side assert triggered -Search for `cudaErrorAssert' in https://docs.nvidia.com/cuda/cuda-runtime-api/group__CUDART__TYPES.html for more information. -CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect. -For debugging consider passing CUDA_LAUNCH_BLOCKING=1 -Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions. - -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 464, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 445, in train - trainer.train() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1424, in train - return inner_training_loop( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1506, in _inner_training_loop - self._run_epoch( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1734, in _run_epoch - tr_loss_step = self.training_step(model, inputs, num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1906, in training_step - loss = self.compute_loss(model, inputs, num_items_in_batch=num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1978, in compute_loss - outputs = model(**inputs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 823, in forward - return model_forward(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 811, in __call__ - return convert_to_fp32(self.model_forward(*args, **kwargs)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/amp/autocast_mode.py", line 44, in decorate_autocast - return func(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 843, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 1139, in forward - outputs = self.bert( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 917, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/output_capturing.py", line 253, in wrapper - outputs = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 680, in forward - embedding_output = self.embeddings( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 110, in forward - embeddings = self.LayerNorm(embeddings) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/normalization.py", line 229, in forward - return F.layer_norm( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/functional.py", line 2935, in layer_norm - return torch.layer_norm( -torch.AcceleratorError: CUDA error: device-side assert triggered -Search for `cudaErrorAssert' in https://docs.nvidia.com/cuda/cuda-runtime-api/group__CUDART__TYPES.html for more information. -CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect. -For debugging consider passing CUDA_LAUNCH_BLOCKING=1 -Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions. diff --git a/wandb/run-20260305_044119-dvqho4ti/files/requirements.txt b/wandb/run-20260305_044119-dvqho4ti/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_044119-dvqho4ti/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 -accelerate==1.13.0 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -triton==3.6.0 -nvidia-nccl-cu12==2.27.5 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -cuda-pathfinder==1.4.0 -shellingham==1.5.4 -torchaudio==2.5.1 -nvidia-cufile-cu12==1.13.1.3 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -nvidia-nvjitlink-cu12==12.8.93 -click==8.3.1 -MarkupSafe==3.0.2 -nvidia-nvshmem-cu12==3.4.5 -urllib3==2.6.3 -cuda-bindings==12.9.4 -propcache==0.4.1 -nvidia-cusolver-cu12==11.7.3.90 -sympy==1.14.0 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -nvidia-cuda-runtime-cu12==12.8.90 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_044119-dvqho4ti/files/wandb-metadata.json b/wandb/run-20260305_044119-dvqho4ti/files/wandb-metadata.json deleted file mode 100644 index dbfb05002adcff4dd52b93e4bb5fd9fa5b6e334b..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_044119-dvqho4ti/files/wandb-metadata.json +++ /dev/null @@ -1,134 +0,0 @@ -{ - "os": "Linux-5.15.0-72-generic-x86_64-with-glibc2.35", - "python": "CPython 3.10.19", - "startedAt": "2026-03-05T04:41:19.332474Z", - "args": [ - "--model_name_or_path", - "/home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000", - "--tokenizer_path", - "/home/n5huang/dna_token/tokenizer_evaluation/merge_bpe/merge_tokenizer_unigram_len.json", - "--trust_remote_code", - "True", - "--data_path", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/H4K20me1/split", - "--kmer", - "-1", - "--run_name", - "hg38_BPE_base__merge_bpe_merge_tokenizer_unigram_len_3e-5_H4K20me1_seed42", - "--model_max_length", - "220", - "--per_device_train_batch_size", - "128", - "--per_device_eval_batch_size", - "128", - "--gradient_accumulation_steps", - "1", - "--learning_rate", - "3e-5", - 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"True" - - --data_path - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/enhancers/split - - --kmer - - "-1" - - --run_name - - hg38_BPE_base__merge_bpe_merge_tokenizer_unigram_len2_3e-5_enhancers_seed42 - - --model_max_length - - "100" - - --per_device_train_batch_size - - "128" - - --per_device_eval_batch_size - - "128" - - --gradient_accumulation_steps - - "1" - - --learning_rate - - "3e-5" - - --num_train_epochs - - "4" - - --fp16 - - --save_steps - - "200" - - --output_dir - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_len2/enhancers - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "547013275648" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:41:36.619164Z" - writerId: wxacsj796eucmm7kpdmtfz1wbqaingzm - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_044136-gmf863h1/files/output.log b/wandb/run-20260305_044136-gmf863h1/files/output.log deleted file mode 100644 index 823f01e38119015534dcd09407e46553c3f193dc..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_044136-gmf863h1/files/output.log +++ /dev/null @@ -1,150 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 21426.57it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -bert.pooler.dense.bias | MISSING | -classifier.bias | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 4 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 828 - Number of trainable parameters = 44,302,082 - 0%| | 0/828 [00:00 - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 445, in train - trainer.train() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1424, in train - return inner_training_loop( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1506, in _inner_training_loop - self._run_epoch( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1734, in _run_epoch - tr_loss_step = self.training_step(model, inputs, num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1906, in training_step - loss = self.compute_loss(model, inputs, num_items_in_batch=num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1978, in compute_loss - outputs = model(**inputs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 823, in forward - return model_forward(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 811, in __call__ - return convert_to_fp32(self.model_forward(*args, **kwargs)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/amp/autocast_mode.py", line 44, in decorate_autocast - return func(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 843, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 1139, in forward - outputs = self.bert( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 917, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/output_capturing.py", line 253, in wrapper - outputs = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 680, in forward - embedding_output = self.embeddings( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 110, in forward - embeddings = self.LayerNorm(embeddings) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/normalization.py", line 229, in forward - return F.layer_norm( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/functional.py", line 2935, in layer_norm - return torch.layer_norm( -torch.AcceleratorError: CUDA error: device-side assert triggered -Search for `cudaErrorAssert' in https://docs.nvidia.com/cuda/cuda-runtime-api/group__CUDART__TYPES.html for more information. -CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect. -For debugging consider passing CUDA_LAUNCH_BLOCKING=1 -Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions. - -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 464, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 445, in train - trainer.train() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1424, in train - return inner_training_loop( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1506, in _inner_training_loop - self._run_epoch( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1734, in _run_epoch - tr_loss_step = self.training_step(model, inputs, num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1906, in training_step - loss = self.compute_loss(model, inputs, num_items_in_batch=num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1978, in compute_loss - outputs = model(**inputs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 823, in forward - return model_forward(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 811, in __call__ - return convert_to_fp32(self.model_forward(*args, **kwargs)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/amp/autocast_mode.py", line 44, in decorate_autocast - return func(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 843, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 1139, in forward - outputs = self.bert( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 917, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/output_capturing.py", line 253, in wrapper - outputs = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 680, in forward - embedding_output = self.embeddings( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 110, in forward - embeddings = self.LayerNorm(embeddings) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/normalization.py", line 229, in forward - return F.layer_norm( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/functional.py", line 2935, in layer_norm - return torch.layer_norm( -torch.AcceleratorError: CUDA error: device-side assert triggered -Search for `cudaErrorAssert' in https://docs.nvidia.com/cuda/cuda-runtime-api/group__CUDART__TYPES.html for more information. -CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect. -For debugging consider passing CUDA_LAUNCH_BLOCKING=1 -Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions. diff --git a/wandb/run-20260305_044136-gmf863h1/files/requirements.txt b/wandb/run-20260305_044136-gmf863h1/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_044136-gmf863h1/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 -accelerate==1.13.0 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -triton==3.6.0 -nvidia-nccl-cu12==2.27.5 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -cuda-pathfinder==1.4.0 -shellingham==1.5.4 -torchaudio==2.5.1 -nvidia-cufile-cu12==1.13.1.3 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -nvidia-nvjitlink-cu12==12.8.93 -click==8.3.1 -MarkupSafe==3.0.2 -nvidia-nvshmem-cu12==3.4.5 -urllib3==2.6.3 -cuda-bindings==12.9.4 -propcache==0.4.1 -nvidia-cusolver-cu12==11.7.3.90 -sympy==1.14.0 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -nvidia-cuda-runtime-cu12==12.8.90 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_044136-gmf863h1/files/wandb-metadata.json b/wandb/run-20260305_044136-gmf863h1/files/wandb-metadata.json deleted file mode 100644 index f473ccb82da55997fe08d8341d98d32059c569d9..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_044136-gmf863h1/files/wandb-metadata.json +++ /dev/null @@ -1,134 +0,0 @@ -{ - "os": "Linux-5.15.0-72-generic-x86_64-with-glibc2.35", - "python": "CPython 3.10.19", - "startedAt": "2026-03-05T04:41:36.619164Z", - "args": [ - "--model_name_or_path", - "/home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000", - "--tokenizer_path", - "/home/n5huang/dna_token/tokenizer_evaluation/merge_bpe/merge_tokenizer_unigram_len2.json", - "--trust_remote_code", - "True", - "--data_path", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/enhancers/split", - "--kmer", - "-1", - "--run_name", - "hg38_BPE_base__merge_bpe_merge_tokenizer_unigram_len2_3e-5_enhancers_seed42", - "--model_max_length", - "100", - "--per_device_train_batch_size", - "128", - "--per_device_eval_batch_size", - "128", - "--gradient_accumulation_steps", - "1", - "--learning_rate", - "3e-5", - 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genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "547013419008" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: 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ta8bnjm07cdillcmzvlye52coby8pcp5 - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_044150-gy9qxjip/files/output.log b/wandb/run-20260305_044150-gy9qxjip/files/output.log deleted file mode 100644 index 3a43486eca806fde2d7721a2519e4583095d2439..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_044150-gy9qxjip/files/output.log +++ /dev/null @@ -1,150 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 20773.04it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -classifier.bias | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.weight | MISSING | -bert.pooler.dense.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 4 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 828 - Number of trainable parameters = 44,302,851 - 0%| | 0/828 [00:00 - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 445, in train - trainer.train() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1424, in train - return inner_training_loop( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1506, in _inner_training_loop - self._run_epoch( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1734, in _run_epoch - tr_loss_step = self.training_step(model, inputs, num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1906, in training_step - loss = self.compute_loss(model, inputs, num_items_in_batch=num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1978, in compute_loss - outputs = model(**inputs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 823, in forward - return model_forward(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 811, in __call__ - return convert_to_fp32(self.model_forward(*args, **kwargs)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/amp/autocast_mode.py", line 44, in decorate_autocast - return func(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 843, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 1139, in forward - outputs = self.bert( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 917, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/output_capturing.py", line 253, in wrapper - outputs = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 680, in forward - embedding_output = self.embeddings( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 110, in forward - embeddings = self.LayerNorm(embeddings) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/normalization.py", line 229, in forward - return F.layer_norm( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/functional.py", line 2935, in layer_norm - return torch.layer_norm( -torch.AcceleratorError: CUDA error: device-side assert triggered -Search for `cudaErrorAssert' in https://docs.nvidia.com/cuda/cuda-runtime-api/group__CUDART__TYPES.html for more information. -CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect. -For debugging consider passing CUDA_LAUNCH_BLOCKING=1 -Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions. - -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 464, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 445, in train - trainer.train() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1424, in train - return inner_training_loop( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1506, in _inner_training_loop - self._run_epoch( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1734, in _run_epoch - tr_loss_step = self.training_step(model, inputs, num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1906, in training_step - loss = self.compute_loss(model, inputs, num_items_in_batch=num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1978, in compute_loss - outputs = model(**inputs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 823, in forward - return model_forward(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 811, in __call__ - return convert_to_fp32(self.model_forward(*args, **kwargs)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/amp/autocast_mode.py", line 44, in decorate_autocast - return func(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 843, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 1139, in forward - outputs = self.bert( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 917, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/output_capturing.py", line 253, in wrapper - outputs = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 680, in forward - embedding_output = self.embeddings( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 110, in forward - embeddings = self.LayerNorm(embeddings) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/normalization.py", line 229, in forward - return F.layer_norm( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/functional.py", line 2935, in layer_norm - return torch.layer_norm( -torch.AcceleratorError: CUDA error: device-side assert triggered -Search for `cudaErrorAssert' in https://docs.nvidia.com/cuda/cuda-runtime-api/group__CUDART__TYPES.html for more information. -CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect. -For debugging consider passing CUDA_LAUNCH_BLOCKING=1 -Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions. diff --git a/wandb/run-20260305_044150-gy9qxjip/files/requirements.txt b/wandb/run-20260305_044150-gy9qxjip/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_044150-gy9qxjip/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 -accelerate==1.13.0 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -triton==3.6.0 -nvidia-nccl-cu12==2.27.5 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -cuda-pathfinder==1.4.0 -shellingham==1.5.4 -torchaudio==2.5.1 -nvidia-cufile-cu12==1.13.1.3 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -nvidia-nvjitlink-cu12==12.8.93 -click==8.3.1 -MarkupSafe==3.0.2 -nvidia-nvshmem-cu12==3.4.5 -urllib3==2.6.3 -cuda-bindings==12.9.4 -propcache==0.4.1 -nvidia-cusolver-cu12==11.7.3.90 -sympy==1.14.0 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -nvidia-cuda-runtime-cu12==12.8.90 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_044150-gy9qxjip/files/wandb-metadata.json b/wandb/run-20260305_044150-gy9qxjip/files/wandb-metadata.json deleted file mode 100644 index a4d165a7030717ca5976362c1a7ec5313bc7a160..0000000000000000000000000000000000000000 --- 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b/wandb/run-20260305_044150-gy9qxjip/run-gy9qxjip.wandb deleted file mode 100644 index e3f3fac4180c14c8458793f20ad626d9cf5cfb23..0000000000000000000000000000000000000000 Binary files a/wandb/run-20260305_044150-gy9qxjip/run-gy9qxjip.wandb and /dev/null differ diff --git a/wandb/run-20260305_044204-fbt4t9q2/files/config.yaml b/wandb/run-20260305_044204-fbt4t9q2/files/config.yaml deleted file mode 100644 index edcbaf9de698a3bace42d8f04dc612ddd4fb2581..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_044204-fbt4t9q2/files/config.yaml +++ /dev/null @@ -1,139 +0,0 @@ -_wandb: - value: - cli_version: 0.25.0 - e: - p1pvtnl23vbxrh56dm8y7dfgz381kde4: - args: - - --model_name_or_path - - /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 - - --tokenizer_path - - /home/n5huang/dna_token/tokenizer_evaluation/merge_bpe/merge_tokenizer_unigram_len2.json - - --trust_remote_code - - "True" - - --data_path - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/promoter_all/split - - --kmer - - "-1" - - --run_name - - hg38_BPE_base__merge_bpe_merge_tokenizer_unigram_len2_3e-5_promoter_all_seed42 - - --model_max_length - - "80" - - --per_device_train_batch_size - - "128" - - --per_device_eval_batch_size - - "128" - - --gradient_accumulation_steps - - "1" - - --learning_rate - - "3e-5" - - --num_train_epochs - - "2" - - --fp16 - - --save_steps - - "200" - - --output_dir - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_len2/promoter_all - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "547013537792" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:42:04.945571Z" - writerId: p1pvtnl23vbxrh56dm8y7dfgz381kde4 - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_044204-fbt4t9q2/files/output.log b/wandb/run-20260305_044204-fbt4t9q2/files/output.log deleted file mode 100644 index 4f0e4730bed2f89d122ed3cc62b259e2d23e4725..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_044204-fbt4t9q2/files/output.log +++ /dev/null @@ -1,150 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 19974.76it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -classifier.weight | MISSING | -bert.pooler.dense.weight | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 25,267 - Num Epochs = 2 - Num update steps per epoch = 198 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 396 - Number of trainable parameters = 44,302,082 - 0%| | 0/396 [00:00 - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 445, in train - trainer.train() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1424, in train - return inner_training_loop( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1506, in _inner_training_loop - self._run_epoch( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1734, in _run_epoch - tr_loss_step = self.training_step(model, inputs, num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1906, in training_step - loss = self.compute_loss(model, inputs, num_items_in_batch=num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1978, in compute_loss - outputs = model(**inputs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 823, in forward - return model_forward(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 811, in __call__ - return convert_to_fp32(self.model_forward(*args, **kwargs)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/amp/autocast_mode.py", line 44, in decorate_autocast - return func(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 843, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 1139, in forward - outputs = self.bert( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 917, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/output_capturing.py", line 253, in wrapper - outputs = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 680, in forward - embedding_output = self.embeddings( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 110, in forward - embeddings = self.LayerNorm(embeddings) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/normalization.py", line 229, in forward - return F.layer_norm( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/functional.py", line 2935, in layer_norm - return torch.layer_norm( -torch.AcceleratorError: CUDA error: device-side assert triggered -Search for `cudaErrorAssert' in https://docs.nvidia.com/cuda/cuda-runtime-api/group__CUDART__TYPES.html for more information. -CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect. -For debugging consider passing CUDA_LAUNCH_BLOCKING=1 -Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions. - -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 464, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 445, in train - trainer.train() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1424, in train - return inner_training_loop( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1506, in _inner_training_loop - self._run_epoch( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1734, in _run_epoch - tr_loss_step = self.training_step(model, inputs, num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1906, in training_step - loss = self.compute_loss(model, inputs, num_items_in_batch=num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1978, in compute_loss - outputs = model(**inputs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 823, in forward - return model_forward(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 811, in __call__ - return convert_to_fp32(self.model_forward(*args, **kwargs)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/amp/autocast_mode.py", line 44, in decorate_autocast - return func(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 843, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 1139, in forward - outputs = self.bert( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 917, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/output_capturing.py", line 253, in wrapper - outputs = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 680, in forward - embedding_output = self.embeddings( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 110, in forward - embeddings = self.LayerNorm(embeddings) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/normalization.py", line 229, in forward - return F.layer_norm( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/functional.py", line 2935, in layer_norm - return torch.layer_norm( -torch.AcceleratorError: CUDA error: device-side assert triggered -Search for `cudaErrorAssert' in https://docs.nvidia.com/cuda/cuda-runtime-api/group__CUDART__TYPES.html for more information. -CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect. -For debugging consider passing CUDA_LAUNCH_BLOCKING=1 -Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions. diff --git a/wandb/run-20260305_044204-fbt4t9q2/files/requirements.txt b/wandb/run-20260305_044204-fbt4t9q2/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_044204-fbt4t9q2/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 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python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_044218-43wifp9k/files/output.log b/wandb/run-20260305_044218-43wifp9k/files/output.log deleted file mode 100644 index c146435ac08569bfc4831c9e6fcf598fe4911789..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_044218-43wifp9k/files/output.log +++ /dev/null @@ -1,150 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 21982.50it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -classifier.weight | MISSING | -classifier.bias | MISSING | -bert.pooler.dense.bias | MISSING | -bert.pooler.dense.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 25,097 - Num Epochs = 2 - Num update steps per epoch = 197 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 394 - Number of trainable parameters = 44,302,082 - 0%| | 0/394 [00:00 - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 445, in train - trainer.train() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1424, in train - return inner_training_loop( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1506, in _inner_training_loop - self._run_epoch( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1734, in _run_epoch - tr_loss_step = self.training_step(model, inputs, num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1906, in training_step - loss = self.compute_loss(model, inputs, num_items_in_batch=num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1978, in compute_loss - outputs = model(**inputs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 823, in forward - return model_forward(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 811, in __call__ - return convert_to_fp32(self.model_forward(*args, **kwargs)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/amp/autocast_mode.py", line 44, in decorate_autocast - return func(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 843, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 1139, in forward - outputs = self.bert( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 917, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/output_capturing.py", line 253, in wrapper - outputs = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 680, in forward - embedding_output = self.embeddings( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 110, in forward - embeddings = self.LayerNorm(embeddings) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/normalization.py", line 229, in forward - return F.layer_norm( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/functional.py", line 2935, in layer_norm - return torch.layer_norm( -torch.AcceleratorError: CUDA error: device-side assert triggered -Search for `cudaErrorAssert' in https://docs.nvidia.com/cuda/cuda-runtime-api/group__CUDART__TYPES.html for more information. -CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect. -For debugging consider passing CUDA_LAUNCH_BLOCKING=1 -Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions. - -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 464, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 445, in train - trainer.train() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1424, in train - return inner_training_loop( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1506, in _inner_training_loop - self._run_epoch( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1734, in _run_epoch - tr_loss_step = self.training_step(model, inputs, num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1906, in training_step - loss = self.compute_loss(model, inputs, num_items_in_batch=num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1978, in compute_loss - outputs = model(**inputs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 823, in forward - return model_forward(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 811, in __call__ - return convert_to_fp32(self.model_forward(*args, **kwargs)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/amp/autocast_mode.py", line 44, in decorate_autocast - return func(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 843, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 1139, in forward - outputs = self.bert( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 917, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/output_capturing.py", line 253, in wrapper - outputs = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 680, in forward - embedding_output = self.embeddings( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 110, in forward - embeddings = self.LayerNorm(embeddings) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/normalization.py", line 229, in forward - return F.layer_norm( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/functional.py", line 2935, in layer_norm - return torch.layer_norm( -torch.AcceleratorError: CUDA error: device-side assert triggered -Search for `cudaErrorAssert' in https://docs.nvidia.com/cuda/cuda-runtime-api/group__CUDART__TYPES.html for more information. -CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect. -For debugging consider passing CUDA_LAUNCH_BLOCKING=1 -Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions. diff --git a/wandb/run-20260305_044218-43wifp9k/files/requirements.txt b/wandb/run-20260305_044218-43wifp9k/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_044218-43wifp9k/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 -accelerate==1.13.0 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -triton==3.6.0 -nvidia-nccl-cu12==2.27.5 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -cuda-pathfinder==1.4.0 -shellingham==1.5.4 -torchaudio==2.5.1 -nvidia-cufile-cu12==1.13.1.3 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -nvidia-nvjitlink-cu12==12.8.93 -click==8.3.1 -MarkupSafe==3.0.2 -nvidia-nvshmem-cu12==3.4.5 -urllib3==2.6.3 -cuda-bindings==12.9.4 -propcache==0.4.1 -nvidia-cusolver-cu12==11.7.3.90 -sympy==1.14.0 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -nvidia-cuda-runtime-cu12==12.8.90 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_044218-43wifp9k/files/wandb-metadata.json b/wandb/run-20260305_044218-43wifp9k/files/wandb-metadata.json deleted file mode 100644 index 1f4abd1aa6f8a7547f4ec309bc2c90ebca164807..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_044218-43wifp9k/files/wandb-metadata.json +++ /dev/null @@ -1,134 +0,0 @@ -{ - "os": "Linux-5.15.0-72-generic-x86_64-with-glibc2.35", - "python": "CPython 3.10.19", - "startedAt": "2026-03-05T04:42:18.201866Z", - "args": [ - "--model_name_or_path", - "/home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000", - "--tokenizer_path", - "/home/n5huang/dna_token/tokenizer_evaluation/merge_bpe/merge_tokenizer_unigram_len2.json", - "--trust_remote_code", - "True", - "--data_path", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/promoter_no_tata/split", - "--kmer", - "-1", - "--run_name", - "hg38_BPE_base__merge_bpe_merge_tokenizer_unigram_len2_3e-5_promoter_no_tata_seed42", - "--model_max_length", - "80", - "--per_device_train_batch_size", - "128", - "--per_device_eval_batch_size", - "128", - "--gradient_accumulation_steps", - "1", - "--learning_rate", - "3e-5", - 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/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/promoter_tata/split - - --kmer - - "-1" - - --run_name - - hg38_BPE_base__merge_bpe_merge_tokenizer_unigram_len2_3e-5_promoter_tata_seed42 - - --model_max_length - - "80" - - --per_device_train_batch_size - - "128" - - --per_device_eval_batch_size - - "128" - - --gradient_accumulation_steps - - "1" - - --learning_rate - - "3e-5" - - --num_train_epochs - - "2" - - --fp16 - - --save_steps - - "200" - - --output_dir - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_len2/promoter_tata - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "547013750784" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:42:31.981433Z" - writerId: rhro7vydlh9znr4bz6mn4868xzahmkc7 - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_044231-4mgqr9x5/files/output.log b/wandb/run-20260305_044231-4mgqr9x5/files/output.log deleted file mode 100644 index 43b3288ee7aec515cb9a66afbed15e652f22261b..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_044231-4mgqr9x5/files/output.log +++ /dev/null @@ -1,150 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 23058.17it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -classifier.bias | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 4,219 - Num Epochs = 2 - Num update steps per epoch = 33 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 66 - Number of trainable parameters = 44,302,082 - 0%| | 0/66 [00:00 - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 445, in train - trainer.train() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1424, in train - return inner_training_loop( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1506, in _inner_training_loop - self._run_epoch( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1734, in _run_epoch - tr_loss_step = self.training_step(model, inputs, num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1906, in training_step - loss = self.compute_loss(model, inputs, num_items_in_batch=num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1978, in compute_loss - outputs = model(**inputs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 823, in forward - return model_forward(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 811, in __call__ - return convert_to_fp32(self.model_forward(*args, **kwargs)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/amp/autocast_mode.py", line 44, in decorate_autocast - return func(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 843, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 1139, in forward - outputs = self.bert( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 917, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/output_capturing.py", line 253, in wrapper - outputs = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 680, in forward - embedding_output = self.embeddings( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 110, in forward - embeddings = self.LayerNorm(embeddings) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/normalization.py", line 229, in forward - return F.layer_norm( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/functional.py", line 2935, in layer_norm - return torch.layer_norm( -torch.AcceleratorError: CUDA error: device-side assert triggered -Search for `cudaErrorAssert' in https://docs.nvidia.com/cuda/cuda-runtime-api/group__CUDART__TYPES.html for more information. -CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect. -For debugging consider passing CUDA_LAUNCH_BLOCKING=1 -Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions. - -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 464, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 445, in train - trainer.train() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1424, in train - return inner_training_loop( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1506, in _inner_training_loop - self._run_epoch( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1734, in _run_epoch - tr_loss_step = self.training_step(model, inputs, num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1906, in training_step - loss = self.compute_loss(model, inputs, num_items_in_batch=num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1978, in compute_loss - outputs = model(**inputs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 823, in forward - return model_forward(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 811, in __call__ - return convert_to_fp32(self.model_forward(*args, **kwargs)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/amp/autocast_mode.py", line 44, in decorate_autocast - return func(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 843, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 1139, in forward - outputs = self.bert( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 917, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/output_capturing.py", line 253, in wrapper - outputs = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 680, in forward - embedding_output = self.embeddings( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 110, in forward - embeddings = self.LayerNorm(embeddings) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/normalization.py", line 229, in forward - return F.layer_norm( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/functional.py", line 2935, in layer_norm - return torch.layer_norm( -torch.AcceleratorError: CUDA error: device-side assert triggered -Search for `cudaErrorAssert' in https://docs.nvidia.com/cuda/cuda-runtime-api/group__CUDART__TYPES.html for more information. -CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect. -For debugging consider passing CUDA_LAUNCH_BLOCKING=1 -Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions. diff --git a/wandb/run-20260305_044231-4mgqr9x5/files/requirements.txt b/wandb/run-20260305_044231-4mgqr9x5/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_044231-4mgqr9x5/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 -accelerate==1.13.0 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -triton==3.6.0 -nvidia-nccl-cu12==2.27.5 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -cuda-pathfinder==1.4.0 -shellingham==1.5.4 -torchaudio==2.5.1 -nvidia-cufile-cu12==1.13.1.3 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -nvidia-nvjitlink-cu12==12.8.93 -click==8.3.1 -MarkupSafe==3.0.2 -nvidia-nvshmem-cu12==3.4.5 -urllib3==2.6.3 -cuda-bindings==12.9.4 -propcache==0.4.1 -nvidia-cusolver-cu12==11.7.3.90 -sympy==1.14.0 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -nvidia-cuda-runtime-cu12==12.8.90 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_044231-4mgqr9x5/files/wandb-metadata.json b/wandb/run-20260305_044231-4mgqr9x5/files/wandb-metadata.json deleted file mode 100644 index f2c42ebcacf13e385889f5bbc6d16560cc58f926..0000000000000000000000000000000000000000 --- 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/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/splice_sites_acceptors/split - - --kmer - - "-1" - - --run_name - - hg38_BPE_base__merge_bpe_merge_tokenizer_unigram_len2_3e-5_splice_sites_acceptors_seed42 - - --model_max_length - - "140" - - --per_device_train_batch_size - - "128" - - --per_device_eval_batch_size - - "128" - - --gradient_accumulation_steps - - "1" - - --learning_rate - - "3e-5" - - --num_train_epochs - - "4" - - --fp16 - - --save_steps - - "200" - - --output_dir - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_acceptors - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "547015798784" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:42:43.002992Z" - writerId: 1cywhhme9w3c5ziiwrd4vagpmle37l83 - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_044243-gm8fw5qs/files/output.log b/wandb/run-20260305_044243-gm8fw5qs/files/output.log deleted file mode 100644 index ad72a836f099109d79b1107a562db08c54df0dc5..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_044243-gm8fw5qs/files/output.log +++ /dev/null @@ -1,150 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 24164.32it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -bert.pooler.dense.bias | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.weight | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 4 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 828 - Number of trainable parameters = 44,302,082 - 0%| | 0/828 [00:00 - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 445, in train - trainer.train() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1424, in train - return inner_training_loop( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1506, in _inner_training_loop - self._run_epoch( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1734, in _run_epoch - tr_loss_step = self.training_step(model, inputs, num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1906, in training_step - loss = self.compute_loss(model, inputs, num_items_in_batch=num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1978, in compute_loss - outputs = model(**inputs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 823, in forward - return model_forward(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 811, in __call__ - return convert_to_fp32(self.model_forward(*args, **kwargs)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/amp/autocast_mode.py", line 44, in decorate_autocast - return func(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 843, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 1139, in forward - outputs = self.bert( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 917, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/output_capturing.py", line 253, in wrapper - outputs = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 680, in forward - embedding_output = self.embeddings( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 110, in forward - embeddings = self.LayerNorm(embeddings) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/normalization.py", line 229, in forward - return F.layer_norm( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/functional.py", line 2935, in layer_norm - return torch.layer_norm( -torch.AcceleratorError: CUDA error: device-side assert triggered -Search for `cudaErrorAssert' in https://docs.nvidia.com/cuda/cuda-runtime-api/group__CUDART__TYPES.html for more information. -CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect. -For debugging consider passing CUDA_LAUNCH_BLOCKING=1 -Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions. - -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 464, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 445, in train - trainer.train() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1424, in train - return inner_training_loop( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1506, in _inner_training_loop - self._run_epoch( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1734, in _run_epoch - tr_loss_step = self.training_step(model, inputs, num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1906, in training_step - loss = self.compute_loss(model, inputs, num_items_in_batch=num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1978, in compute_loss - outputs = model(**inputs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 823, in forward - return model_forward(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 811, in __call__ - return convert_to_fp32(self.model_forward(*args, **kwargs)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/amp/autocast_mode.py", line 44, in decorate_autocast - return func(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 843, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 1139, in forward - outputs = self.bert( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 917, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/output_capturing.py", line 253, in wrapper - outputs = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 680, in forward - embedding_output = self.embeddings( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 110, in forward - embeddings = self.LayerNorm(embeddings) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/normalization.py", line 229, in forward - return F.layer_norm( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/functional.py", line 2935, in layer_norm - return torch.layer_norm( -torch.AcceleratorError: CUDA error: device-side assert triggered -Search for `cudaErrorAssert' in https://docs.nvidia.com/cuda/cuda-runtime-api/group__CUDART__TYPES.html for more information. -CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect. -For debugging consider passing CUDA_LAUNCH_BLOCKING=1 -Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions. diff --git a/wandb/run-20260305_044243-gm8fw5qs/files/requirements.txt b/wandb/run-20260305_044243-gm8fw5qs/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_044243-gm8fw5qs/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 -accelerate==1.13.0 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -triton==3.6.0 -nvidia-nccl-cu12==2.27.5 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -cuda-pathfinder==1.4.0 -shellingham==1.5.4 -torchaudio==2.5.1 -nvidia-cufile-cu12==1.13.1.3 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -nvidia-nvjitlink-cu12==12.8.93 -click==8.3.1 -MarkupSafe==3.0.2 -nvidia-nvshmem-cu12==3.4.5 -urllib3==2.6.3 -cuda-bindings==12.9.4 -propcache==0.4.1 -nvidia-cusolver-cu12==11.7.3.90 -sympy==1.14.0 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -nvidia-cuda-runtime-cu12==12.8.90 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_044243-gm8fw5qs/files/wandb-metadata.json b/wandb/run-20260305_044243-gm8fw5qs/files/wandb-metadata.json deleted file mode 100644 index b61bebde1c5f0d60e15e8a4066837fe4a9ef5dae..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_044243-gm8fw5qs/files/wandb-metadata.json +++ /dev/null @@ -1,134 +0,0 @@ -{ - "os": "Linux-5.15.0-72-generic-x86_64-with-glibc2.35", - "python": "CPython 3.10.19", - "startedAt": "2026-03-05T04:42:43.002992Z", - "args": [ - "--model_name_or_path", - "/home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000", - "--tokenizer_path", - "/home/n5huang/dna_token/tokenizer_evaluation/merge_bpe/merge_tokenizer_unigram_len2.json", - "--trust_remote_code", - "True", - "--data_path", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/splice_sites_acceptors/split", - "--kmer", - "-1", - "--run_name", - "hg38_BPE_base__merge_bpe_merge_tokenizer_unigram_len2_3e-5_splice_sites_acceptors_seed42", - "--model_max_length", - "140", - "--per_device_train_batch_size", - "128", - "--per_device_eval_batch_size", - "128", - "--gradient_accumulation_steps", - "1", - "--learning_rate", - 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genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "547015921664" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:42:57.969793Z" - writerId: wpcezff8pn3hdae8xt8jysl5vzi4iv4r - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_044257-hu29qoha/files/output.log b/wandb/run-20260305_044257-hu29qoha/files/output.log deleted file mode 100644 index b5ed8f4ba42baf3f904f58c1bd74466211c88401..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_044257-hu29qoha/files/output.log +++ /dev/null @@ -1,150 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 22473.46it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -classifier.bias | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 4 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 828 - Number of trainable parameters = 44,302,851 - 0%| | 0/828 [00:00 - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 445, in train - trainer.train() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1424, in train - return inner_training_loop( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1506, in _inner_training_loop - self._run_epoch( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1734, in _run_epoch - tr_loss_step = self.training_step(model, inputs, num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1906, in training_step - loss = self.compute_loss(model, inputs, num_items_in_batch=num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1978, in compute_loss - outputs = model(**inputs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 823, in forward - return model_forward(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 811, in __call__ - return convert_to_fp32(self.model_forward(*args, **kwargs)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/amp/autocast_mode.py", line 44, in decorate_autocast - return func(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 843, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 1139, in forward - outputs = self.bert( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 917, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/output_capturing.py", line 253, in wrapper - outputs = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 680, in forward - embedding_output = self.embeddings( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 110, in forward - embeddings = self.LayerNorm(embeddings) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/normalization.py", line 229, in forward - return F.layer_norm( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/functional.py", line 2935, in layer_norm - return torch.layer_norm( -torch.AcceleratorError: CUDA error: device-side assert triggered -Search for `cudaErrorAssert' in https://docs.nvidia.com/cuda/cuda-runtime-api/group__CUDART__TYPES.html for more information. -CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect. -For debugging consider passing CUDA_LAUNCH_BLOCKING=1 -Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions. - -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 464, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 445, in train - trainer.train() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1424, in train - return inner_training_loop( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1506, in _inner_training_loop - self._run_epoch( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1734, in _run_epoch - tr_loss_step = self.training_step(model, inputs, num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1906, in training_step - loss = self.compute_loss(model, inputs, num_items_in_batch=num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1978, in compute_loss - outputs = model(**inputs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 823, in forward - return model_forward(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 811, in __call__ - return convert_to_fp32(self.model_forward(*args, **kwargs)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/amp/autocast_mode.py", line 44, in decorate_autocast - return func(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 843, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 1139, in forward - outputs = self.bert( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 917, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/output_capturing.py", line 253, in wrapper - outputs = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 680, in forward - embedding_output = self.embeddings( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 110, in forward - embeddings = self.LayerNorm(embeddings) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/normalization.py", line 229, in forward - return F.layer_norm( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/functional.py", line 2935, in layer_norm - return torch.layer_norm( -torch.AcceleratorError: CUDA error: device-side assert triggered -Search for `cudaErrorAssert' in https://docs.nvidia.com/cuda/cuda-runtime-api/group__CUDART__TYPES.html for more information. -CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect. -For debugging consider passing CUDA_LAUNCH_BLOCKING=1 -Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions. diff --git a/wandb/run-20260305_044257-hu29qoha/files/requirements.txt b/wandb/run-20260305_044257-hu29qoha/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_044257-hu29qoha/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 -accelerate==1.13.0 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -triton==3.6.0 -nvidia-nccl-cu12==2.27.5 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -cuda-pathfinder==1.4.0 -shellingham==1.5.4 -torchaudio==2.5.1 -nvidia-cufile-cu12==1.13.1.3 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -nvidia-nvjitlink-cu12==12.8.93 -click==8.3.1 -MarkupSafe==3.0.2 -nvidia-nvshmem-cu12==3.4.5 -urllib3==2.6.3 -cuda-bindings==12.9.4 -propcache==0.4.1 -nvidia-cusolver-cu12==11.7.3.90 -sympy==1.14.0 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -nvidia-cuda-runtime-cu12==12.8.90 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_044257-hu29qoha/files/wandb-metadata.json b/wandb/run-20260305_044257-hu29qoha/files/wandb-metadata.json deleted file mode 100644 index 667083dead509382db54d09efc90285eadeb7d70..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_044257-hu29qoha/files/wandb-metadata.json +++ /dev/null @@ -1,134 +0,0 @@ -{ - "os": "Linux-5.15.0-72-generic-x86_64-with-glibc2.35", - "python": "CPython 3.10.19", - "startedAt": "2026-03-05T04:42:57.969793Z", - "args": [ - "--model_name_or_path", - "/home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000", - "--tokenizer_path", - "/home/n5huang/dna_token/tokenizer_evaluation/merge_bpe/merge_tokenizer_unigram_len2.json", - "--trust_remote_code", - "True", - "--data_path", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/splice_sites_all/split", - "--kmer", - "-1", - "--run_name", - "hg38_BPE_base__merge_bpe_merge_tokenizer_unigram_len2_3e-5_splice_sites_all_seed42", - "--model_max_length", - "140", - "--per_device_train_batch_size", - "128", - "--per_device_eval_batch_size", - "128", - "--gradient_accumulation_steps", - "1", - "--learning_rate", - "3e-5", - 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handles. diff --git a/wandb/run-20260305_044257-hu29qoha/run-hu29qoha.wandb b/wandb/run-20260305_044257-hu29qoha/run-hu29qoha.wandb deleted file mode 100644 index 6e91d1aec683fd2fad04052ed848a7787266e5bf..0000000000000000000000000000000000000000 Binary files a/wandb/run-20260305_044257-hu29qoha/run-hu29qoha.wandb and /dev/null differ diff --git a/wandb/run-20260305_044313-0ijw2mvb/files/config.yaml b/wandb/run-20260305_044313-0ijw2mvb/files/config.yaml deleted file mode 100644 index 8ababdc04cc203d489a6d7d78e24b245a6bdb933..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_044313-0ijw2mvb/files/config.yaml +++ /dev/null @@ -1,139 +0,0 @@ -_wandb: - value: - cli_version: 0.25.0 - e: - xrnfcbx55b05cx3h06ajwwitqhuibwm6: - args: - - --model_name_or_path - - /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 - - --tokenizer_path - - /home/n5huang/dna_token/tokenizer_evaluation/merge_bpe/merge_tokenizer_unigram_len2.json - - --trust_remote_code - - "True" - - --data_path - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/splice_sites_donors/split - - --kmer - - "-1" - - --run_name - - hg38_BPE_base__merge_bpe_merge_tokenizer_unigram_len2_3e-5_splice_sites_donors_seed42 - - --model_max_length - - "140" - - --per_device_train_batch_size - - "128" - - --per_device_eval_batch_size - - "128" - - --gradient_accumulation_steps - - "1" - - --learning_rate - - "3e-5" - - --num_train_epochs - - "4" - - --fp16 - - --save_steps - - "200" - - --output_dir - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_donors - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "547016056832" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:43:13.046368Z" - writerId: xrnfcbx55b05cx3h06ajwwitqhuibwm6 - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_044313-0ijw2mvb/files/output.log b/wandb/run-20260305_044313-0ijw2mvb/files/output.log deleted file mode 100644 index a006e3246c998bef89d55f79453a53d251e3b35c..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_044313-0ijw2mvb/files/output.log +++ /dev/null @@ -1,150 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 23166.61it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -classifier.bias | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 4 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 828 - Number of trainable parameters = 44,302,082 - 0%| | 0/828 [00:00 - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 445, in train - trainer.train() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1424, in train - return inner_training_loop( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1506, in _inner_training_loop - self._run_epoch( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1734, in _run_epoch - tr_loss_step = self.training_step(model, inputs, num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1906, in training_step - loss = self.compute_loss(model, inputs, num_items_in_batch=num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1978, in compute_loss - outputs = model(**inputs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 823, in forward - return model_forward(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 811, in __call__ - return convert_to_fp32(self.model_forward(*args, **kwargs)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/amp/autocast_mode.py", line 44, in decorate_autocast - return func(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 843, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 1139, in forward - outputs = self.bert( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 917, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/output_capturing.py", line 253, in wrapper - outputs = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 680, in forward - embedding_output = self.embeddings( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 110, in forward - embeddings = self.LayerNorm(embeddings) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/normalization.py", line 229, in forward - return F.layer_norm( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/functional.py", line 2935, in layer_norm - return torch.layer_norm( -torch.AcceleratorError: CUDA error: device-side assert triggered -Search for `cudaErrorAssert' in https://docs.nvidia.com/cuda/cuda-runtime-api/group__CUDART__TYPES.html for more information. -CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect. -For debugging consider passing CUDA_LAUNCH_BLOCKING=1 -Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions. - -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 464, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 445, in train - trainer.train() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1424, in train - return inner_training_loop( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1506, in _inner_training_loop - self._run_epoch( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1734, in _run_epoch - tr_loss_step = self.training_step(model, inputs, num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1906, in training_step - loss = self.compute_loss(model, inputs, num_items_in_batch=num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1978, in compute_loss - outputs = model(**inputs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 823, in forward - return model_forward(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 811, in __call__ - return convert_to_fp32(self.model_forward(*args, **kwargs)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/amp/autocast_mode.py", line 44, in decorate_autocast - return func(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 843, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 1139, in forward - outputs = self.bert( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 917, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/output_capturing.py", line 253, in wrapper - outputs = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 680, in forward - embedding_output = self.embeddings( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 110, in forward - embeddings = self.LayerNorm(embeddings) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/normalization.py", line 229, in forward - return F.layer_norm( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/functional.py", line 2935, in layer_norm - return torch.layer_norm( -torch.AcceleratorError: CUDA error: device-side assert triggered -Search for `cudaErrorAssert' in https://docs.nvidia.com/cuda/cuda-runtime-api/group__CUDART__TYPES.html for more information. -CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect. -For debugging consider passing CUDA_LAUNCH_BLOCKING=1 -Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions. diff --git a/wandb/run-20260305_044313-0ijw2mvb/files/requirements.txt b/wandb/run-20260305_044313-0ijw2mvb/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_044313-0ijw2mvb/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 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python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_044328-llwl2v0t/files/output.log b/wandb/run-20260305_044328-llwl2v0t/files/output.log deleted file mode 100644 index e3520fd69947ed058781c23a6b577629197da428..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_044328-llwl2v0t/files/output.log +++ /dev/null @@ -1,150 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 22478.23it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -bert.pooler.dense.bias | MISSING | -classifier.bias | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 2 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 414 - Number of trainable parameters = 44,302,082 - 0%| | 0/414 [00:00 - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 445, in train - trainer.train() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1424, in train - return inner_training_loop( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1506, in _inner_training_loop - self._run_epoch( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1734, in _run_epoch - tr_loss_step = self.training_step(model, inputs, num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1906, in training_step - loss = self.compute_loss(model, inputs, num_items_in_batch=num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1978, in compute_loss - outputs = model(**inputs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 823, in forward - return model_forward(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 811, in __call__ - return convert_to_fp32(self.model_forward(*args, **kwargs)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/amp/autocast_mode.py", line 44, in decorate_autocast - return func(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 843, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 1139, in forward - outputs = self.bert( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 917, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/output_capturing.py", line 253, in wrapper - outputs = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 680, in forward - embedding_output = self.embeddings( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 110, in forward - embeddings = self.LayerNorm(embeddings) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/normalization.py", line 229, in forward - return F.layer_norm( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/functional.py", line 2935, in layer_norm - return torch.layer_norm( -torch.AcceleratorError: CUDA error: device-side assert triggered -Search for `cudaErrorAssert' in https://docs.nvidia.com/cuda/cuda-runtime-api/group__CUDART__TYPES.html for more information. -CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect. -For debugging consider passing CUDA_LAUNCH_BLOCKING=1 -Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions. - -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 464, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 445, in train - trainer.train() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1424, in train - return inner_training_loop( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1506, in _inner_training_loop - self._run_epoch( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1734, in _run_epoch - tr_loss_step = self.training_step(model, inputs, num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1906, in training_step - loss = self.compute_loss(model, inputs, num_items_in_batch=num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1978, in compute_loss - outputs = model(**inputs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 823, in forward - return model_forward(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 811, in __call__ - return convert_to_fp32(self.model_forward(*args, **kwargs)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/amp/autocast_mode.py", line 44, in decorate_autocast - return func(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 843, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 1139, in forward - outputs = self.bert( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 917, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/output_capturing.py", line 253, in wrapper - outputs = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 680, in forward - embedding_output = self.embeddings( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 110, in forward - embeddings = self.LayerNorm(embeddings) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/normalization.py", line 229, in forward - return F.layer_norm( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/functional.py", line 2935, in layer_norm - return torch.layer_norm( -torch.AcceleratorError: CUDA error: device-side assert triggered -Search for `cudaErrorAssert' in https://docs.nvidia.com/cuda/cuda-runtime-api/group__CUDART__TYPES.html for more information. -CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect. -For debugging consider passing CUDA_LAUNCH_BLOCKING=1 -Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions. diff --git a/wandb/run-20260305_044328-llwl2v0t/files/requirements.txt b/wandb/run-20260305_044328-llwl2v0t/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_044328-llwl2v0t/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 -accelerate==1.13.0 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -triton==3.6.0 -nvidia-nccl-cu12==2.27.5 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -cuda-pathfinder==1.4.0 -shellingham==1.5.4 -torchaudio==2.5.1 -nvidia-cufile-cu12==1.13.1.3 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -nvidia-nvjitlink-cu12==12.8.93 -click==8.3.1 -MarkupSafe==3.0.2 -nvidia-nvshmem-cu12==3.4.5 -urllib3==2.6.3 -cuda-bindings==12.9.4 -propcache==0.4.1 -nvidia-cusolver-cu12==11.7.3.90 -sympy==1.14.0 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -nvidia-cuda-runtime-cu12==12.8.90 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_044328-llwl2v0t/files/wandb-metadata.json b/wandb/run-20260305_044328-llwl2v0t/files/wandb-metadata.json deleted file mode 100644 index b2fc073c9ecfadb6ffa17298bd6ee6d844c76c82..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_044328-llwl2v0t/files/wandb-metadata.json +++ /dev/null @@ -1,134 +0,0 @@ -{ - "os": "Linux-5.15.0-72-generic-x86_64-with-glibc2.35", - "python": "CPython 3.10.19", - "startedAt": "2026-03-05T04:43:28.663433Z", - "args": [ - "--model_name_or_path", - "/home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000", - "--tokenizer_path", - "/home/n5huang/dna_token/tokenizer_evaluation/merge_bpe/merge_tokenizer_unigram_len2.json", - "--trust_remote_code", - "True", - "--data_path", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/H2AFZ/split", - "--kmer", - "-1", - "--run_name", - "hg38_BPE_base__merge_bpe_merge_tokenizer_unigram_len2_3e-5_H2AFZ_seed42", - "--model_max_length", - "220", - "--per_device_train_batch_size", - "128", - "--per_device_eval_batch_size", - "128", - "--gradient_accumulation_steps", - "1", - "--learning_rate", - "3e-5", - "--num_train_epochs", - 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handles. diff --git a/wandb/run-20260305_044328-llwl2v0t/run-llwl2v0t.wandb b/wandb/run-20260305_044328-llwl2v0t/run-llwl2v0t.wandb deleted file mode 100644 index b176d44b652e61357e9d2e7a9438253f593f5eeb..0000000000000000000000000000000000000000 Binary files a/wandb/run-20260305_044328-llwl2v0t/run-llwl2v0t.wandb and /dev/null differ diff --git a/wandb/run-20260305_044346-j34q8e7l/files/config.yaml b/wandb/run-20260305_044346-j34q8e7l/files/config.yaml deleted file mode 100644 index e1a48583e34b21be2b1dabcf37e114061e069f96..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_044346-j34q8e7l/files/config.yaml +++ /dev/null @@ -1,139 +0,0 @@ -_wandb: - value: - cli_version: 0.25.0 - e: - sqp642zsv3jb9gewhxqgnrgca7bgazgo: - args: - - --model_name_or_path - - /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 - - --tokenizer_path - - /home/n5huang/dna_token/tokenizer_evaluation/merge_bpe/merge_tokenizer_unigram_len2.json - - --trust_remote_code - - "True" - - --data_path - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/H3K27ac/split - - --kmer - - "-1" - - --run_name - - hg38_BPE_base__merge_bpe_merge_tokenizer_unigram_len2_3e-5_H3K27ac_seed42 - - --model_max_length - - "220" - - --per_device_train_batch_size - - "128" - - --per_device_eval_batch_size - - "128" - - --gradient_accumulation_steps - - "1" - - --learning_rate - - "3e-5" - - --num_train_epochs - - "2" - - --fp16 - - --save_steps - - "200" - - --output_dir - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_len2/H3K27ac - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "547018252288" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:43:46.740182Z" - writerId: sqp642zsv3jb9gewhxqgnrgca7bgazgo - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_044346-j34q8e7l/files/output.log b/wandb/run-20260305_044346-j34q8e7l/files/output.log deleted file mode 100644 index ae97ac0f757c5c688a4edd1e2c9b9687d004f7ad..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_044346-j34q8e7l/files/output.log +++ /dev/null @@ -1,150 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 8917.85it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -classifier.weight | MISSING | -classifier.bias | MISSING | -bert.pooler.dense.bias | MISSING | -bert.pooler.dense.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 25,292 - Num Epochs = 2 - Num update steps per epoch = 198 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 396 - Number of trainable parameters = 44,302,082 - 0%| | 0/396 [00:00 - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 445, in train - trainer.train() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1424, in train - return inner_training_loop( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1506, in _inner_training_loop - self._run_epoch( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1734, in _run_epoch - tr_loss_step = self.training_step(model, inputs, num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1906, in training_step - loss = self.compute_loss(model, inputs, num_items_in_batch=num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1978, in compute_loss - outputs = model(**inputs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 823, in forward - return model_forward(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 811, in __call__ - return convert_to_fp32(self.model_forward(*args, **kwargs)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/amp/autocast_mode.py", line 44, in decorate_autocast - return func(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 843, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 1139, in forward - outputs = self.bert( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 917, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/output_capturing.py", line 253, in wrapper - outputs = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 680, in forward - embedding_output = self.embeddings( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 110, in forward - embeddings = self.LayerNorm(embeddings) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/normalization.py", line 229, in forward - return F.layer_norm( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/functional.py", line 2935, in layer_norm - return torch.layer_norm( -torch.AcceleratorError: CUDA error: device-side assert triggered -Search for `cudaErrorAssert' in https://docs.nvidia.com/cuda/cuda-runtime-api/group__CUDART__TYPES.html for more information. -CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect. -For debugging consider passing CUDA_LAUNCH_BLOCKING=1 -Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions. - -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 464, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 445, in train - trainer.train() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1424, in train - return inner_training_loop( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1506, in _inner_training_loop - self._run_epoch( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1734, in _run_epoch - tr_loss_step = self.training_step(model, inputs, num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1906, in training_step - loss = self.compute_loss(model, inputs, num_items_in_batch=num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1978, in compute_loss - outputs = model(**inputs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 823, in forward - return model_forward(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 811, in __call__ - return convert_to_fp32(self.model_forward(*args, **kwargs)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/amp/autocast_mode.py", line 44, in decorate_autocast - return func(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 843, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 1139, in forward - outputs = self.bert( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 917, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/output_capturing.py", line 253, in wrapper - outputs = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 680, in forward - embedding_output = self.embeddings( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 110, in forward - embeddings = self.LayerNorm(embeddings) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/normalization.py", line 229, in forward - return F.layer_norm( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/functional.py", line 2935, in layer_norm - return torch.layer_norm( -torch.AcceleratorError: CUDA error: device-side assert triggered -Search for `cudaErrorAssert' in https://docs.nvidia.com/cuda/cuda-runtime-api/group__CUDART__TYPES.html for more information. -CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect. -For debugging consider passing CUDA_LAUNCH_BLOCKING=1 -Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions. diff --git a/wandb/run-20260305_044346-j34q8e7l/files/requirements.txt b/wandb/run-20260305_044346-j34q8e7l/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_044346-j34q8e7l/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 -accelerate==1.13.0 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -triton==3.6.0 -nvidia-nccl-cu12==2.27.5 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -cuda-pathfinder==1.4.0 -shellingham==1.5.4 -torchaudio==2.5.1 -nvidia-cufile-cu12==1.13.1.3 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -nvidia-nvjitlink-cu12==12.8.93 -click==8.3.1 -MarkupSafe==3.0.2 -nvidia-nvshmem-cu12==3.4.5 -urllib3==2.6.3 -cuda-bindings==12.9.4 -propcache==0.4.1 -nvidia-cusolver-cu12==11.7.3.90 -sympy==1.14.0 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -nvidia-cuda-runtime-cu12==12.8.90 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_044346-j34q8e7l/files/wandb-metadata.json b/wandb/run-20260305_044346-j34q8e7l/files/wandb-metadata.json deleted file mode 100644 index 4ca6e2904596ce0b940676ab9bcdf848de335f63..0000000000000000000000000000000000000000 --- 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handles. diff --git a/wandb/run-20260305_044346-j34q8e7l/run-j34q8e7l.wandb b/wandb/run-20260305_044346-j34q8e7l/run-j34q8e7l.wandb deleted file mode 100644 index 3771162f7d6dc8d25e901e67c4d91da92aba52ac..0000000000000000000000000000000000000000 Binary files a/wandb/run-20260305_044346-j34q8e7l/run-j34q8e7l.wandb and /dev/null differ diff --git a/wandb/run-20260305_044404-cud5qtuo/files/config.yaml b/wandb/run-20260305_044404-cud5qtuo/files/config.yaml deleted file mode 100644 index 437ee729a6e61de5a34d2daa62f2ab763e2f5a76..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_044404-cud5qtuo/files/config.yaml +++ /dev/null @@ -1,139 +0,0 @@ -_wandb: - value: - cli_version: 0.25.0 - e: - hf39ds1g2b82bh0izhit714fb064l83j: - args: - - --model_name_or_path - - /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 - - --tokenizer_path - - /home/n5huang/dna_token/tokenizer_evaluation/merge_bpe/merge_tokenizer_unigram_len2.json - - --trust_remote_code - - "True" - - --data_path - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/H3K27me3/split - - --kmer - - "-1" - - --run_name - - hg38_BPE_base__merge_bpe_merge_tokenizer_unigram_len2_3e-5_H3K27me3_seed42 - - --model_max_length - - "220" - - --per_device_train_batch_size - - "128" - - --per_device_eval_batch_size - - "128" - - --gradient_accumulation_steps - - "1" - - --learning_rate - - "3e-5" - - --num_train_epochs - - "2" - - --fp16 - - --save_steps - - "200" - - --output_dir - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_len2/H3K27me3 - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "547018407936" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:44:04.439709Z" - writerId: hf39ds1g2b82bh0izhit714fb064l83j - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_044404-cud5qtuo/files/output.log b/wandb/run-20260305_044404-cud5qtuo/files/output.log deleted file mode 100644 index 0751294942a30662a27c3f250fb5549638961b28..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_044404-cud5qtuo/files/output.log +++ /dev/null @@ -1,150 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 19872.62it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -classifier.weight | MISSING | -bert.pooler.dense.weight | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 2 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 414 - Number of trainable parameters = 44,302,082 - 0%| | 0/414 [00:00 - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 445, in train - trainer.train() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1424, in train - return inner_training_loop( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1506, in _inner_training_loop - self._run_epoch( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1734, in _run_epoch - tr_loss_step = self.training_step(model, inputs, num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1906, in training_step - loss = self.compute_loss(model, inputs, num_items_in_batch=num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1978, in compute_loss - outputs = model(**inputs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 823, in forward - return model_forward(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 811, in __call__ - return convert_to_fp32(self.model_forward(*args, **kwargs)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/amp/autocast_mode.py", line 44, in decorate_autocast - return func(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 843, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 1139, in forward - outputs = self.bert( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 917, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/output_capturing.py", line 253, in wrapper - outputs = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 680, in forward - embedding_output = self.embeddings( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 110, in forward - embeddings = self.LayerNorm(embeddings) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/normalization.py", line 229, in forward - return F.layer_norm( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/functional.py", line 2935, in layer_norm - return torch.layer_norm( -torch.AcceleratorError: CUDA error: device-side assert triggered -Search for `cudaErrorAssert' in https://docs.nvidia.com/cuda/cuda-runtime-api/group__CUDART__TYPES.html for more information. -CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect. -For debugging consider passing CUDA_LAUNCH_BLOCKING=1 -Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions. - -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 464, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 445, in train - trainer.train() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1424, in train - return inner_training_loop( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1506, in _inner_training_loop - self._run_epoch( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1734, in _run_epoch - tr_loss_step = self.training_step(model, inputs, num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1906, in training_step - loss = self.compute_loss(model, inputs, num_items_in_batch=num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1978, in compute_loss - outputs = model(**inputs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 823, in forward - return model_forward(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 811, in __call__ - return convert_to_fp32(self.model_forward(*args, **kwargs)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/amp/autocast_mode.py", line 44, in decorate_autocast - return func(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 843, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 1139, in forward - outputs = self.bert( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 917, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/output_capturing.py", line 253, in wrapper - outputs = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 680, in forward - embedding_output = self.embeddings( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 110, in forward - embeddings = self.LayerNorm(embeddings) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/normalization.py", line 229, in forward - return F.layer_norm( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/functional.py", line 2935, in layer_norm - return torch.layer_norm( -torch.AcceleratorError: CUDA error: device-side assert triggered -Search for `cudaErrorAssert' in https://docs.nvidia.com/cuda/cuda-runtime-api/group__CUDART__TYPES.html for more information. -CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect. -For debugging consider passing CUDA_LAUNCH_BLOCKING=1 -Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions. diff --git a/wandb/run-20260305_044404-cud5qtuo/files/requirements.txt b/wandb/run-20260305_044404-cud5qtuo/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_044404-cud5qtuo/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 -accelerate==1.13.0 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -triton==3.6.0 -nvidia-nccl-cu12==2.27.5 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -cuda-pathfinder==1.4.0 -shellingham==1.5.4 -torchaudio==2.5.1 -nvidia-cufile-cu12==1.13.1.3 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -nvidia-nvjitlink-cu12==12.8.93 -click==8.3.1 -MarkupSafe==3.0.2 -nvidia-nvshmem-cu12==3.4.5 -urllib3==2.6.3 -cuda-bindings==12.9.4 -propcache==0.4.1 -nvidia-cusolver-cu12==11.7.3.90 -sympy==1.14.0 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -nvidia-cuda-runtime-cu12==12.8.90 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_044404-cud5qtuo/files/wandb-metadata.json b/wandb/run-20260305_044404-cud5qtuo/files/wandb-metadata.json deleted file mode 100644 index 3499fb145d7b31304c297dadcc18bb219c1d5f19..0000000000000000000000000000000000000000 --- 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ni4jjwciiivfx8arjwd73rb6m755rhjv - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_044423-fz7f3rxq/files/output.log b/wandb/run-20260305_044423-fz7f3rxq/files/output.log deleted file mode 100644 index 3b842d78acf63ddee5d805f9f6e9c67e6a7f673e..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_044423-fz7f3rxq/files/output.log +++ /dev/null @@ -1,150 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 24464.35it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.dense.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -classifier.weight | MISSING | -classifier.bias | MISSING | -bert.pooler.dense.weight | MISSING | -bert.pooler.dense.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 2 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 414 - Number of trainable parameters = 44,302,082 - 0%| | 0/414 [00:00 - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 445, in train - trainer.train() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1424, in train - return inner_training_loop( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1506, in _inner_training_loop - self._run_epoch( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1734, in _run_epoch - tr_loss_step = self.training_step(model, inputs, num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1906, in training_step - loss = self.compute_loss(model, inputs, num_items_in_batch=num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1978, in compute_loss - outputs = model(**inputs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 823, in forward - return model_forward(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 811, in __call__ - return convert_to_fp32(self.model_forward(*args, **kwargs)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/amp/autocast_mode.py", line 44, in decorate_autocast - return func(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 843, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 1139, in forward - outputs = self.bert( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 917, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/output_capturing.py", line 253, in wrapper - outputs = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 680, in forward - embedding_output = self.embeddings( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 110, in forward - embeddings = self.LayerNorm(embeddings) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/normalization.py", line 229, in forward - return F.layer_norm( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/functional.py", line 2935, in layer_norm - return torch.layer_norm( -torch.AcceleratorError: CUDA error: device-side assert triggered -Search for `cudaErrorAssert' in https://docs.nvidia.com/cuda/cuda-runtime-api/group__CUDART__TYPES.html for more information. -CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect. -For debugging consider passing CUDA_LAUNCH_BLOCKING=1 -Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions. - -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 464, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 445, in train - trainer.train() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1424, in train - return inner_training_loop( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1506, in _inner_training_loop - self._run_epoch( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1734, in _run_epoch - tr_loss_step = self.training_step(model, inputs, num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1906, in training_step - loss = self.compute_loss(model, inputs, num_items_in_batch=num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1978, in compute_loss - outputs = model(**inputs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 823, in forward - return model_forward(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 811, in __call__ - return convert_to_fp32(self.model_forward(*args, **kwargs)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/amp/autocast_mode.py", line 44, in decorate_autocast - return func(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 843, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 1139, in forward - outputs = self.bert( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 917, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/output_capturing.py", line 253, in wrapper - outputs = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 680, in forward - embedding_output = self.embeddings( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 110, in forward - embeddings = self.LayerNorm(embeddings) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/normalization.py", line 229, in forward - return F.layer_norm( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/functional.py", line 2935, in layer_norm - return torch.layer_norm( -torch.AcceleratorError: CUDA error: device-side assert triggered -Search for `cudaErrorAssert' in https://docs.nvidia.com/cuda/cuda-runtime-api/group__CUDART__TYPES.html for more information. -CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect. -For debugging consider passing CUDA_LAUNCH_BLOCKING=1 -Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions. diff --git a/wandb/run-20260305_044423-fz7f3rxq/files/requirements.txt b/wandb/run-20260305_044423-fz7f3rxq/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_044423-fz7f3rxq/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 -accelerate==1.13.0 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -triton==3.6.0 -nvidia-nccl-cu12==2.27.5 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -cuda-pathfinder==1.4.0 -shellingham==1.5.4 -torchaudio==2.5.1 -nvidia-cufile-cu12==1.13.1.3 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -nvidia-nvjitlink-cu12==12.8.93 -click==8.3.1 -MarkupSafe==3.0.2 -nvidia-nvshmem-cu12==3.4.5 -urllib3==2.6.3 -cuda-bindings==12.9.4 -propcache==0.4.1 -nvidia-cusolver-cu12==11.7.3.90 -sympy==1.14.0 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -nvidia-cuda-runtime-cu12==12.8.90 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_044423-fz7f3rxq/files/wandb-metadata.json b/wandb/run-20260305_044423-fz7f3rxq/files/wandb-metadata.json deleted file mode 100644 index 4f1e81133996e18f00815c132b5fb3f8993deee0..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_044423-fz7f3rxq/files/wandb-metadata.json +++ /dev/null @@ -1,134 +0,0 @@ -{ - "os": "Linux-5.15.0-72-generic-x86_64-with-glibc2.35", - "python": "CPython 3.10.19", - "startedAt": "2026-03-05T04:44:23.539028Z", - "args": [ - "--model_name_or_path", - "/home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000", - "--tokenizer_path", - "/home/n5huang/dna_token/tokenizer_evaluation/merge_bpe/merge_tokenizer_unigram_len2.json", - "--trust_remote_code", - "True", - "--data_path", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/H3K36me3/split", - "--kmer", - "-1", - "--run_name", - "hg38_BPE_base__merge_bpe_merge_tokenizer_unigram_len2_3e-5_H3K36me3_seed42", - "--model_max_length", - "220", - "--per_device_train_batch_size", - "128", - "--per_device_eval_batch_size", - "128", - "--gradient_accumulation_steps", - "1", - "--learning_rate", - "3e-5", - 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handles. diff --git a/wandb/run-20260305_044423-fz7f3rxq/run-fz7f3rxq.wandb b/wandb/run-20260305_044423-fz7f3rxq/run-fz7f3rxq.wandb deleted file mode 100644 index 2938c61a2c57ac40527c0cac7688daaebd62069f..0000000000000000000000000000000000000000 Binary files a/wandb/run-20260305_044423-fz7f3rxq/run-fz7f3rxq.wandb and /dev/null differ diff --git a/wandb/run-20260305_044441-wzl23ecz/files/config.yaml b/wandb/run-20260305_044441-wzl23ecz/files/config.yaml deleted file mode 100644 index 423ebdeced368bc83baa46ba9b3e7b60df89e8e5..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_044441-wzl23ecz/files/config.yaml +++ /dev/null @@ -1,139 +0,0 @@ -_wandb: - value: - cli_version: 0.25.0 - e: - z8xgnar6vrkbvjynq6um98po0erewuj7: - args: - - --model_name_or_path - - /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 - - --tokenizer_path - - /home/n5huang/dna_token/tokenizer_evaluation/merge_bpe/merge_tokenizer_unigram_len2.json - - --trust_remote_code - - "True" - - --data_path - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/H3K4me1/split - - --kmer - - "-1" - - --run_name - - hg38_BPE_base__merge_bpe_merge_tokenizer_unigram_len2_3e-5_H3K4me1_seed42 - - --model_max_length - - "220" - - --per_device_train_batch_size - - "128" - - --per_device_eval_batch_size - - "128" - - --gradient_accumulation_steps - - "1" - - --learning_rate - - "3e-5" - - --num_train_epochs - - "2" - - --fp16 - - --save_steps - - "200" - - --output_dir - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_len2/H3K4me1 - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "547020627968" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:44:41.771393Z" - writerId: z8xgnar6vrkbvjynq6um98po0erewuj7 - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_044441-wzl23ecz/files/output.log b/wandb/run-20260305_044441-wzl23ecz/files/output.log deleted file mode 100644 index bb89e9d142b717ac2592a99ce1bcfa1e701013f5..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_044441-wzl23ecz/files/output.log +++ /dev/null @@ -1,150 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 24173.97it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -classifier.bias | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 2 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 414 - Number of trainable parameters = 44,302,082 - 0%| | 0/414 [00:00 - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 445, in train - trainer.train() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1424, in train - return inner_training_loop( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1506, in _inner_training_loop - self._run_epoch( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1734, in _run_epoch - tr_loss_step = self.training_step(model, inputs, num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1906, in training_step - loss = self.compute_loss(model, inputs, num_items_in_batch=num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1978, in compute_loss - outputs = model(**inputs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 823, in forward - return model_forward(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 811, in __call__ - return convert_to_fp32(self.model_forward(*args, **kwargs)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/amp/autocast_mode.py", line 44, in decorate_autocast - return func(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 843, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 1139, in forward - outputs = self.bert( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 917, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/output_capturing.py", line 253, in wrapper - outputs = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 680, in forward - embedding_output = self.embeddings( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 110, in forward - embeddings = self.LayerNorm(embeddings) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/normalization.py", line 229, in forward - return F.layer_norm( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/functional.py", line 2935, in layer_norm - return torch.layer_norm( -torch.AcceleratorError: CUDA error: device-side assert triggered -Search for `cudaErrorAssert' in https://docs.nvidia.com/cuda/cuda-runtime-api/group__CUDART__TYPES.html for more information. -CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect. -For debugging consider passing CUDA_LAUNCH_BLOCKING=1 -Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions. - -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 464, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 445, in train - trainer.train() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1424, in train - return inner_training_loop( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1506, in _inner_training_loop - self._run_epoch( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1734, in _run_epoch - tr_loss_step = self.training_step(model, inputs, num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1906, in training_step - loss = self.compute_loss(model, inputs, num_items_in_batch=num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1978, in compute_loss - outputs = model(**inputs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 823, in forward - return model_forward(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 811, in __call__ - return convert_to_fp32(self.model_forward(*args, **kwargs)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/amp/autocast_mode.py", line 44, in decorate_autocast - return func(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 843, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 1139, in forward - outputs = self.bert( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 917, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/output_capturing.py", line 253, in wrapper - outputs = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 680, in forward - embedding_output = self.embeddings( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 110, in forward - embeddings = self.LayerNorm(embeddings) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/normalization.py", line 229, in forward - return F.layer_norm( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/functional.py", line 2935, in layer_norm - return torch.layer_norm( -torch.AcceleratorError: CUDA error: device-side assert triggered -Search for `cudaErrorAssert' in https://docs.nvidia.com/cuda/cuda-runtime-api/group__CUDART__TYPES.html for more information. -CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect. -For debugging consider passing CUDA_LAUNCH_BLOCKING=1 -Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions. diff --git a/wandb/run-20260305_044441-wzl23ecz/files/requirements.txt b/wandb/run-20260305_044441-wzl23ecz/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_044441-wzl23ecz/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 -accelerate==1.13.0 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -triton==3.6.0 -nvidia-nccl-cu12==2.27.5 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -cuda-pathfinder==1.4.0 -shellingham==1.5.4 -torchaudio==2.5.1 -nvidia-cufile-cu12==1.13.1.3 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -nvidia-nvjitlink-cu12==12.8.93 -click==8.3.1 -MarkupSafe==3.0.2 -nvidia-nvshmem-cu12==3.4.5 -urllib3==2.6.3 -cuda-bindings==12.9.4 -propcache==0.4.1 -nvidia-cusolver-cu12==11.7.3.90 -sympy==1.14.0 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -nvidia-cuda-runtime-cu12==12.8.90 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_044441-wzl23ecz/files/wandb-metadata.json b/wandb/run-20260305_044441-wzl23ecz/files/wandb-metadata.json deleted file mode 100644 index c5eb143f67724fde31bdc07ac51dfe3c53366d94..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_044441-wzl23ecz/files/wandb-metadata.json +++ /dev/null @@ -1,134 +0,0 @@ -{ - "os": "Linux-5.15.0-72-generic-x86_64-with-glibc2.35", - "python": "CPython 3.10.19", - "startedAt": "2026-03-05T04:44:41.771393Z", - "args": [ - "--model_name_or_path", - "/home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000", - "--tokenizer_path", - "/home/n5huang/dna_token/tokenizer_evaluation/merge_bpe/merge_tokenizer_unigram_len2.json", - "--trust_remote_code", - "True", - "--data_path", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/H3K4me1/split", - "--kmer", - "-1", - "--run_name", - "hg38_BPE_base__merge_bpe_merge_tokenizer_unigram_len2_3e-5_H3K4me1_seed42", - "--model_max_length", - "220", - "--per_device_train_batch_size", - "128", - "--per_device_eval_batch_size", - "128", - "--gradient_accumulation_steps", - "1", - "--learning_rate", - "3e-5", - 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"True" - - --data_path - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/H3K4me2/split - - --kmer - - "-1" - - --run_name - - hg38_BPE_base__merge_bpe_merge_tokenizer_unigram_len2_3e-5_H3K4me2_seed42 - - --model_max_length - - "220" - - --per_device_train_batch_size - - "128" - - --per_device_eval_batch_size - - "128" - - --gradient_accumulation_steps - - "1" - - --learning_rate - - "3e-5" - - --num_train_epochs - - "2" - - --fp16 - - --save_steps - - "200" - - --output_dir - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_len2/H3K4me2 - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "547020775424" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:44:59.394355Z" - writerId: nalotxbistds412db0ldimpop3mg18al - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_044459-8svfel3c/files/output.log b/wandb/run-20260305_044459-8svfel3c/files/output.log deleted file mode 100644 index f934ac9c81127c882ff8bb1b579bdda48a56ead0..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_044459-8svfel3c/files/output.log +++ /dev/null @@ -1,150 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 23837.98it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -classifier.bias | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 25,710 - Num Epochs = 2 - Num update steps per epoch = 201 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 402 - Number of trainable parameters = 44,302,082 - 0%| | 0/402 [00:00 - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 445, in train - trainer.train() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1424, in train - return inner_training_loop( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1506, in _inner_training_loop - self._run_epoch( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1734, in _run_epoch - tr_loss_step = self.training_step(model, inputs, num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1906, in training_step - loss = self.compute_loss(model, inputs, num_items_in_batch=num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1978, in compute_loss - outputs = model(**inputs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 823, in forward - return model_forward(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 811, in __call__ - return convert_to_fp32(self.model_forward(*args, **kwargs)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/amp/autocast_mode.py", line 44, in decorate_autocast - return func(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 843, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 1139, in forward - outputs = self.bert( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 917, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/output_capturing.py", line 253, in wrapper - outputs = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 680, in forward - embedding_output = self.embeddings( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 110, in forward - embeddings = self.LayerNorm(embeddings) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/normalization.py", line 229, in forward - return F.layer_norm( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/functional.py", line 2935, in layer_norm - return torch.layer_norm( -torch.AcceleratorError: CUDA error: device-side assert triggered -Search for `cudaErrorAssert' in https://docs.nvidia.com/cuda/cuda-runtime-api/group__CUDART__TYPES.html for more information. -CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect. -For debugging consider passing CUDA_LAUNCH_BLOCKING=1 -Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions. - -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 464, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 445, in train - trainer.train() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1424, in train - return inner_training_loop( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1506, in _inner_training_loop - self._run_epoch( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1734, in _run_epoch - tr_loss_step = self.training_step(model, inputs, num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1906, in training_step - loss = self.compute_loss(model, inputs, num_items_in_batch=num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1978, in compute_loss - outputs = model(**inputs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 823, in forward - return model_forward(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 811, in __call__ - return convert_to_fp32(self.model_forward(*args, **kwargs)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/amp/autocast_mode.py", line 44, in decorate_autocast - return func(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 843, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 1139, in forward - outputs = self.bert( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 917, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/output_capturing.py", line 253, in wrapper - outputs = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 680, in forward - embedding_output = self.embeddings( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 110, in forward - embeddings = self.LayerNorm(embeddings) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/normalization.py", line 229, in forward - return F.layer_norm( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/functional.py", line 2935, in layer_norm - return torch.layer_norm( -torch.AcceleratorError: CUDA error: device-side assert triggered -Search for `cudaErrorAssert' in https://docs.nvidia.com/cuda/cuda-runtime-api/group__CUDART__TYPES.html for more information. -CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect. -For debugging consider passing CUDA_LAUNCH_BLOCKING=1 -Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions. diff --git a/wandb/run-20260305_044459-8svfel3c/files/requirements.txt b/wandb/run-20260305_044459-8svfel3c/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_044459-8svfel3c/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 -accelerate==1.13.0 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -triton==3.6.0 -nvidia-nccl-cu12==2.27.5 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -cuda-pathfinder==1.4.0 -shellingham==1.5.4 -torchaudio==2.5.1 -nvidia-cufile-cu12==1.13.1.3 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -nvidia-nvjitlink-cu12==12.8.93 -click==8.3.1 -MarkupSafe==3.0.2 -nvidia-nvshmem-cu12==3.4.5 -urllib3==2.6.3 -cuda-bindings==12.9.4 -propcache==0.4.1 -nvidia-cusolver-cu12==11.7.3.90 -sympy==1.14.0 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -nvidia-cuda-runtime-cu12==12.8.90 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_044459-8svfel3c/files/wandb-metadata.json b/wandb/run-20260305_044459-8svfel3c/files/wandb-metadata.json deleted file mode 100644 index 8bb43f0003dc362edfcc7d538425a7916b086bee..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_044459-8svfel3c/files/wandb-metadata.json +++ /dev/null @@ -1,134 +0,0 @@ -{ - "os": "Linux-5.15.0-72-generic-x86_64-with-glibc2.35", - "python": "CPython 3.10.19", - "startedAt": "2026-03-05T04:44:59.394355Z", - "args": [ - "--model_name_or_path", - "/home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000", - "--tokenizer_path", - "/home/n5huang/dna_token/tokenizer_evaluation/merge_bpe/merge_tokenizer_unigram_len2.json", - "--trust_remote_code", - "True", - "--data_path", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/H3K4me2/split", - "--kmer", - "-1", - "--run_name", - "hg38_BPE_base__merge_bpe_merge_tokenizer_unigram_len2_3e-5_H3K4me2_seed42", - "--model_max_length", - "220", - "--per_device_train_batch_size", - "128", - "--per_device_eval_batch_size", - "128", - "--gradient_accumulation_steps", - "1", - "--learning_rate", - "3e-5", - 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GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:45:17.080233Z" - writerId: 1xxd5fyqxc8berdew2x9xv5fvkr54m4d - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_044517-29xu457t/files/output.log b/wandb/run-20260305_044517-29xu457t/files/output.log deleted file mode 100644 index 64fd89c91430dd5d1e8a6d02a8e740324b695af6..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_044517-29xu457t/files/output.log +++ /dev/null @@ -1,150 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 21861.12it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -bert.pooler.dense.weight | MISSING | -classifier.weight | MISSING | -classifier.bias | MISSING | -bert.pooler.dense.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 14,595 - Num Epochs = 2 - Num update steps per epoch = 115 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 230 - Number of trainable parameters = 44,302,082 - 0%| | 0/230 [00:00 - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 445, in train - trainer.train() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1424, in train - return inner_training_loop( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1506, in _inner_training_loop - self._run_epoch( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1734, in _run_epoch - tr_loss_step = self.training_step(model, inputs, num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1906, in training_step - loss = self.compute_loss(model, inputs, num_items_in_batch=num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1978, in compute_loss - outputs = model(**inputs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 823, in forward - return model_forward(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 811, in __call__ - return convert_to_fp32(self.model_forward(*args, **kwargs)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/amp/autocast_mode.py", line 44, in decorate_autocast - return func(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 843, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 1139, in forward - outputs = self.bert( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 917, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/output_capturing.py", line 253, in wrapper - outputs = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 680, in forward - embedding_output = self.embeddings( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 110, in forward - embeddings = self.LayerNorm(embeddings) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/normalization.py", line 229, in forward - return F.layer_norm( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/functional.py", line 2935, in layer_norm - return torch.layer_norm( -torch.AcceleratorError: CUDA error: device-side assert triggered -Search for `cudaErrorAssert' in https://docs.nvidia.com/cuda/cuda-runtime-api/group__CUDART__TYPES.html for more information. -CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect. -For debugging consider passing CUDA_LAUNCH_BLOCKING=1 -Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions. - -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 464, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 445, in train - trainer.train() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1424, in train - return inner_training_loop( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1506, in _inner_training_loop - self._run_epoch( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1734, in _run_epoch - tr_loss_step = self.training_step(model, inputs, num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1906, in training_step - loss = self.compute_loss(model, inputs, num_items_in_batch=num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1978, in compute_loss - outputs = model(**inputs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 823, in forward - return model_forward(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 811, in __call__ - return convert_to_fp32(self.model_forward(*args, **kwargs)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/amp/autocast_mode.py", line 44, in decorate_autocast - return func(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 843, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 1139, in forward - outputs = self.bert( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 917, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/output_capturing.py", line 253, in wrapper - outputs = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 680, in forward - embedding_output = self.embeddings( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 110, in forward - embeddings = self.LayerNorm(embeddings) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/normalization.py", line 229, in forward - return F.layer_norm( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/functional.py", line 2935, in layer_norm - return torch.layer_norm( -torch.AcceleratorError: CUDA error: device-side assert triggered -Search for `cudaErrorAssert' in https://docs.nvidia.com/cuda/cuda-runtime-api/group__CUDART__TYPES.html for more information. -CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect. -For debugging consider passing CUDA_LAUNCH_BLOCKING=1 -Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions. diff --git a/wandb/run-20260305_044517-29xu457t/files/requirements.txt b/wandb/run-20260305_044517-29xu457t/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_044517-29xu457t/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 -accelerate==1.13.0 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -triton==3.6.0 -nvidia-nccl-cu12==2.27.5 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -cuda-pathfinder==1.4.0 -shellingham==1.5.4 -torchaudio==2.5.1 -nvidia-cufile-cu12==1.13.1.3 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -nvidia-nvjitlink-cu12==12.8.93 -click==8.3.1 -MarkupSafe==3.0.2 -nvidia-nvshmem-cu12==3.4.5 -urllib3==2.6.3 -cuda-bindings==12.9.4 -propcache==0.4.1 -nvidia-cusolver-cu12==11.7.3.90 -sympy==1.14.0 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -nvidia-cuda-runtime-cu12==12.8.90 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_044517-29xu457t/files/wandb-metadata.json b/wandb/run-20260305_044517-29xu457t/files/wandb-metadata.json deleted file mode 100644 index 97cc488bcc28d823bf0e2bdf7513e8856b5b78a1..0000000000000000000000000000000000000000 --- 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04:45:17,316 INFO MainThread:2323194 [wandb_init.py:init():997] communicating run to backend with 90.0 second timeout -2026-03-05 04:45:18,041 INFO MainThread:2323194 [wandb_init.py:init():1042] starting run threads in backend -2026-03-05 04:45:18,137 INFO MainThread:2323194 [wandb_run.py:_console_start():2524] atexit reg -2026-03-05 04:45:18,137 INFO MainThread:2323194 [wandb_run.py:_redirect():2373] redirect: wrap_raw -2026-03-05 04:45:18,137 INFO MainThread:2323194 [wandb_run.py:_redirect():2442] Wrapping output streams. -2026-03-05 04:45:18,137 INFO MainThread:2323194 [wandb_run.py:_redirect():2465] Redirects installed. -2026-03-05 04:45:18,141 INFO MainThread:2323194 [wandb_init.py:init():1082] run started, returning control to user process -2026-03-05 04:45:23,425 INFO wandb-AsyncioManager-main:2323194 [service_client.py:_forward_responses():134] Reached EOF. -2026-03-05 04:45:23,426 INFO wandb-AsyncioManager-main:2323194 [mailbox.py:close():155] Closing mailbox, abandoning 1 handles. diff --git a/wandb/run-20260305_044517-29xu457t/run-29xu457t.wandb b/wandb/run-20260305_044517-29xu457t/run-29xu457t.wandb deleted file mode 100644 index 9f809995b571efa064abf1d4d09328fe11249511..0000000000000000000000000000000000000000 Binary files a/wandb/run-20260305_044517-29xu457t/run-29xu457t.wandb and /dev/null differ diff --git a/wandb/run-20260305_044531-ftihtv6w/files/config.yaml b/wandb/run-20260305_044531-ftihtv6w/files/config.yaml deleted file mode 100644 index 31498563651c611d3914957690f74e5122902dfb..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_044531-ftihtv6w/files/config.yaml +++ /dev/null @@ -1,139 +0,0 @@ -_wandb: - value: - cli_version: 0.25.0 - e: - 1t0ifirlp1hzggfun8icsfkx6hf2rpd2: - args: - - --model_name_or_path - - /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 - - --tokenizer_path - - /home/n5huang/dna_token/tokenizer_evaluation/merge_bpe/merge_tokenizer_unigram_len2.json - - --trust_remote_code - - "True" - - --data_path - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/H3K9ac/split - - --kmer - - "-1" - - --run_name - - hg38_BPE_base__merge_bpe_merge_tokenizer_unigram_len2_3e-5_H3K9ac_seed42 - - --model_max_length - - "220" - - --per_device_train_batch_size - - "128" - - --per_device_eval_batch_size - - "128" - - --gradient_accumulation_steps - - "1" - - --learning_rate - - "3e-5" - - --num_train_epochs - - "2" - - --fp16 - - --save_steps - - "200" - - --output_dir - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_len2/H3K9ac - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "547021041664" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:45:31.863083Z" - writerId: 1t0ifirlp1hzggfun8icsfkx6hf2rpd2 - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_044531-ftihtv6w/files/output.log b/wandb/run-20260305_044531-ftihtv6w/files/output.log deleted file mode 100644 index 3a3745c402b5e0dd85ddb3e3277c81b69c22927a..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_044531-ftihtv6w/files/output.log +++ /dev/null @@ -1,150 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 22475.84it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -bert.pooler.dense.bias | MISSING | -classifier.bias | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 19,422 - Num Epochs = 2 - Num update steps per epoch = 152 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 304 - Number of trainable parameters = 44,302,082 - 0%| | 0/304 [00:00 - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 445, in train - trainer.train() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1424, in train - return inner_training_loop( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1506, in _inner_training_loop - self._run_epoch( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1734, in _run_epoch - tr_loss_step = self.training_step(model, inputs, num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1906, in training_step - loss = self.compute_loss(model, inputs, num_items_in_batch=num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1978, in compute_loss - outputs = model(**inputs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 823, in forward - return model_forward(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 811, in __call__ - return convert_to_fp32(self.model_forward(*args, **kwargs)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/amp/autocast_mode.py", line 44, in decorate_autocast - return func(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 843, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 1139, in forward - outputs = self.bert( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 917, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/output_capturing.py", line 253, in wrapper - outputs = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 680, in forward - embedding_output = self.embeddings( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 110, in forward - embeddings = self.LayerNorm(embeddings) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/normalization.py", line 229, in forward - return F.layer_norm( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/functional.py", line 2935, in layer_norm - return torch.layer_norm( -torch.AcceleratorError: CUDA error: device-side assert triggered -Search for `cudaErrorAssert' in https://docs.nvidia.com/cuda/cuda-runtime-api/group__CUDART__TYPES.html for more information. -CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect. -For debugging consider passing CUDA_LAUNCH_BLOCKING=1 -Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions. - -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 464, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 445, in train - trainer.train() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1424, in train - return inner_training_loop( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1506, in _inner_training_loop - self._run_epoch( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1734, in _run_epoch - tr_loss_step = self.training_step(model, inputs, num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1906, in training_step - loss = self.compute_loss(model, inputs, num_items_in_batch=num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1978, in compute_loss - outputs = model(**inputs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 823, in forward - return model_forward(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 811, in __call__ - return convert_to_fp32(self.model_forward(*args, **kwargs)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/amp/autocast_mode.py", line 44, in decorate_autocast - return func(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 843, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 1139, in forward - outputs = self.bert( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 917, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/output_capturing.py", line 253, in wrapper - outputs = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 680, in forward - embedding_output = self.embeddings( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 110, in forward - embeddings = self.LayerNorm(embeddings) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/normalization.py", line 229, in forward - return F.layer_norm( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/functional.py", line 2935, in layer_norm - return torch.layer_norm( -torch.AcceleratorError: CUDA error: device-side assert triggered -Search for `cudaErrorAssert' in https://docs.nvidia.com/cuda/cuda-runtime-api/group__CUDART__TYPES.html for more information. -CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect. -For debugging consider passing CUDA_LAUNCH_BLOCKING=1 -Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions. diff --git a/wandb/run-20260305_044531-ftihtv6w/files/requirements.txt b/wandb/run-20260305_044531-ftihtv6w/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_044531-ftihtv6w/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 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GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:45:48.964492Z" - writerId: 6oout2o4bnwacmr3jv4bi3mjmdafeq7f - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_044548-52al4qgb/files/output.log b/wandb/run-20260305_044548-52al4qgb/files/output.log deleted file mode 100644 index 4836f4d580f44d3987e1f070f09ad0171b3137ee..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_044548-52al4qgb/files/output.log +++ /dev/null @@ -1,150 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 21498.34it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.decoder.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -classifier.weight | MISSING | -bert.pooler.dense.weight | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 22,630 - Num Epochs = 2 - Num update steps per epoch = 177 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 354 - Number of trainable parameters = 44,302,082 - 0%| | 0/354 [00:00 - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 445, in train - trainer.train() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1424, in train - return inner_training_loop( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1506, in _inner_training_loop - self._run_epoch( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1734, in _run_epoch - tr_loss_step = self.training_step(model, inputs, num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1906, in training_step - loss = self.compute_loss(model, inputs, num_items_in_batch=num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1978, in compute_loss - outputs = model(**inputs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 823, in forward - return model_forward(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 811, in __call__ - return convert_to_fp32(self.model_forward(*args, **kwargs)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/amp/autocast_mode.py", line 44, in decorate_autocast - return func(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 843, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 1139, in forward - outputs = self.bert( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 917, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/output_capturing.py", line 253, in wrapper - outputs = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 680, in forward - embedding_output = self.embeddings( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 110, in forward - embeddings = self.LayerNorm(embeddings) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/normalization.py", line 229, in forward - return F.layer_norm( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/functional.py", line 2935, in layer_norm - return torch.layer_norm( -torch.AcceleratorError: CUDA error: device-side assert triggered -Search for `cudaErrorAssert' in https://docs.nvidia.com/cuda/cuda-runtime-api/group__CUDART__TYPES.html for more information. -CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect. -For debugging consider passing CUDA_LAUNCH_BLOCKING=1 -Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions. - -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 464, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 445, in train - trainer.train() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1424, in train - return inner_training_loop( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1506, in _inner_training_loop - self._run_epoch( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1734, in _run_epoch - tr_loss_step = self.training_step(model, inputs, num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1906, in training_step - loss = self.compute_loss(model, inputs, num_items_in_batch=num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1978, in compute_loss - outputs = model(**inputs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 823, in forward - return model_forward(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 811, in __call__ - return convert_to_fp32(self.model_forward(*args, **kwargs)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/amp/autocast_mode.py", line 44, in decorate_autocast - return func(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 843, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 1139, in forward - outputs = self.bert( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 917, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/output_capturing.py", line 253, in wrapper - outputs = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 680, in forward - embedding_output = self.embeddings( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 110, in forward - embeddings = self.LayerNorm(embeddings) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/normalization.py", line 229, in forward - return F.layer_norm( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/functional.py", line 2935, in layer_norm - return torch.layer_norm( -torch.AcceleratorError: CUDA error: device-side assert triggered -Search for `cudaErrorAssert' in https://docs.nvidia.com/cuda/cuda-runtime-api/group__CUDART__TYPES.html for more information. -CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect. -For debugging consider passing CUDA_LAUNCH_BLOCKING=1 -Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions. diff --git a/wandb/run-20260305_044548-52al4qgb/files/requirements.txt b/wandb/run-20260305_044548-52al4qgb/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_044548-52al4qgb/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 -accelerate==1.13.0 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -triton==3.6.0 -nvidia-nccl-cu12==2.27.5 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -cuda-pathfinder==1.4.0 -shellingham==1.5.4 -torchaudio==2.5.1 -nvidia-cufile-cu12==1.13.1.3 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -nvidia-nvjitlink-cu12==12.8.93 -click==8.3.1 -MarkupSafe==3.0.2 -nvidia-nvshmem-cu12==3.4.5 -urllib3==2.6.3 -cuda-bindings==12.9.4 -propcache==0.4.1 -nvidia-cusolver-cu12==11.7.3.90 -sympy==1.14.0 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -nvidia-cuda-runtime-cu12==12.8.90 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_044548-52al4qgb/files/wandb-metadata.json b/wandb/run-20260305_044548-52al4qgb/files/wandb-metadata.json deleted file mode 100644 index f0f7171c7cd4530f9e90a9862e30debcac45faba..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_044548-52al4qgb/files/wandb-metadata.json +++ /dev/null @@ -1,134 +0,0 @@ -{ - "os": "Linux-5.15.0-72-generic-x86_64-with-glibc2.35", - "python": "CPython 3.10.19", - "startedAt": "2026-03-05T04:45:48.964492Z", - "args": [ - "--model_name_or_path", - "/home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000", - "--tokenizer_path", - "/home/n5huang/dna_token/tokenizer_evaluation/merge_bpe/merge_tokenizer_unigram_len2.json", - "--trust_remote_code", - "True", - "--data_path", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/H3K9me3/split", - "--kmer", - "-1", - "--run_name", - "hg38_BPE_base__merge_bpe_merge_tokenizer_unigram_len2_3e-5_H3K9me3_seed42", - "--model_max_length", - "220", - "--per_device_train_batch_size", - "128", - "--per_device_eval_batch_size", - "128", - "--gradient_accumulation_steps", - "1", - "--learning_rate", - "3e-5", - "--num_train_epochs", - "2", - "--fp16", - "--save_steps", - "200", - "--output_dir", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_len2/H3K9me3", - "--evaluation_strategy", - "steps", - "--eval_steps", - "200", - "--warmup_steps", - "30", - "--logging_steps", - "100000", - "--log_level", - "info", - "--seed", - "42", - "--find_unused_parameters", - "False", - "--project_name", - "genomic_bench_tune_hg38_1024" - ], - "program": "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", - "git": { - "remote": "https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks", - "commit": "5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6" - }, - "email": "mtapiapacheco@ucsd.edu", - "root": "/data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data", - "host": "sn4622116170", - "executable": "/home/n5huang/miniconda3/envs/nt_ft/bin/python", - "cpu_count": 128, - 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"True" - - --data_path - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/H4K20me1/split - - --kmer - - "-1" - - --run_name - - hg38_BPE_base__merge_bpe_merge_tokenizer_unigram_len2_3e-5_H4K20me1_seed42 - - --model_max_length - - "220" - - --per_device_train_batch_size - - "128" - - --per_device_eval_batch_size - - "128" - - --gradient_accumulation_steps - - "1" - - --learning_rate - - "3e-5" - - --num_train_epochs - - "2" - - --fp16 - - --save_steps - - "200" - - --output_dir - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_len2/H4K20me1 - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "547023233024" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:46:07.149502Z" - writerId: tp40pxgwsetofj9i19cokp7z8nkzpx8d - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_044607-o54sle96/files/output.log b/wandb/run-20260305_044607-o54sle96/files/output.log deleted file mode 100644 index 5194cd70d5036fa2f638a6bef9c662313fda7f95..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_044607-o54sle96/files/output.log +++ /dev/null @@ -1,150 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 22456.78it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -classifier.weight | MISSING | -classifier.bias | MISSING | -bert.pooler.dense.bias | MISSING | -bert.pooler.dense.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 25,816 - Num Epochs = 2 - Num update steps per epoch = 202 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 404 - Number of trainable parameters = 44,302,082 - 0%| | 0/404 [00:00 - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 445, in train - trainer.train() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1424, in train - return inner_training_loop( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1506, in _inner_training_loop - self._run_epoch( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1734, in _run_epoch - tr_loss_step = self.training_step(model, inputs, num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1906, in training_step - loss = self.compute_loss(model, inputs, num_items_in_batch=num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1978, in compute_loss - outputs = model(**inputs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 823, in forward - return model_forward(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 811, in __call__ - return convert_to_fp32(self.model_forward(*args, **kwargs)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/amp/autocast_mode.py", line 44, in decorate_autocast - return func(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 843, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 1139, in forward - outputs = self.bert( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 917, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/output_capturing.py", line 253, in wrapper - outputs = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 680, in forward - embedding_output = self.embeddings( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 110, in forward - embeddings = self.LayerNorm(embeddings) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/normalization.py", line 229, in forward - return F.layer_norm( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/functional.py", line 2935, in layer_norm - return torch.layer_norm( -torch.AcceleratorError: CUDA error: device-side assert triggered -Search for `cudaErrorAssert' in https://docs.nvidia.com/cuda/cuda-runtime-api/group__CUDART__TYPES.html for more information. -CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect. -For debugging consider passing CUDA_LAUNCH_BLOCKING=1 -Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions. - -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 464, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 445, in train - trainer.train() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1424, in train - return inner_training_loop( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1506, in _inner_training_loop - self._run_epoch( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1734, in _run_epoch - tr_loss_step = self.training_step(model, inputs, num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1906, in training_step - loss = self.compute_loss(model, inputs, num_items_in_batch=num_items_in_batch) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1978, in compute_loss - outputs = model(**inputs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 823, in forward - return model_forward(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/accelerate/utils/operations.py", line 811, in __call__ - return convert_to_fp32(self.model_forward(*args, **kwargs)) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/amp/autocast_mode.py", line 44, in decorate_autocast - return func(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 843, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 1139, in forward - outputs = self.bert( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/generic.py", line 917, in wrapper - output = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/output_capturing.py", line 253, in wrapper - outputs = func(self, *args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 680, in forward - embedding_output = self.embeddings( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/bert/modeling_bert.py", line 110, in forward - embeddings = self.LayerNorm(embeddings) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1776, in _wrapped_call_impl - return self._call_impl(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/module.py", line 1787, in _call_impl - return forward_call(*args, **kwargs) - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/modules/normalization.py", line 229, in forward - return F.layer_norm( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/nn/functional.py", line 2935, in layer_norm - return torch.layer_norm( -torch.AcceleratorError: CUDA error: device-side assert triggered -Search for `cudaErrorAssert' in https://docs.nvidia.com/cuda/cuda-runtime-api/group__CUDART__TYPES.html for more information. -CUDA kernel errors might be asynchronously reported at some other API call, so the stacktrace below might be incorrect. -For debugging consider passing CUDA_LAUNCH_BLOCKING=1 -Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions. diff --git a/wandb/run-20260305_044607-o54sle96/files/requirements.txt b/wandb/run-20260305_044607-o54sle96/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_044607-o54sle96/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 -accelerate==1.13.0 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -triton==3.6.0 -nvidia-nccl-cu12==2.27.5 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -cuda-pathfinder==1.4.0 -shellingham==1.5.4 -torchaudio==2.5.1 -nvidia-cufile-cu12==1.13.1.3 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -nvidia-nvjitlink-cu12==12.8.93 -click==8.3.1 -MarkupSafe==3.0.2 -nvidia-nvshmem-cu12==3.4.5 -urllib3==2.6.3 -cuda-bindings==12.9.4 -propcache==0.4.1 -nvidia-cusolver-cu12==11.7.3.90 -sympy==1.14.0 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -nvidia-cuda-runtime-cu12==12.8.90 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_044607-o54sle96/files/wandb-metadata.json b/wandb/run-20260305_044607-o54sle96/files/wandb-metadata.json deleted file mode 100644 index 837d55ad90f615e896a291e7b27508d5776c753a..0000000000000000000000000000000000000000 --- 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handles. diff --git a/wandb/run-20260305_044607-o54sle96/run-o54sle96.wandb b/wandb/run-20260305_044607-o54sle96/run-o54sle96.wandb deleted file mode 100644 index 4d3a3c1c1f0371ab658fcddbd1c03b5deba8b3eb..0000000000000000000000000000000000000000 Binary files a/wandb/run-20260305_044607-o54sle96/run-o54sle96.wandb and /dev/null differ diff --git a/wandb/run-20260305_044626-rx74ejua/files/config.yaml b/wandb/run-20260305_044626-rx74ejua/files/config.yaml deleted file mode 100644 index ba270f79fa471f8e18fb79d881b9e8fe52f27660..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_044626-rx74ejua/files/config.yaml +++ /dev/null @@ -1,139 +0,0 @@ -_wandb: - value: - cli_version: 0.25.0 - e: - hylaou3doldl42r3sm5fa6lwfrocaexc: - args: - - --model_name_or_path - - /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 - - --tokenizer_path - - /home/n5huang/dna_token/tokenizer_evaluation/merge_bpe/merge_tokenizer_unigram_tf_idf.json - - --trust_remote_code - - "True" - - --data_path - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/enhancers/split - - --kmer - - "-1" - - --run_name - - hg38_BPE_base__merge_bpe_merge_tokenizer_unigram_tf_idf_3e-5_enhancers_seed42 - - --model_max_length - - "100" - - --per_device_train_batch_size - - "128" - - --per_device_eval_batch_size - - "128" - - --gradient_accumulation_steps - - "1" - - --learning_rate - - "3e-5" - - --num_train_epochs - - "4" - - --fp16 - - --save_steps - - "200" - - --output_dir - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "547023441920" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:46:26.683052Z" - writerId: hylaou3doldl42r3sm5fa6lwfrocaexc - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_044626-rx74ejua/files/output.log b/wandb/run-20260305_044626-rx74ejua/files/output.log deleted file mode 100644 index d7629e064d09f1d6e1899a25bbfcb7e3eee70f6d..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_044626-rx74ejua/files/output.log +++ /dev/null @@ -1,70 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 22106.39it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -bert.pooler.dense.weight | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 755}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 4 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 828 - Number of trainable parameters = 44,302,082 - 24%|██▍ | 199/828 [00:09<00:27, 22.76it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.41it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers/checkpoint-200/tokenizer_config.json - 48%|████▊ | 400/828 [00:19<00:19, 22.07it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.04it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers/checkpoint-400/tokenizer_config.json - 72%|███████▏ | 598/828 [00:28<00:09, 24.52it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers/checkpoint-600 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers/checkpoint-600/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 2.87it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers/checkpoint-600/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers/checkpoint-600/tokenizer_config.json - 96%|█████████▋| 799/828 [00:38<00:01, 22.69it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers/checkpoint-800 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers/checkpoint-800/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 2.95it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers/checkpoint-800/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers/checkpoint-800/tokenizer_config.json -100%|█████████▉| 826/828 [00:40<00:00, 21.03it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers/checkpoint-828 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers/checkpoint-828/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 2.97it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers/checkpoint-828/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers/checkpoint-828/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 828/828 [00:41<00:00, 19.97it/s] -{'train_runtime': '41.45', 'train_samples_per_second': '2547', 'train_steps_per_second': '19.97', 'train_loss': '0.5676', 'epoch': '4'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 83.28it/s] diff --git a/wandb/run-20260305_044626-rx74ejua/files/requirements.txt b/wandb/run-20260305_044626-rx74ejua/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_044626-rx74ejua/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 -accelerate==1.13.0 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -triton==3.6.0 -nvidia-nccl-cu12==2.27.5 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -cuda-pathfinder==1.4.0 -shellingham==1.5.4 -torchaudio==2.5.1 -nvidia-cufile-cu12==1.13.1.3 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -nvidia-nvjitlink-cu12==12.8.93 -click==8.3.1 -MarkupSafe==3.0.2 -nvidia-nvshmem-cu12==3.4.5 -urllib3==2.6.3 -cuda-bindings==12.9.4 -propcache==0.4.1 -nvidia-cusolver-cu12==11.7.3.90 -sympy==1.14.0 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -nvidia-cuda-runtime-cu12==12.8.90 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_044626-rx74ejua/files/wandb-metadata.json b/wandb/run-20260305_044626-rx74ejua/files/wandb-metadata.json deleted file mode 100644 index 322bff748855b0194f4e39391693e1b34dff6607..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_044626-rx74ejua/files/wandb-metadata.json +++ /dev/null @@ -1,134 +0,0 @@ -{ - "os": "Linux-5.15.0-72-generic-x86_64-with-glibc2.35", - "python": "CPython 3.10.19", - "startedAt": "2026-03-05T04:46:26.683052Z", - "args": [ - "--model_name_or_path", - "/home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000", - "--tokenizer_path", - "/home/n5huang/dna_token/tokenizer_evaluation/merge_bpe/merge_tokenizer_unigram_tf_idf.json", - "--trust_remote_code", - "True", - "--data_path", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/enhancers/split", - "--kmer", - "-1", - "--run_name", - "hg38_BPE_base__merge_bpe_merge_tokenizer_unigram_tf_idf_3e-5_enhancers_seed42", - "--model_max_length", - "100", - "--per_device_train_batch_size", - "128", - 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/data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:47:22.860124Z" - writerId: nzbxsu353o1c89ah64wr36fc0i1ak6nq - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_044722-r33vg9iv/files/output.log b/wandb/run-20260305_044722-r33vg9iv/files/output.log deleted file mode 100644 index 39ccb5542923b1a1b7bcf9e3103b25b1c051853e..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_044722-r33vg9iv/files/output.log +++ /dev/null @@ -1,70 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 20531.42it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -classifier.bias | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.weight | MISSING | -bert.pooler.dense.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 755}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 4 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 828 - Number of trainable parameters = 44,302,851 - 24%|██▍ | 199/828 [00:08<00:25, 24.46it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers_types/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers_types/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.15it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers_types/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers_types/checkpoint-200/tokenizer_config.json - 48%|████▊ | 400/828 [00:17<00:18, 23.66it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers_types/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers_types/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.94it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers_types/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers_types/checkpoint-400/tokenizer_config.json - 72%|███████▏ | 598/828 [00:26<00:09, 23.52it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers_types/checkpoint-600 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers_types/checkpoint-600/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 5.10it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers_types/checkpoint-600/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers_types/checkpoint-600/tokenizer_config.json - 96%|█████████▋| 799/828 [00:35<00:01, 23.12it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers_types/checkpoint-800 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers_types/checkpoint-800/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.96it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers_types/checkpoint-800/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers_types/checkpoint-800/tokenizer_config.json -100%|█████████▉| 826/828 [00:37<00:00, 21.11it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers_types/checkpoint-828 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers_types/checkpoint-828/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.06it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers_types/checkpoint-828/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers_types/checkpoint-828/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 828/828 [00:37<00:00, 21.79it/s] -{'train_runtime': '37.99', 'train_samples_per_second': '2780', 'train_steps_per_second': '21.8', 'train_loss': '0.6981', 'epoch': '4'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 82.90it/s] diff --git a/wandb/run-20260305_044722-r33vg9iv/files/requirements.txt b/wandb/run-20260305_044722-r33vg9iv/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_044722-r33vg9iv/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:48:15.396015Z" - writerId: 04sw5dhn4r8ijsxu6y3r8i2aeohaloaz - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_044815-t403r93p/files/output.log b/wandb/run-20260305_044815-t403r93p/files/output.log deleted file mode 100644 index 7cb24ea80c2c2ef3b34437701d9a6d7512e64c67..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_044815-t403r93p/files/output.log +++ /dev/null @@ -1,55 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 24024.54it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -classifier.bias | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.weight | MISSING | -bert.pooler.dense.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 755}. -***** Running training ***** - Num examples = 25,267 - Num Epochs = 2 - Num update steps per epoch = 198 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 396 - Number of trainable parameters = 44,302,082 - 51%|█████ | 200/396 [00:07<00:06, 29.70it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/promoter_all/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/promoter_all/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.33it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/promoter_all/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/promoter_all/checkpoint-200/tokenizer_config.json -100%|█████████▉| 395/396 [00:15<00:00, 27.57it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/promoter_all/checkpoint-396 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/promoter_all/checkpoint-396/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.89it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/promoter_all/checkpoint-396/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/promoter_all/checkpoint-396/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 396/396 [00:16<00:00, 24.56it/s] -{'train_runtime': '16.12', 'train_samples_per_second': '3134', 'train_steps_per_second': '24.56', 'train_loss': '0.3975', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3159 - Batch size = 128 -100%|██████████| 25/25 [00:00<00:00, 99.12it/s] diff --git a/wandb/run-20260305_044815-t403r93p/files/requirements.txt b/wandb/run-20260305_044815-t403r93p/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_044815-t403r93p/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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- - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "547030319104" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - 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/data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:48:45.045003Z" - writerId: clcc7rwiwiuhyexgzhbhubd7gurh871a - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_044845-aelf79gh/files/output.log b/wandb/run-20260305_044845-aelf79gh/files/output.log deleted file mode 100644 index ec72481ea6073c08eba0d3fca50a5c4310c92084..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_044845-aelf79gh/files/output.log +++ /dev/null @@ -1,55 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 12305.37it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -bert.pooler.dense.bias | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 755}. -***** Running training ***** - Num examples = 25,097 - Num Epochs = 2 - Num update steps per epoch = 197 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 394 - Number of trainable parameters = 44,302,082 - 51%|█████ | 199/394 [00:08<00:08, 24.12it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/promoter_no_tata/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/promoter_no_tata/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.69it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/promoter_no_tata/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/promoter_no_tata/checkpoint-200/tokenizer_config.json - 99%|█████████▉| 391/394 [00:16<00:00, 23.46it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/promoter_no_tata/checkpoint-394 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/promoter_no_tata/checkpoint-394/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 2.61it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/promoter_no_tata/checkpoint-394/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/promoter_no_tata/checkpoint-394/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 394/394 [00:17<00:00, 22.41it/s] -{'train_runtime': '17.58', 'train_samples_per_second': '2855', 'train_steps_per_second': '22.41', 'train_loss': '0.3692', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3138 - Batch size = 128 -100%|██████████| 25/25 [00:00<00:00, 99.44it/s] diff --git a/wandb/run-20260305_044845-aelf79gh/files/requirements.txt b/wandb/run-20260305_044845-aelf79gh/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_044845-aelf79gh/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 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/home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -classifier.bias | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 755}. -***** Running training ***** - Num examples = 4,219 - Num Epochs = 2 - Num update steps per epoch = 33 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 66 - Number of trainable parameters = 44,302,082 - 97%|█████████▋| 64/66 [00:03<00:00, 28.51it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/promoter_tata/checkpoint-66 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/promoter_tata/checkpoint-66/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.61it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/promoter_tata/checkpoint-66/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/promoter_tata/checkpoint-66/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 66/66 [00:04<00:00, 16.11it/s] -{'train_runtime': '4.096', 'train_samples_per_second': '2060', 'train_steps_per_second': '16.11', 'train_loss': '0.5832', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 528 - Batch size = 128 -100%|██████████| 5/5 [00:00<00:00, 80.58it/s] diff --git a/wandb/run-20260305_044916-sdj0nfrw/files/requirements.txt b/wandb/run-20260305_044916-sdj0nfrw/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_044916-sdj0nfrw/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 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python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:49:31.800349Z" - writerId: op4zf7052dflakmcmf9716ed8g5zmhn9 - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_044931-mat73596/files/output.log b/wandb/run-20260305_044931-mat73596/files/output.log deleted file mode 100644 index 338fe8b4b8c87f8d78df8338b8a24ea360a9e0d8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_044931-mat73596/files/output.log +++ /dev/null @@ -1,70 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 20646.49it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -classifier.bias | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 755}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 4 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 828 - Number of trainable parameters = 44,302,082 - 24%|██▍ | 199/828 [00:12<00:36, 17.30it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_acceptors/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_acceptors/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.52it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_acceptors/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_acceptors/checkpoint-200/tokenizer_config.json - 48%|████▊ | 400/828 [00:24<00:24, 17.48it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_acceptors/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_acceptors/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.19it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_acceptors/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_acceptors/checkpoint-400/tokenizer_config.json - 72%|███████▏ | 599/828 [00:36<00:13, 17.39it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_acceptors/checkpoint-600 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_acceptors/checkpoint-600/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 5.42it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_acceptors/checkpoint-600/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_acceptors/checkpoint-600/tokenizer_config.json - 97%|█████████▋| 800/828 [00:48<00:01, 17.73it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_acceptors/checkpoint-800 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_acceptors/checkpoint-800/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 5.53it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_acceptors/checkpoint-800/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_acceptors/checkpoint-800/tokenizer_config.json -100%|█████████▉| 826/828 [00:50<00:00, 16.93it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_acceptors/checkpoint-828 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_acceptors/checkpoint-828/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.30it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_acceptors/checkpoint-828/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_acceptors/checkpoint-828/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 828/828 [00:51<00:00, 16.12it/s] -{'train_runtime': '51.37', 'train_samples_per_second': '2056', 'train_steps_per_second': '16.12', 'train_loss': '0.6054', 'epoch': '4'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 60.06it/s] diff --git a/wandb/run-20260305_044931-mat73596/files/requirements.txt b/wandb/run-20260305_044931-mat73596/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_044931-mat73596/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 -accelerate==1.13.0 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -triton==3.6.0 -nvidia-nccl-cu12==2.27.5 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -cuda-pathfinder==1.4.0 -shellingham==1.5.4 -torchaudio==2.5.1 -nvidia-cufile-cu12==1.13.1.3 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -nvidia-nvjitlink-cu12==12.8.93 -click==8.3.1 -MarkupSafe==3.0.2 -nvidia-nvshmem-cu12==3.4.5 -urllib3==2.6.3 -cuda-bindings==12.9.4 -propcache==0.4.1 -nvidia-cusolver-cu12==11.7.3.90 -sympy==1.14.0 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -nvidia-cuda-runtime-cu12==12.8.90 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_044931-mat73596/files/wandb-metadata.json b/wandb/run-20260305_044931-mat73596/files/wandb-metadata.json deleted file mode 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/home/n5huang/dna_token/tokenizer_evaluation/merge_bpe/merge_tokenizer_unigram_tf_idf.json - - --trust_remote_code - - "True" - - --data_path - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/splice_sites_all/split - - --kmer - - "-1" - - --run_name - - hg38_BPE_base__merge_bpe_merge_tokenizer_unigram_tf_idf_3e-5_splice_sites_all_seed42 - - --model_max_length - - "140" - - --per_device_train_batch_size - - "128" - - --per_device_eval_batch_size - - "128" - - --gradient_accumulation_steps - - "1" - - --learning_rate - - "3e-5" - - --num_train_epochs - - "4" - - --fp16 - - --save_steps - - "200" - - --output_dir - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_all - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "547035111424" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:50:38.897780Z" - writerId: 7wcf0o8v0qji4d4e563gsbb11s122z5h - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_045038-0trwei28/files/output.log b/wandb/run-20260305_045038-0trwei28/files/output.log deleted file mode 100644 index 0b26bd3f75c44862f2dc5e57d83c4a843f1e0db6..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_045038-0trwei28/files/output.log +++ /dev/null @@ -1,70 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 24291.80it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -bert.pooler.dense.bias | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 755}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 4 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 828 - Number of trainable parameters = 44,302,851 - 24%|██▍ | 199/828 [00:12<00:35, 17.68it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_all/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_all/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.14it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_all/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_all/checkpoint-200/tokenizer_config.json - 48%|████▊ | 400/828 [00:24<00:24, 17.33it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_all/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_all/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.47it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_all/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_all/checkpoint-400/tokenizer_config.json - 72%|███████▏ | 599/828 [00:37<00:13, 17.29it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_all/checkpoint-600 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_all/checkpoint-600/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 2.96it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_all/checkpoint-600/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_all/checkpoint-600/tokenizer_config.json - 97%|█████████▋| 800/828 [00:50<00:01, 16.50it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_all/checkpoint-800 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_all/checkpoint-800/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.82it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_all/checkpoint-800/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_all/checkpoint-800/tokenizer_config.json -100%|█████████▉| 826/828 [00:52<00:00, 16.88it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_all/checkpoint-828 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_all/checkpoint-828/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.60it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_all/checkpoint-828/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_all/checkpoint-828/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 828/828 [00:53<00:00, 15.42it/s] -{'train_runtime': '53.7', 'train_samples_per_second': '1966', 'train_steps_per_second': '15.42', 'train_loss': '0.9322', 'epoch': '4'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 59.34it/s] diff --git a/wandb/run-20260305_045038-0trwei28/files/requirements.txt b/wandb/run-20260305_045038-0trwei28/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_045038-0trwei28/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:51:48.437477Z" - writerId: p1nzr5lmorls2po4xred1uqn6deh1t28 - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_045148-lo9v7ma2/files/output.log b/wandb/run-20260305_045148-lo9v7ma2/files/output.log deleted file mode 100644 index b8941ee11dc75309bdffbe0a5327d7db994d9ada..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_045148-lo9v7ma2/files/output.log +++ /dev/null @@ -1,70 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 20933.18it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -classifier.bias | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 755}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 4 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 828 - Number of trainable parameters = 44,302,082 - 24%|██▍ | 199/828 [00:12<00:37, 16.90it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_donors/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_donors/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.71it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_donors/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_donors/checkpoint-200/tokenizer_config.json - 48%|████▊ | 400/828 [00:24<00:24, 17.55it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_donors/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_donors/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 5.09it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_donors/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_donors/checkpoint-400/tokenizer_config.json - 72%|███████▏ | 599/828 [00:36<00:13, 17.51it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_donors/checkpoint-600 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_donors/checkpoint-600/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.25it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_donors/checkpoint-600/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_donors/checkpoint-600/tokenizer_config.json - 97%|█████████▋| 800/828 [00:48<00:01, 17.22it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_donors/checkpoint-800 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_donors/checkpoint-800/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 5.11it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_donors/checkpoint-800/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_donors/checkpoint-800/tokenizer_config.json -100%|█████████▉| 826/828 [00:50<00:00, 16.95it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_donors/checkpoint-828 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_donors/checkpoint-828/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.90it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_donors/checkpoint-828/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_donors/checkpoint-828/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 828/828 [00:51<00:00, 16.09it/s] -{'train_runtime': '51.46', 'train_samples_per_second': '2052', 'train_steps_per_second': '16.09', 'train_loss': '0.5413', 'epoch': '4'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 61.13it/s] diff --git a/wandb/run-20260305_045148-lo9v7ma2/files/requirements.txt b/wandb/run-20260305_045148-lo9v7ma2/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_045148-lo9v7ma2/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 -accelerate==1.13.0 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -triton==3.6.0 -nvidia-nccl-cu12==2.27.5 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -cuda-pathfinder==1.4.0 -shellingham==1.5.4 -torchaudio==2.5.1 -nvidia-cufile-cu12==1.13.1.3 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -nvidia-nvjitlink-cu12==12.8.93 -click==8.3.1 -MarkupSafe==3.0.2 -nvidia-nvshmem-cu12==3.4.5 -urllib3==2.6.3 -cuda-bindings==12.9.4 -propcache==0.4.1 -nvidia-cusolver-cu12==11.7.3.90 -sympy==1.14.0 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -nvidia-cuda-runtime-cu12==12.8.90 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_045148-lo9v7ma2/files/wandb-metadata.json b/wandb/run-20260305_045148-lo9v7ma2/files/wandb-metadata.json deleted file mode 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cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:52:54.704074Z" - writerId: kgki8cdimxbjurviy9cc7y9vm93adsy0 - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_045254-2uy6si7z/files/output.log b/wandb/run-20260305_045254-2uy6si7z/files/output.log deleted file mode 100644 index 668c398282f5200832b8e179b5eaaad5b598a69f..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_045254-2uy6si7z/files/output.log +++ /dev/null @@ -1,60 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 20948.70it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -classifier.weight | MISSING | -bert.pooler.dense.bias | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 755}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 2 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 414 - Number of trainable parameters = 44,302,082 - 48%|████▊ | 199/414 [00:15<00:16, 12.91it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H2AFZ/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H2AFZ/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.76it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H2AFZ/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H2AFZ/checkpoint-200/tokenizer_config.json - 96%|█████████▋| 399/414 [00:32<00:01, 12.71it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H2AFZ/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H2AFZ/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.49it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H2AFZ/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H2AFZ/checkpoint-400/tokenizer_config.json -100%|█████████▉| 413/414 [00:34<00:00, 10.79it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H2AFZ/checkpoint-414 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H2AFZ/checkpoint-414/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 2.88it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H2AFZ/checkpoint-414/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H2AFZ/checkpoint-414/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 414/414 [00:34<00:00, 11.87it/s] -{'train_runtime': '34.89', 'train_samples_per_second': '1513', 'train_steps_per_second': '11.87', 'train_loss': '0.5928', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 44.00it/s] diff --git a/wandb/run-20260305_045254-2uy6si7z/files/requirements.txt b/wandb/run-20260305_045254-2uy6si7z/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_045254-2uy6si7z/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 -accelerate==1.13.0 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -triton==3.6.0 -nvidia-nccl-cu12==2.27.5 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -cuda-pathfinder==1.4.0 -shellingham==1.5.4 -torchaudio==2.5.1 -nvidia-cufile-cu12==1.13.1.3 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -nvidia-nvjitlink-cu12==12.8.93 -click==8.3.1 -MarkupSafe==3.0.2 -nvidia-nvshmem-cu12==3.4.5 -urllib3==2.6.3 -cuda-bindings==12.9.4 -propcache==0.4.1 -nvidia-cusolver-cu12==11.7.3.90 -sympy==1.14.0 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -nvidia-cuda-runtime-cu12==12.8.90 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_045254-2uy6si7z/files/wandb-metadata.json b/wandb/run-20260305_045254-2uy6si7z/files/wandb-metadata.json deleted file mode 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/home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -bert.pooler.dense.weight | MISSING | -classifier.weight | MISSING | -classifier.bias | MISSING | -bert.pooler.dense.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 755}. -***** Running training ***** - Num examples = 25,292 - Num Epochs = 2 - Num update steps per epoch = 198 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 396 - Number of trainable parameters = 44,302,082 - 50%|█████ | 199/396 [00:15<00:14, 13.51it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K27ac/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K27ac/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.08it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K27ac/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K27ac/checkpoint-200/tokenizer_config.json -100%|█████████▉| 395/396 [00:31<00:00, 12.75it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K27ac/checkpoint-396 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K27ac/checkpoint-396/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.89it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K27ac/checkpoint-396/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K27ac/checkpoint-396/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 396/396 [00:32<00:00, 12.19it/s] -{'train_runtime': '32.5', 'train_samples_per_second': '1557', 'train_steps_per_second': '12.19', 'train_loss': '0.6105', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3163 - Batch size = 128 -100%|██████████| 25/25 [00:00<00:00, 43.62it/s] diff --git a/wandb/run-20260305_045347-7npd9bzt/files/requirements.txt b/wandb/run-20260305_045347-7npd9bzt/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_045347-7npd9bzt/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:54:37.168068Z" - writerId: artdz7hkmytl4nysr4r7xjrc5dlrurqb - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_045437-0u1ivpgs/files/output.log b/wandb/run-20260305_045437-0u1ivpgs/files/output.log deleted file mode 100644 index 6d2091bcdd30b8813e82184131df82e6f57a284d..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_045437-0u1ivpgs/files/output.log +++ /dev/null @@ -1,60 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 12212.78it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.decoder.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -classifier.weight | MISSING | -bert.pooler.dense.weight | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 755}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 2 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 414 - Number of trainable parameters = 44,302,082 - 48%|████▊ | 199/414 [00:15<00:16, 12.94it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K27me3/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K27me3/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.98it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K27me3/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K27me3/checkpoint-200/tokenizer_config.json - 96%|█████████▋| 399/414 [00:31<00:01, 12.91it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K27me3/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K27me3/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.48it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K27me3/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K27me3/checkpoint-400/tokenizer_config.json -100%|█████████▉| 413/414 [00:33<00:00, 11.44it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K27me3/checkpoint-414 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K27me3/checkpoint-414/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.50it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K27me3/checkpoint-414/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K27me3/checkpoint-414/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 414/414 [00:34<00:00, 12.11it/s] -{'train_runtime': '34.19', 'train_samples_per_second': '1544', 'train_steps_per_second': '12.11', 'train_loss': '0.5461', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 43.78it/s] diff --git a/wandb/run-20260305_045437-0u1ivpgs/files/requirements.txt b/wandb/run-20260305_045437-0u1ivpgs/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_045437-0u1ivpgs/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 -accelerate==1.13.0 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -triton==3.6.0 -nvidia-nccl-cu12==2.27.5 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -cuda-pathfinder==1.4.0 -shellingham==1.5.4 -torchaudio==2.5.1 -nvidia-cufile-cu12==1.13.1.3 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -nvidia-nvjitlink-cu12==12.8.93 -click==8.3.1 -MarkupSafe==3.0.2 -nvidia-nvshmem-cu12==3.4.5 -urllib3==2.6.3 -cuda-bindings==12.9.4 -propcache==0.4.1 -nvidia-cusolver-cu12==11.7.3.90 -sympy==1.14.0 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -nvidia-cuda-runtime-cu12==12.8.90 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_045437-0u1ivpgs/files/wandb-metadata.json b/wandb/run-20260305_045437-0u1ivpgs/files/wandb-metadata.json deleted file mode 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Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:55:29.090626Z" - writerId: ircp478wa6sqe42gcs1xatbm5f05cyja - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_045529-49h18pcw/files/output.log b/wandb/run-20260305_045529-49h18pcw/files/output.log deleted file mode 100644 index 473d389ba9d87453943de18df156bf86cc555dd7..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_045529-49h18pcw/files/output.log +++ /dev/null @@ -1,60 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 20184.14it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -classifier.weight | MISSING | -bert.pooler.dense.bias | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 755}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 2 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 414 - Number of trainable parameters = 44,302,082 - 48%|████▊ | 199/414 [00:15<00:16, 12.85it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K36me3/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K36me3/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.52it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K36me3/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K36me3/checkpoint-200/tokenizer_config.json - 96%|█████████▋| 399/414 [00:31<00:01, 12.82it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K36me3/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K36me3/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.71it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K36me3/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K36me3/checkpoint-400/tokenizer_config.json -100%|█████████▉| 413/414 [00:33<00:00, 11.19it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K36me3/checkpoint-414 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K36me3/checkpoint-414/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.56it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K36me3/checkpoint-414/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K36me3/checkpoint-414/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 414/414 [00:34<00:00, 11.99it/s] -{'train_runtime': '34.54', 'train_samples_per_second': '1529', 'train_steps_per_second': '11.99', 'train_loss': '0.5452', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 43.75it/s] diff --git a/wandb/run-20260305_045529-49h18pcw/files/requirements.txt b/wandb/run-20260305_045529-49h18pcw/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_045529-49h18pcw/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 -accelerate==1.13.0 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -triton==3.6.0 -nvidia-nccl-cu12==2.27.5 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -cuda-pathfinder==1.4.0 -shellingham==1.5.4 -torchaudio==2.5.1 -nvidia-cufile-cu12==1.13.1.3 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -nvidia-nvjitlink-cu12==12.8.93 -click==8.3.1 -MarkupSafe==3.0.2 -nvidia-nvshmem-cu12==3.4.5 -urllib3==2.6.3 -cuda-bindings==12.9.4 -propcache==0.4.1 -nvidia-cusolver-cu12==11.7.3.90 -sympy==1.14.0 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -nvidia-cuda-runtime-cu12==12.8.90 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_045529-49h18pcw/files/wandb-metadata.json b/wandb/run-20260305_045529-49h18pcw/files/wandb-metadata.json deleted file mode 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/data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:56:21.448921Z" - writerId: jr2nvomjqulnlxemrq3veg3zh6nal65r - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_045621-vb6bnge1/files/output.log b/wandb/run-20260305_045621-vb6bnge1/files/output.log deleted file mode 100644 index b18640bca67181f6f562ddc11e48955c16d32735..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_045621-vb6bnge1/files/output.log +++ /dev/null @@ -1,60 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 18330.80it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -bert.pooler.dense.weight | MISSING | -classifier.bias | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 755}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 2 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 414 - Number of trainable parameters = 44,302,082 - 48%|████▊ | 199/414 [00:16<00:16, 13.02it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me1/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me1/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.51it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me1/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me1/checkpoint-200/tokenizer_config.json - 96%|█████████▋| 399/414 [00:32<00:01, 12.78it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me1/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me1/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.59it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me1/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me1/checkpoint-400/tokenizer_config.json -100%|█████████▉| 413/414 [00:34<00:00, 11.38it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me1/checkpoint-414 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me1/checkpoint-414/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.81it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me1/checkpoint-414/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me1/checkpoint-414/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 414/414 [00:34<00:00, 11.88it/s] -{'train_runtime': '34.86', 'train_samples_per_second': '1515', 'train_steps_per_second': '11.88', 'train_loss': '0.6189', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 43.92it/s] diff --git a/wandb/run-20260305_045621-vb6bnge1/files/requirements.txt b/wandb/run-20260305_045621-vb6bnge1/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_045621-vb6bnge1/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:57:13.844988Z" - writerId: sqhydwlk23d6c6rxq0jkp1hna2okbxie - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_045713-nhupfaag/files/output.log b/wandb/run-20260305_045713-nhupfaag/files/output.log deleted file mode 100644 index ccdbce6e7d22615561f5c259c09f25f4f6762b71..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_045713-nhupfaag/files/output.log +++ /dev/null @@ -1,60 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 14036.14it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -classifier.weight | MISSING | -bert.pooler.dense.weight | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 755}. -***** Running training ***** - Num examples = 25,710 - Num Epochs = 2 - Num update steps per epoch = 201 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 402 - Number of trainable parameters = 44,302,082 - 50%|████▉ | 199/402 [00:15<00:15, 13.09it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me2/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me2/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.47it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me2/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me2/checkpoint-200/tokenizer_config.json - 99%|█████████▉| 399/402 [00:31<00:00, 13.11it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me2/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me2/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.70it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me2/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me2/checkpoint-400/tokenizer_config.json -100%|█████████▉| 401/402 [00:32<00:00, 5.33it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me2/checkpoint-402 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me2/checkpoint-402/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.41it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me2/checkpoint-402/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me2/checkpoint-402/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 402/402 [00:33<00:00, 11.97it/s] -{'train_runtime': '33.57', 'train_samples_per_second': '1532', 'train_steps_per_second': '11.97', 'train_loss': '0.565', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3215 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 44.70it/s] diff --git a/wandb/run-20260305_045713-nhupfaag/files/requirements.txt b/wandb/run-20260305_045713-nhupfaag/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_045713-nhupfaag/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 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- --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "547052232704" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - 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/data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:58:05.254580Z" - writerId: rsxfjsw7ovby63hbxiq39k7j1skpn4ii - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_045805-q6udn5as/files/output.log b/wandb/run-20260305_045805-q6udn5as/files/output.log deleted file mode 100644 index 7ddb5149e2574685fde426983e53105a56e73a63..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_045805-q6udn5as/files/output.log +++ /dev/null @@ -1,55 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 22866.50it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -bert.pooler.dense.weight | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.weight | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 755}. -***** Running training ***** - Num examples = 14,595 - Num Epochs = 2 - Num update steps per epoch = 115 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 230 - Number of trainable parameters = 44,302,082 - 87%|████████▋ | 199/230 [00:15<00:02, 12.91it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me3/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me3/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.12it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me3/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me3/checkpoint-200/tokenizer_config.json -100%|█████████▉| 229/230 [00:19<00:00, 12.94it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me3/checkpoint-230 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me3/checkpoint-230/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.25it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me3/checkpoint-230/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me3/checkpoint-230/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 230/230 [00:19<00:00, 11.65it/s] -{'train_runtime': '19.74', 'train_samples_per_second': '1479', 'train_steps_per_second': '11.65', 'train_loss': '0.4853', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 1825 - Batch size = 128 -100%|██████████| 15/15 [00:00<00:00, 46.85it/s] diff --git a/wandb/run-20260305_045805-q6udn5as/files/requirements.txt b/wandb/run-20260305_045805-q6udn5as/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_045805-q6udn5as/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 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/data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:58:39.203801Z" - writerId: 1dxd4swqkctq2noelw3t4yxdv6ne0k3t - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_045839-uo42pjbt/files/output.log b/wandb/run-20260305_045839-uo42pjbt/files/output.log deleted file mode 100644 index 7269677960dfda41fd758683c7f30b6515747291..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_045839-uo42pjbt/files/output.log +++ /dev/null @@ -1,55 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 20135.21it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -bert.pooler.dense.weight | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.weight | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 755}. -***** Running training ***** - Num examples = 19,422 - Num Epochs = 2 - Num update steps per epoch = 152 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 304 - Number of trainable parameters = 44,302,082 - 65%|██████▌ | 199/304 [00:15<00:08, 13.12it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K9ac/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K9ac/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.69it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K9ac/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K9ac/checkpoint-200/tokenizer_config.json -100%|█████████▉| 303/304 [00:24<00:00, 13.09it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K9ac/checkpoint-304 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K9ac/checkpoint-304/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.98it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K9ac/checkpoint-304/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K9ac/checkpoint-304/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 304/304 [00:25<00:00, 12.00it/s] -{'train_runtime': '25.33', 'train_samples_per_second': '1534', 'train_steps_per_second': '12', 'train_loss': '0.5826', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 2429 - Batch size = 128 -100%|██████████| 19/19 [00:00<00:00, 42.96it/s] diff --git a/wandb/run-20260305_045839-uo42pjbt/files/requirements.txt b/wandb/run-20260305_045839-uo42pjbt/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_045839-uo42pjbt/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T04:59:20.695454Z" - writerId: w19q2zkqamfxspijhxbncsjo5z1rd4at - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_045920-pcna4urr/files/output.log b/wandb/run-20260305_045920-pcna4urr/files/output.log deleted file mode 100644 index 3d3bec67a09c21c8cab5ba2698fda79ed69a33b0..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_045920-pcna4urr/files/output.log +++ /dev/null @@ -1,55 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 15743.45it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -classifier.weight | MISSING | -classifier.bias | MISSING | -bert.pooler.dense.weight | MISSING | -bert.pooler.dense.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 755}. -***** Running training ***** - Num examples = 22,630 - Num Epochs = 2 - Num update steps per epoch = 177 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 354 - Number of trainable parameters = 44,302,082 - 56%|█████▋ | 200/354 [00:16<00:11, 12.96it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K9me3/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K9me3/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.54it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K9me3/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K9me3/checkpoint-200/tokenizer_config.json -100%|██████████| 354/354 [00:29<00:00, 13.38it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K9me3/checkpoint-354 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K9me3/checkpoint-354/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.66it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K9me3/checkpoint-354/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K9me3/checkpoint-354/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 354/354 [00:30<00:00, 11.66it/s] -{'train_runtime': '30.36', 'train_samples_per_second': '1491', 'train_steps_per_second': '11.66', 'train_loss': '0.6671', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 2830 - Batch size = 128 -100%|██████████| 23/23 [00:00<00:00, 43.12it/s] diff --git a/wandb/run-20260305_045920-pcna4urr/files/requirements.txt b/wandb/run-20260305_045920-pcna4urr/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_045920-pcna4urr/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 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Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T05:00:08.346678Z" - writerId: mx9p2j9wat11rdtvul601ojymx9120r6 - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_050008-3nefo53q/files/output.log b/wandb/run-20260305_050008-3nefo53q/files/output.log deleted file mode 100644 index b66d2994367472aa793e818fb65a649ae4b52f11..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_050008-3nefo53q/files/output.log +++ /dev/null @@ -1,60 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 9092.02it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -classifier.bias | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.weight | MISSING | -bert.pooler.dense.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 755}. -***** Running training ***** - Num examples = 25,816 - Num Epochs = 2 - Num update steps per epoch = 202 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 404 - Number of trainable parameters = 44,302,082 - 49%|████▉ | 199/404 [00:15<00:15, 12.82it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H4K20me1/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H4K20me1/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.09it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H4K20me1/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H4K20me1/checkpoint-200/tokenizer_config.json - 99%|█████████▉| 399/404 [00:32<00:00, 12.66it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H4K20me1/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H4K20me1/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.98it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H4K20me1/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H4K20me1/checkpoint-400/tokenizer_config.json -100%|█████████▉| 403/404 [00:33<00:00, 6.47it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H4K20me1/checkpoint-404 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H4K20me1/checkpoint-404/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.50it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H4K20me1/checkpoint-404/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/H4K20me1/checkpoint-404/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 404/404 [00:33<00:00, 11.93it/s] -{'train_runtime': '33.87', 'train_samples_per_second': '1524', 'train_steps_per_second': '11.93', 'train_loss': '0.5072', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3227 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 44.59it/s] diff --git a/wandb/run-20260305_050008-3nefo53q/files/requirements.txt b/wandb/run-20260305_050008-3nefo53q/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_050008-3nefo53q/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 -accelerate==1.13.0 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -triton==3.6.0 -nvidia-nccl-cu12==2.27.5 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -cuda-pathfinder==1.4.0 -shellingham==1.5.4 -torchaudio==2.5.1 -nvidia-cufile-cu12==1.13.1.3 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -nvidia-nvjitlink-cu12==12.8.93 -click==8.3.1 -MarkupSafe==3.0.2 -nvidia-nvshmem-cu12==3.4.5 -urllib3==2.6.3 -cuda-bindings==12.9.4 -propcache==0.4.1 -nvidia-cusolver-cu12==11.7.3.90 -sympy==1.14.0 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -nvidia-cuda-runtime-cu12==12.8.90 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_050008-3nefo53q/files/wandb-metadata.json b/wandb/run-20260305_050008-3nefo53q/files/wandb-metadata.json deleted file mode 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/data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T05:01:00.568842Z" - writerId: cjfrzj08shdlacrz90qqppfloujjpg4m - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_050100-56e8zy5n/files/output.log b/wandb/run-20260305_050100-56e8zy5n/files/output.log deleted file mode 100644 index 87927f6b56e5141b4c217ca21e73c62000fe8ea1..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_050100-56e8zy5n/files/output.log +++ /dev/null @@ -1,69 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 24750.22it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_reg/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -bert.pooler.dense.bias | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 4 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 828 - Number of trainable parameters = 45,088,514 - 24%|██▍ | 199/828 [00:08<00:25, 24.35it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/enhancers/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/enhancers/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.21it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/enhancers/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/enhancers/checkpoint-200/tokenizer_config.json - 48%|████▊ | 400/828 [00:18<00:17, 24.37it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/enhancers/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/enhancers/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.04it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/enhancers/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/enhancers/checkpoint-400/tokenizer_config.json - 72%|███████▏ | 598/828 [00:27<00:09, 24.61it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/enhancers/checkpoint-600 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/enhancers/checkpoint-600/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.59it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/enhancers/checkpoint-600/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/enhancers/checkpoint-600/tokenizer_config.json - 96%|█████████▋| 799/828 [00:36<00:01, 24.49it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/enhancers/checkpoint-800 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/enhancers/checkpoint-800/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.40it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/enhancers/checkpoint-800/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/enhancers/checkpoint-800/tokenizer_config.json -100%|█████████▉| 826/828 [00:38<00:00, 21.82it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/enhancers/checkpoint-828 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/enhancers/checkpoint-828/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.98it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/enhancers/checkpoint-828/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/enhancers/checkpoint-828/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 828/828 [00:38<00:00, 21.30it/s] -{'train_runtime': '38.87', 'train_samples_per_second': '2717', 'train_steps_per_second': '21.3', 'train_loss': '0.5709', 'epoch': '4'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 79.98it/s] diff --git a/wandb/run-20260305_050100-56e8zy5n/files/requirements.txt b/wandb/run-20260305_050100-56e8zy5n/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_050100-56e8zy5n/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 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wandb-AsyncioManager-main:2794545 [mailbox.py:close():155] Closing mailbox, abandoning 1 handles. diff --git a/wandb/run-20260305_050100-56e8zy5n/run-56e8zy5n.wandb b/wandb/run-20260305_050100-56e8zy5n/run-56e8zy5n.wandb deleted file mode 100644 index 665d9a379d30a3ff0ed4073b994f56ccb018a0e2..0000000000000000000000000000000000000000 Binary files a/wandb/run-20260305_050100-56e8zy5n/run-56e8zy5n.wandb and /dev/null differ diff --git a/wandb/run-20260305_050154-dn8q78i3/files/config.yaml b/wandb/run-20260305_050154-dn8q78i3/files/config.yaml deleted file mode 100644 index 56cd0802e5442da8bc11e67c80767ed2393bd68d..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_050154-dn8q78i3/files/config.yaml +++ /dev/null @@ -1,139 +0,0 @@ -_wandb: - value: - cli_version: 0.25.0 - e: - nqkh3vuapoxymsdroehv12jf3fw94idq: - args: - - --model_name_or_path - - /home/n5huang/dna_token/pretrain/models/model_len_reg/checkpoint-100000 - - --tokenizer_path - - /home/n5huang/dna_token/tokenizer_evaluation/baseline_bpe/tokenizer.json - - --trust_remote_code - - "True" - - --data_path - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/enhancers_types/split - - --kmer - - "-1" - - --run_name - - hg38_BPE_len_reg__baseline_bpe_tokenizer_3e-5_enhancers_types_seed42 - - --model_max_length - - "100" - - --per_device_train_batch_size - - "128" - - --per_device_eval_batch_size - - "128" - - --gradient_accumulation_steps - - "1" - - --learning_rate - - "3e-5" - - --num_train_epochs - - "4" - - --fp16 - - --save_steps - - "200" - - --output_dir - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/enhancers_types - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "547061575680" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T05:01:54.801468Z" - writerId: nqkh3vuapoxymsdroehv12jf3fw94idq - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_050154-dn8q78i3/files/output.log b/wandb/run-20260305_050154-dn8q78i3/files/output.log deleted file mode 100644 index 52d5d7cead7271a8a103d6e4130afc7c7eabecee..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_050154-dn8q78i3/files/output.log +++ /dev/null @@ -1,69 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 15385.51it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_reg/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -bert.pooler.dense.weight | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 4 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 828 - Number of trainable parameters = 45,089,283 - 24%|██▍ | 199/828 [00:08<00:26, 23.30it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/enhancers_types/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/enhancers_types/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.06it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/enhancers_types/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/enhancers_types/checkpoint-200/tokenizer_config.json - 48%|████▊ | 400/828 [00:18<00:18, 23.21it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/enhancers_types/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/enhancers_types/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.15it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/enhancers_types/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/enhancers_types/checkpoint-400/tokenizer_config.json - 72%|███████▏ | 598/828 [00:27<00:09, 23.15it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/enhancers_types/checkpoint-600 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/enhancers_types/checkpoint-600/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.59it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/enhancers_types/checkpoint-600/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/enhancers_types/checkpoint-600/tokenizer_config.json - 96%|█████████▋| 799/828 [00:36<00:01, 23.84it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/enhancers_types/checkpoint-800 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/enhancers_types/checkpoint-800/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.28it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/enhancers_types/checkpoint-800/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/enhancers_types/checkpoint-800/tokenizer_config.json -100%|█████████▉| 826/828 [00:37<00:00, 22.02it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/enhancers_types/checkpoint-828 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/enhancers_types/checkpoint-828/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.43it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/enhancers_types/checkpoint-828/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/enhancers_types/checkpoint-828/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 828/828 [00:38<00:00, 21.34it/s] -{'train_runtime': '38.8', 'train_samples_per_second': '2721', 'train_steps_per_second': '21.34', 'train_loss': '0.7039', 'epoch': '4'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 81.66it/s] diff --git a/wandb/run-20260305_050154-dn8q78i3/files/requirements.txt b/wandb/run-20260305_050154-dn8q78i3/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_050154-dn8q78i3/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 -accelerate==1.13.0 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -triton==3.6.0 -nvidia-nccl-cu12==2.27.5 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -cuda-pathfinder==1.4.0 -shellingham==1.5.4 -torchaudio==2.5.1 -nvidia-cufile-cu12==1.13.1.3 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -nvidia-nvjitlink-cu12==12.8.93 -click==8.3.1 -MarkupSafe==3.0.2 -nvidia-nvshmem-cu12==3.4.5 -urllib3==2.6.3 -cuda-bindings==12.9.4 -propcache==0.4.1 -nvidia-cusolver-cu12==11.7.3.90 -sympy==1.14.0 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -nvidia-cuda-runtime-cu12==12.8.90 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_050154-dn8q78i3/files/wandb-metadata.json b/wandb/run-20260305_050154-dn8q78i3/files/wandb-metadata.json deleted file mode 100644 index fe9e4ecd97f5118b158216136a5ec583adfd5018..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_050154-dn8q78i3/files/wandb-metadata.json +++ /dev/null @@ -1,134 +0,0 @@ -{ - "os": "Linux-5.15.0-72-generic-x86_64-with-glibc2.35", - "python": "CPython 3.10.19", - "startedAt": "2026-03-05T05:01:54.801468Z", - "args": [ - "--model_name_or_path", - "/home/n5huang/dna_token/pretrain/models/model_len_reg/checkpoint-100000", - "--tokenizer_path", - "/home/n5huang/dna_token/tokenizer_evaluation/baseline_bpe/tokenizer.json", - "--trust_remote_code", - "True", - "--data_path", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/enhancers_types/split", - "--kmer", - "-1", - "--run_name", - "hg38_BPE_len_reg__baseline_bpe_tokenizer_3e-5_enhancers_types_seed42", - "--model_max_length", - "100", - "--per_device_train_batch_size", - "128", - "--per_device_eval_batch_size", - "128", - 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memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T05:02:48.039063Z" - writerId: anpbfe7z9it8opmebk8yyvdvme3tdx17 - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_050248-qr7kw8vd/files/output.log b/wandb/run-20260305_050248-qr7kw8vd/files/output.log deleted file mode 100644 index 8a292dff4918eb87ef8e24b652df3508bf3ca5d4..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_050248-qr7kw8vd/files/output.log +++ /dev/null @@ -1,54 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 22676.77it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_reg/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -classifier.weight | MISSING | -classifier.bias | MISSING | -bert.pooler.dense.bias | MISSING | -bert.pooler.dense.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 25,267 - Num Epochs = 2 - Num update steps per epoch = 198 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 396 - Number of trainable parameters = 45,088,514 - 50%|█████ | 199/396 [00:08<00:07, 27.64it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/promoter_all/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/promoter_all/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.12it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/promoter_all/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/promoter_all/checkpoint-200/tokenizer_config.json - 99%|█████████▉| 394/396 [00:16<00:00, 27.61it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/promoter_all/checkpoint-396 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/promoter_all/checkpoint-396/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.31it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/promoter_all/checkpoint-396/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/promoter_all/checkpoint-396/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 396/396 [00:17<00:00, 23.02it/s] -{'train_runtime': '17.2', 'train_samples_per_second': '2939', 'train_steps_per_second': '23.03', 'train_loss': '0.3866', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3159 - Batch size = 128 -100%|██████████| 25/25 [00:00<00:00, 90.10it/s] diff --git a/wandb/run-20260305_050248-qr7kw8vd/files/requirements.txt b/wandb/run-20260305_050248-qr7kw8vd/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_050248-qr7kw8vd/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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/data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T05:03:18.495394Z" - writerId: tbh44dfuupvwcschwusd4pgb5kv0wf7w - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_050318-nlfpso96/files/output.log b/wandb/run-20260305_050318-nlfpso96/files/output.log deleted file mode 100644 index fd90ac911e385fac46deba0cce85feebd5ee77eb..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_050318-nlfpso96/files/output.log +++ /dev/null @@ -1,54 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 22556.02it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_reg/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -classifier.weight | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.bias | MISSING | -bert.pooler.dense.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 25,097 - Num Epochs = 2 - Num update steps per epoch = 197 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 394 - Number of trainable parameters = 45,088,514 - 51%|█████ | 200/394 [00:07<00:06, 28.24it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/promoter_no_tata/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/promoter_no_tata/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.65it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/promoter_no_tata/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/promoter_no_tata/checkpoint-200/tokenizer_config.json - 99%|█████████▉| 392/394 [00:15<00:00, 28.77it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/promoter_no_tata/checkpoint-394 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/promoter_no_tata/checkpoint-394/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.44it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/promoter_no_tata/checkpoint-394/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/promoter_no_tata/checkpoint-394/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 394/394 [00:16<00:00, 24.48it/s] -{'train_runtime': '16.09', 'train_samples_per_second': '3119', 'train_steps_per_second': '24.48', 'train_loss': '0.3685', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3138 - Batch size = 128 -100%|██████████| 25/25 [00:00<00:00, 94.13it/s] diff --git a/wandb/run-20260305_050318-nlfpso96/files/requirements.txt b/wandb/run-20260305_050318-nlfpso96/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_050318-nlfpso96/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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--find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "547066343424" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T05:03:53.080868Z" - writerId: a4gpbwbbtw2x1l8vexel3g7mxmqenca2 - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_050353-ne2ts5o4/files/output.log b/wandb/run-20260305_050353-ne2ts5o4/files/output.log deleted file mode 100644 index d1d65722efd38358b4787e9abe93e6a97516176d..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_050353-ne2ts5o4/files/output.log +++ /dev/null @@ -1,49 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 23641.09it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_reg/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.decoder.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -bert.pooler.dense.weight | MISSING | -classifier.weight | MISSING | -classifier.bias | MISSING | -bert.pooler.dense.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 4,219 - Num Epochs = 2 - Num update steps per epoch = 33 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 66 - Number of trainable parameters = 45,088,514 - 97%|█████████▋| 64/66 [00:02<00:00, 28.32it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/promoter_tata/checkpoint-66 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/promoter_tata/checkpoint-66/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.91it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/promoter_tata/checkpoint-66/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/promoter_tata/checkpoint-66/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 66/66 [00:03<00:00, 17.86it/s] -{'train_runtime': '3.694', 'train_samples_per_second': '2284', 'train_steps_per_second': '17.87', 'train_loss': '0.5513', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 528 - Batch size = 128 -100%|██████████| 5/5 [00:00<00:00, 107.50it/s] diff --git a/wandb/run-20260305_050353-ne2ts5o4/files/requirements.txt b/wandb/run-20260305_050353-ne2ts5o4/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_050353-ne2ts5o4/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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- - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/splice_sites_acceptors/split - - --kmer - - "-1" - - --run_name - - hg38_BPE_len_reg__baseline_bpe_tokenizer_3e-5_splice_sites_acceptors_seed42 - - --model_max_length - - "140" - - --per_device_train_batch_size - - "128" - - --per_device_eval_batch_size - - "128" - - --gradient_accumulation_steps - - "1" - - --learning_rate - - "3e-5" - - --num_train_epochs - - "4" - - --fp16 - - --save_steps - - "200" - - --output_dir - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/splice_sites_acceptors - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "547065724928" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T05:04:07.728611Z" - writerId: ejvhfuuuyegs4ftsc1qcncx6n9pqumy0 - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_050407-yqernv9u/files/output.log b/wandb/run-20260305_050407-yqernv9u/files/output.log deleted file mode 100644 index 285b904fb30f3d76ec37e0306e430f7b23038de7..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_050407-yqernv9u/files/output.log +++ /dev/null @@ -1,69 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 22408.08it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_reg/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.decoder.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -bert.pooler.dense.bias | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 4 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 828 - Number of trainable parameters = 45,088,514 - 24%|██▍ | 199/828 [00:11<00:35, 17.74it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.45it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-200/tokenizer_config.json - 48%|████▊ | 400/828 [00:23<00:24, 17.47it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.47it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-400/tokenizer_config.json - 72%|███████▏ | 599/828 [00:36<00:13, 17.47it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-600 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-600/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.93it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-600/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-600/tokenizer_config.json - 96%|█████████▋| 799/828 [00:48<00:01, 17.35it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-800 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-800/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.10it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-800/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-800/tokenizer_config.json -100%|█████████▉| 827/828 [00:50<00:00, 17.25it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-828 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-828/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.31it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-828/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-828/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 828/828 [00:51<00:00, 16.14it/s] -{'train_runtime': '51.29', 'train_samples_per_second': '2059', 'train_steps_per_second': '16.14', 'train_loss': '0.6061', 'epoch': '4'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 58.13it/s] diff --git a/wandb/run-20260305_050407-yqernv9u/files/requirements.txt b/wandb/run-20260305_050407-yqernv9u/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_050407-yqernv9u/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 -accelerate==1.13.0 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -triton==3.6.0 -nvidia-nccl-cu12==2.27.5 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -cuda-pathfinder==1.4.0 -shellingham==1.5.4 -torchaudio==2.5.1 -nvidia-cufile-cu12==1.13.1.3 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -nvidia-nvjitlink-cu12==12.8.93 -click==8.3.1 -MarkupSafe==3.0.2 -nvidia-nvshmem-cu12==3.4.5 -urllib3==2.6.3 -cuda-bindings==12.9.4 -propcache==0.4.1 -nvidia-cusolver-cu12==11.7.3.90 -sympy==1.14.0 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -nvidia-cuda-runtime-cu12==12.8.90 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_050407-yqernv9u/files/wandb-metadata.json b/wandb/run-20260305_050407-yqernv9u/files/wandb-metadata.json deleted file mode 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/home/n5huang/dna_token/pretrain/models/model_len_reg/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -bert.pooler.dense.weight | MISSING | -classifier.bias | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 4 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 828 - Number of trainable parameters = 45,089,283 - 24%|██▍ | 199/828 [00:11<00:35, 17.59it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/splice_sites_all/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/splice_sites_all/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.60it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/splice_sites_all/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/splice_sites_all/checkpoint-200/tokenizer_config.json - 48%|████▊ | 399/828 [00:24<00:25, 17.04it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/splice_sites_all/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/splice_sites_all/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.60it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/splice_sites_all/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/splice_sites_all/checkpoint-400/tokenizer_config.json - 72%|███████▏ | 600/828 [00:36<00:12, 17.56it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/splice_sites_all/checkpoint-600 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/splice_sites_all/checkpoint-600/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.59it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/splice_sites_all/checkpoint-600/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/splice_sites_all/checkpoint-600/tokenizer_config.json - 96%|█████████▋| 799/828 [00:48<00:01, 17.41it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/splice_sites_all/checkpoint-800 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/splice_sites_all/checkpoint-800/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.26it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/splice_sites_all/checkpoint-800/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/splice_sites_all/checkpoint-800/tokenizer_config.json -100%|█████████▉| 827/828 [00:50<00:00, 16.61it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/splice_sites_all/checkpoint-828 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/splice_sites_all/checkpoint-828/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.17it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/splice_sites_all/checkpoint-828/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/splice_sites_all/checkpoint-828/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 828/828 [00:51<00:00, 16.00it/s] -{'train_runtime': '51.74', 'train_samples_per_second': '2041', 'train_steps_per_second': '16', 'train_loss': '0.9928', 'epoch': '4'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 60.30it/s] diff --git a/wandb/run-20260305_050514-oiqj9wuv/files/requirements.txt b/wandb/run-20260305_050514-oiqj9wuv/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_050514-oiqj9wuv/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 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wandb-AsyncioManager-main:2920991 [mailbox.py:close():155] Closing mailbox, abandoning 1 handles. diff --git a/wandb/run-20260305_050514-oiqj9wuv/run-oiqj9wuv.wandb b/wandb/run-20260305_050514-oiqj9wuv/run-oiqj9wuv.wandb deleted file mode 100644 index 64b9c6a3c3ea1133988f6676ce749d04bd7feebf..0000000000000000000000000000000000000000 Binary files a/wandb/run-20260305_050514-oiqj9wuv/run-oiqj9wuv.wandb and /dev/null differ diff --git a/wandb/run-20260305_050621-3q97bj28/files/config.yaml b/wandb/run-20260305_050621-3q97bj28/files/config.yaml deleted file mode 100644 index b9171e0f40de3f45ef3757d040320aa1b654b2d0..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_050621-3q97bj28/files/config.yaml +++ /dev/null @@ -1,139 +0,0 @@ -_wandb: - value: - cli_version: 0.25.0 - e: - icc6hq19w3hadvmpnfkaimll8horzmr4: - args: - - --model_name_or_path - - /home/n5huang/dna_token/pretrain/models/model_len_reg/checkpoint-100000 - - --tokenizer_path - - /home/n5huang/dna_token/tokenizer_evaluation/baseline_bpe/tokenizer.json - - --trust_remote_code - - "True" - - --data_path - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/splice_sites_donors/split - - --kmer - - "-1" - - --run_name - - hg38_BPE_len_reg__baseline_bpe_tokenizer_3e-5_splice_sites_donors_seed42 - - --model_max_length - - "140" - - --per_device_train_batch_size - - "128" - - --per_device_eval_batch_size - - "128" - - --gradient_accumulation_steps - - "1" - - --learning_rate - - "3e-5" - - --num_train_epochs - - "4" - - --fp16 - - --save_steps - - "200" - - --output_dir - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/splice_sites_donors - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "547070689280" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T05:06:21.380198Z" - writerId: icc6hq19w3hadvmpnfkaimll8horzmr4 - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_050621-3q97bj28/files/output.log b/wandb/run-20260305_050621-3q97bj28/files/output.log deleted file mode 100644 index 090758d04faaaf12c2a4a330cd18787cf83e03f1..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_050621-3q97bj28/files/output.log +++ /dev/null @@ -1,69 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 19092.51it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_reg/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -classifier.weight | MISSING | -bert.pooler.dense.bias | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 4 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 828 - Number of trainable parameters = 45,088,514 - 24%|██▍ | 199/828 [00:12<00:35, 17.53it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 2.96it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-200/tokenizer_config.json - 48%|████▊ | 400/828 [00:24<00:24, 17.52it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.74it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-400/tokenizer_config.json - 72%|███████▏ | 599/828 [00:37<00:13, 16.79it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-600 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-600/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.02it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-600/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-600/tokenizer_config.json - 97%|█████████▋| 800/828 [00:49<00:01, 17.51it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-800 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-800/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.93it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-800/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-800/tokenizer_config.json -100%|█████████▉| 826/828 [00:52<00:00, 16.81it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-828 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-828/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.92it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-828/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-828/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 828/828 [00:53<00:00, 15.58it/s] -{'train_runtime': '53.13', 'train_samples_per_second': '1988', 'train_steps_per_second': '15.59', 'train_loss': '0.5496', 'epoch': '4'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 59.75it/s] diff --git a/wandb/run-20260305_050621-3q97bj28/files/requirements.txt b/wandb/run-20260305_050621-3q97bj28/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_050621-3q97bj28/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 -accelerate==1.13.0 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -triton==3.6.0 -nvidia-nccl-cu12==2.27.5 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -cuda-pathfinder==1.4.0 -shellingham==1.5.4 -torchaudio==2.5.1 -nvidia-cufile-cu12==1.13.1.3 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -nvidia-nvjitlink-cu12==12.8.93 -click==8.3.1 -MarkupSafe==3.0.2 -nvidia-nvshmem-cu12==3.4.5 -urllib3==2.6.3 -cuda-bindings==12.9.4 -propcache==0.4.1 -nvidia-cusolver-cu12==11.7.3.90 -sympy==1.14.0 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -nvidia-cuda-runtime-cu12==12.8.90 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_050621-3q97bj28/files/wandb-metadata.json b/wandb/run-20260305_050621-3q97bj28/files/wandb-metadata.json deleted file mode 100644 index 5932a15d2b93c42167e1eda5f765be75caba2499..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_050621-3q97bj28/files/wandb-metadata.json +++ /dev/null @@ -1,134 +0,0 @@ -{ - "os": "Linux-5.15.0-72-generic-x86_64-with-glibc2.35", - "python": "CPython 3.10.19", - "startedAt": "2026-03-05T05:06:21.380198Z", - "args": [ - "--model_name_or_path", - "/home/n5huang/dna_token/pretrain/models/model_len_reg/checkpoint-100000", - "--tokenizer_path", - "/home/n5huang/dna_token/tokenizer_evaluation/baseline_bpe/tokenizer.json", - "--trust_remote_code", - "True", - "--data_path", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/splice_sites_donors/split", - "--kmer", - "-1", - "--run_name", - "hg38_BPE_len_reg__baseline_bpe_tokenizer_3e-5_splice_sites_donors_seed42", - "--model_max_length", - "140", - "--per_device_train_batch_size", - "128", - "--per_device_eval_batch_size", - "128", - 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"2026-03-05T05:07:29.625295Z" - writerId: yjcxrg5g4vglzvg065asfpse9e4uz0rg - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_050729-3w3exu8r/files/output.log b/wandb/run-20260305_050729-3w3exu8r/files/output.log deleted file mode 100644 index 52e451fea8fcd66ff5e30ada5d49752bdb7603b6..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_050729-3w3exu8r/files/output.log +++ /dev/null @@ -1,59 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 21964.26it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_reg/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -bert.pooler.dense.bias | MISSING | -classifier.bias | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 2 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 414 - Number of trainable parameters = 45,088,514 - 48%|████▊ | 199/414 [00:17<00:18, 11.63it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H2AFZ/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H2AFZ/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.68it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H2AFZ/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H2AFZ/checkpoint-200/tokenizer_config.json - 96%|█████████▋| 399/414 [00:35<00:01, 11.61it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H2AFZ/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H2AFZ/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.80it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H2AFZ/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H2AFZ/checkpoint-400/tokenizer_config.json -100%|█████████▉| 413/414 [00:37<00:00, 9.84it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H2AFZ/checkpoint-414 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H2AFZ/checkpoint-414/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.95it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H2AFZ/checkpoint-414/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H2AFZ/checkpoint-414/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 414/414 [00:38<00:00, 10.71it/s] -{'train_runtime': '38.64', 'train_samples_per_second': '1366', 'train_steps_per_second': '10.71', 'train_loss': '0.598', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 39.98it/s] diff --git a/wandb/run-20260305_050729-3w3exu8r/files/requirements.txt b/wandb/run-20260305_050729-3w3exu8r/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_050729-3w3exu8r/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T05:08:25.617775Z" - writerId: 01nzbvf66h15w8mhlr9bubb0o5sqo5r8 - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_050825-es9xouas/files/output.log b/wandb/run-20260305_050825-es9xouas/files/output.log deleted file mode 100644 index 4591f6b301b2c176b52478a8309bf228130fbc1f..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_050825-es9xouas/files/output.log +++ /dev/null @@ -1,54 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 20963.22it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_reg/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.decoder.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -bert.pooler.dense.bias | MISSING | -classifier.bias | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 25,292 - Num Epochs = 2 - Num update steps per epoch = 198 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 396 - Number of trainable parameters = 45,088,514 - 50%|█████ | 199/396 [00:17<00:16, 11.80it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H3K27ac/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H3K27ac/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.69it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H3K27ac/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H3K27ac/checkpoint-200/tokenizer_config.json -100%|█████████▉| 395/396 [00:35<00:00, 11.50it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H3K27ac/checkpoint-396 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H3K27ac/checkpoint-396/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.84it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H3K27ac/checkpoint-396/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H3K27ac/checkpoint-396/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 396/396 [00:36<00:00, 10.88it/s] -{'train_runtime': '36.39', 'train_samples_per_second': '1390', 'train_steps_per_second': '10.88', 'train_loss': '0.6094', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3163 - Batch size = 128 -100%|██████████| 25/25 [00:00<00:00, 40.59it/s] diff --git a/wandb/run-20260305_050825-es9xouas/files/requirements.txt b/wandb/run-20260305_050825-es9xouas/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_050825-es9xouas/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 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/data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T05:09:19.211288Z" - writerId: q7036opv2mzlezfjq4dghefdsm23mpgt - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_050919-59317kt9/files/output.log b/wandb/run-20260305_050919-59317kt9/files/output.log deleted file mode 100644 index d24738901ef89aa007d01b74dafeaa2db8434afc..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_050919-59317kt9/files/output.log +++ /dev/null @@ -1,59 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 25247.32it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_reg/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -classifier.weight | MISSING | -classifier.bias | MISSING | -bert.pooler.dense.weight | MISSING | -bert.pooler.dense.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 2 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 414 - Number of trainable parameters = 45,088,514 - 48%|████▊ | 199/414 [00:17<00:18, 11.47it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H3K27me3/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H3K27me3/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.33it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H3K27me3/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H3K27me3/checkpoint-200/tokenizer_config.json - 96%|█████████▋| 399/414 [00:35<00:01, 11.45it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H3K27me3/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H3K27me3/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.82it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H3K27me3/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H3K27me3/checkpoint-400/tokenizer_config.json -100%|█████████▉| 413/414 [00:37<00:00, 9.84it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H3K27me3/checkpoint-414 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H3K27me3/checkpoint-414/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.84it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H3K27me3/checkpoint-414/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H3K27me3/checkpoint-414/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 414/414 [00:38<00:00, 10.78it/s] -{'train_runtime': '38.39', 'train_samples_per_second': '1375', 'train_steps_per_second': '10.79', 'train_loss': '0.5525', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 40.28it/s] diff --git a/wandb/run-20260305_050919-59317kt9/files/requirements.txt b/wandb/run-20260305_050919-59317kt9/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_050919-59317kt9/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 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/data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T05:10:15.653871Z" - writerId: xt42exucdoqky0gtmc701crrbdzw9lpe - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_051015-lwqk9g89/files/output.log b/wandb/run-20260305_051015-lwqk9g89/files/output.log deleted file mode 100644 index 6b9c8541fb4d414754433addf19843d97879494d..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_051015-lwqk9g89/files/output.log +++ /dev/null @@ -1,59 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 18023.52it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_reg/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -bert.pooler.dense.bias | MISSING | -classifier.bias | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 2 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 414 - Number of trainable parameters = 45,088,514 - 48%|████▊ | 199/414 [00:17<00:18, 11.59it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H3K36me3/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H3K36me3/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.30it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H3K36me3/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H3K36me3/checkpoint-200/tokenizer_config.json - 96%|█████████▋| 399/414 [00:35<00:01, 11.56it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H3K36me3/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H3K36me3/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.85it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H3K36me3/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H3K36me3/checkpoint-400/tokenizer_config.json -100%|█████████▉| 413/414 [00:37<00:00, 10.18it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H3K36me3/checkpoint-414 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H3K36me3/checkpoint-414/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.92it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H3K36me3/checkpoint-414/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H3K36me3/checkpoint-414/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 414/414 [00:37<00:00, 10.90it/s] -{'train_runtime': '38', 'train_samples_per_second': '1390', 'train_steps_per_second': '10.89', 'train_loss': '0.5515', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 40.31it/s] diff --git a/wandb/run-20260305_051015-lwqk9g89/files/requirements.txt b/wandb/run-20260305_051015-lwqk9g89/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_051015-lwqk9g89/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T05:11:11.623960Z" - writerId: dix2q45zw5u2aqhq0pfoi06gdbj3upcx - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_051111-y6jtosvf/files/output.log b/wandb/run-20260305_051111-y6jtosvf/files/output.log deleted file mode 100644 index 36dd1ca38cbc7c4ad89582507f7126894230dc0a..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_051111-y6jtosvf/files/output.log +++ /dev/null @@ -1,59 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 21857.73it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_reg/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -bert.pooler.dense.weight | MISSING | -classifier.weight | MISSING | -classifier.bias | MISSING | -bert.pooler.dense.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 2 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 414 - Number of trainable parameters = 45,088,514 - 48%|████▊ | 200/414 [00:18<00:18, 11.60it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H3K4me1/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H3K4me1/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 2.75it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H3K4me1/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H3K4me1/checkpoint-200/tokenizer_config.json - 97%|█████████▋| 400/414 [00:36<00:01, 11.52it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H3K4me1/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H3K4me1/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 2.69it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H3K4me1/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H3K4me1/checkpoint-400/tokenizer_config.json -100%|██████████| 414/414 [00:38<00:00, 10.31it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H3K4me1/checkpoint-414 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H3K4me1/checkpoint-414/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 2.99it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H3K4me1/checkpoint-414/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H3K4me1/checkpoint-414/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 414/414 [00:39<00:00, 10.55it/s] -{'train_runtime': '39.24', 'train_samples_per_second': '1346', 'train_steps_per_second': '10.55', 'train_loss': '0.6241', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 40.28it/s] diff --git a/wandb/run-20260305_051111-y6jtosvf/files/requirements.txt b/wandb/run-20260305_051111-y6jtosvf/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_051111-y6jtosvf/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 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"2026-03-05T05:12:09.724783Z" - writerId: hzjele2pkrzc5a31kw3kxy382hthzliv - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_051209-2iu3lqmb/files/output.log b/wandb/run-20260305_051209-2iu3lqmb/files/output.log deleted file mode 100644 index 47ef2822558aaab73465df75cbd707ee8f310025..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_051209-2iu3lqmb/files/output.log +++ /dev/null @@ -1,59 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 16671.57it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_reg/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -classifier.weight | MISSING | -bert.pooler.dense.bias | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 25,710 - Num Epochs = 2 - Num update steps per epoch = 201 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 402 - Number of trainable parameters = 45,088,514 - 50%|████▉ | 199/402 [00:17<00:17, 11.57it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H3K4me2/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H3K4me2/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.52it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H3K4me2/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H3K4me2/checkpoint-200/tokenizer_config.json - 99%|█████████▉| 399/402 [00:35<00:00, 11.57it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H3K4me2/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H3K4me2/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.21it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H3K4me2/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H3K4me2/checkpoint-400/tokenizer_config.json -100%|█████████▉| 401/402 [00:36<00:00, 4.94it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H3K4me2/checkpoint-402 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H3K4me2/checkpoint-402/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.46it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H3K4me2/checkpoint-402/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H3K4me2/checkpoint-402/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 402/402 [00:37<00:00, 10.73it/s] -{'train_runtime': '37.46', 'train_samples_per_second': '1373', 'train_steps_per_second': '10.73', 'train_loss': '0.5622', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3215 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 40.78it/s] diff --git a/wandb/run-20260305_051209-2iu3lqmb/files/requirements.txt b/wandb/run-20260305_051209-2iu3lqmb/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_051209-2iu3lqmb/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 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--------------------------------------------+------------+- -cls.predictions.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -bert.pooler.dense.bias | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 14,595 - Num Epochs = 2 - Num update steps per epoch = 115 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 230 - Number of trainable parameters = 45,088,514 - 87%|████████▋ | 199/230 [00:17<00:02, 11.52it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H3K4me3/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H3K4me3/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.92it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H3K4me3/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H3K4me3/checkpoint-200/tokenizer_config.json -100%|█████████▉| 229/230 [00:21<00:00, 11.57it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H3K4me3/checkpoint-230 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H3K4me3/checkpoint-230/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 2.72it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H3K4me3/checkpoint-230/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H3K4me3/checkpoint-230/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 230/230 [00:22<00:00, 10.43it/s] -{'train_runtime': '22.06', 'train_samples_per_second': '1323', 'train_steps_per_second': '10.43', 'train_loss': '0.473', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 1825 - Batch size = 128 -100%|██████████| 15/15 [00:00<00:00, 43.28it/s] diff --git a/wandb/run-20260305_051304-knt74y0i/files/requirements.txt b/wandb/run-20260305_051304-knt74y0i/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_051304-knt74y0i/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T05:13:40.584519Z" - writerId: 6o0d6w8aapdegm3u9k5pr9tsxad2hrzp - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_051340-w5zz2ox3/files/output.log b/wandb/run-20260305_051340-w5zz2ox3/files/output.log deleted file mode 100644 index 4f9e186a219bdc3da313d8fcd003fb8d99638e98..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_051340-w5zz2ox3/files/output.log +++ /dev/null @@ -1,54 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 24049.09it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_reg/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -classifier.weight | MISSING | -bert.pooler.dense.bias | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 19,422 - Num Epochs = 2 - Num update steps per epoch = 152 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 304 - Number of trainable parameters = 45,088,514 - 65%|██████▌ | 199/304 [00:17<00:08, 11.68it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H3K9ac/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H3K9ac/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.17it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H3K9ac/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H3K9ac/checkpoint-200/tokenizer_config.json -100%|█████████▉| 303/304 [00:27<00:00, 11.51it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H3K9ac/checkpoint-304 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H3K9ac/checkpoint-304/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.73it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H3K9ac/checkpoint-304/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H3K9ac/checkpoint-304/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 304/304 [00:28<00:00, 10.68it/s] -{'train_runtime': '28.45', 'train_samples_per_second': '1365', 'train_steps_per_second': '10.68', 'train_loss': '0.5818', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 2429 - Batch size = 128 -100%|██████████| 19/19 [00:00<00:00, 40.50it/s] diff --git a/wandb/run-20260305_051340-w5zz2ox3/files/requirements.txt b/wandb/run-20260305_051340-w5zz2ox3/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_051340-w5zz2ox3/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 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"2026-03-05T05:14:24.641113Z" - writerId: 3cu9kh4m0kdoq92pkxhvjtkqnq29jsdf - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_051424-g0tq4f6q/files/output.log b/wandb/run-20260305_051424-g0tq4f6q/files/output.log deleted file mode 100644 index bd6821b83fd2098194254eb8406476eb08b0e912..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_051424-g0tq4f6q/files/output.log +++ /dev/null @@ -1,54 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 20458.04it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_reg/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -bert.pooler.dense.bias | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 22,630 - Num Epochs = 2 - Num update steps per epoch = 177 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 354 - Number of trainable parameters = 45,088,514 - 56%|█████▌ | 199/354 [00:17<00:13, 11.52it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H3K9me3/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H3K9me3/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.95it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H3K9me3/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H3K9me3/checkpoint-200/tokenizer_config.json -100%|█████████▉| 353/354 [00:31<00:00, 11.51it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H3K9me3/checkpoint-354 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H3K9me3/checkpoint-354/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.19it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H3K9me3/checkpoint-354/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H3K9me3/checkpoint-354/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 354/354 [00:32<00:00, 10.96it/s] -{'train_runtime': '32.31', 'train_samples_per_second': '1401', 'train_steps_per_second': '10.96', 'train_loss': '0.6708', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 2830 - Batch size = 128 -100%|██████████| 23/23 [00:00<00:00, 41.53it/s] diff --git a/wandb/run-20260305_051424-g0tq4f6q/files/requirements.txt b/wandb/run-20260305_051424-g0tq4f6q/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_051424-g0tq4f6q/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T05:15:13.858594Z" - writerId: rudfhiqearwnz5btsh80r9p5s659pnmq - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_051513-5qbxkiy4/files/output.log b/wandb/run-20260305_051513-5qbxkiy4/files/output.log deleted file mode 100644 index 701148713b908fe7912e1dd046936bb48cf1f61b..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_051513-5qbxkiy4/files/output.log +++ /dev/null @@ -1,59 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 18827.76it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_reg/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -bert.pooler.dense.weight | MISSING | -classifier.weight | MISSING | -classifier.bias | MISSING | -bert.pooler.dense.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 25,816 - Num Epochs = 2 - Num update steps per epoch = 202 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 404 - Number of trainable parameters = 45,088,514 - 49%|████▉ | 199/404 [00:17<00:17, 11.48it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H4K20me1/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H4K20me1/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.71it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H4K20me1/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H4K20me1/checkpoint-200/tokenizer_config.json - 99%|█████████▉| 399/404 [00:35<00:00, 11.62it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H4K20me1/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H4K20me1/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.34it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H4K20me1/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H4K20me1/checkpoint-400/tokenizer_config.json -100%|█████████▉| 403/404 [00:36<00:00, 5.91it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H4K20me1/checkpoint-404 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H4K20me1/checkpoint-404/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.59it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H4K20me1/checkpoint-404/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__baseline_bpe_tokenizer/H4K20me1/checkpoint-404/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 404/404 [00:37<00:00, 10.75it/s] -{'train_runtime': '37.59', 'train_samples_per_second': '1374', 'train_steps_per_second': '10.75', 'train_loss': '0.5187', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3227 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 40.41it/s] diff --git a/wandb/run-20260305_051513-5qbxkiy4/files/requirements.txt b/wandb/run-20260305_051513-5qbxkiy4/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_051513-5qbxkiy4/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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/home/n5huang/dna_token/pretrain/models/model_len_reg/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.dense.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -bert.pooler.dense.weight | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 4 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 828 - Number of trainable parameters = 45,088,514 - 24%|██▍ | 199/828 [00:08<00:27, 23.28it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/enhancers/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/enhancers/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.77it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/enhancers/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/enhancers/checkpoint-200/tokenizer_config.json - 48%|████▊ | 400/828 [00:18<00:18, 23.37it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/enhancers/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/enhancers/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.85it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/enhancers/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/enhancers/checkpoint-400/tokenizer_config.json - 72%|███████▏ | 598/828 [00:27<00:09, 24.42it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/enhancers/checkpoint-600 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/enhancers/checkpoint-600/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.61it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/enhancers/checkpoint-600/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/enhancers/checkpoint-600/tokenizer_config.json - 96%|█████████▋| 799/828 [00:36<00:01, 23.69it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/enhancers/checkpoint-800 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/enhancers/checkpoint-800/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.62it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/enhancers/checkpoint-800/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/enhancers/checkpoint-800/tokenizer_config.json -100%|█████████▉| 826/828 [00:38<00:00, 21.86it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/enhancers/checkpoint-828 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/enhancers/checkpoint-828/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.20it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/enhancers/checkpoint-828/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/enhancers/checkpoint-828/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 828/828 [00:39<00:00, 21.05it/s] -{'train_runtime': '39.34', 'train_samples_per_second': '2684', 'train_steps_per_second': '21.05', 'train_loss': '0.5007', 'epoch': '4'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 81.86it/s] diff --git a/wandb/run-20260305_051609-3o1nj3hz/files/requirements.txt b/wandb/run-20260305_051609-3o1nj3hz/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_051609-3o1nj3hz/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 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/home/n5huang/dna_token/tokenizer_evaluation/merge_bpe/merge_tokenizer_unigram_len.json - - --trust_remote_code - - "True" - - --data_path - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/enhancers_types/split - - --kmer - - "-1" - - --run_name - - hg38_BPE_len_reg__merge_bpe_merge_tokenizer_unigram_len_3e-5_enhancers_types_seed42 - - --model_max_length - - "100" - - --per_device_train_batch_size - - "128" - - --per_device_eval_batch_size - - "128" - - --gradient_accumulation_steps - - "1" - - --learning_rate - - "3e-5" - - --num_train_epochs - - "4" - - --fp16 - - --save_steps - - "200" - - --output_dir - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/enhancers_types - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "547097063424" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T05:17:03.269147Z" - writerId: 3wcatw1h9vwen478iblbsnpyy4x5b3yn - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_051703-krihcn6o/files/output.log b/wandb/run-20260305_051703-krihcn6o/files/output.log deleted file mode 100644 index 8bb5f5ac540f15a27270ef9171a1f78afebdf65c..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_051703-krihcn6o/files/output.log +++ /dev/null @@ -1,70 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 17665.01it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_reg/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -bert.pooler.dense.bias | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 4 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 828 - Number of trainable parameters = 45,089,283 - 24%|██▍ | 198/828 [00:09<00:30, 20.91it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/enhancers_types/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/enhancers_types/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 2.85it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/enhancers_types/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/enhancers_types/checkpoint-200/tokenizer_config.json - 48%|████▊ | 399/828 [00:19<00:18, 23.17it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/enhancers_types/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/enhancers_types/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.55it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/enhancers_types/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/enhancers_types/checkpoint-400/tokenizer_config.json - 72%|███████▏ | 600/828 [00:28<00:09, 23.57it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/enhancers_types/checkpoint-600 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/enhancers_types/checkpoint-600/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.52it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/enhancers_types/checkpoint-600/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/enhancers_types/checkpoint-600/tokenizer_config.json - 96%|█████████▋| 798/828 [00:38<00:01, 23.13it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/enhancers_types/checkpoint-800 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/enhancers_types/checkpoint-800/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.81it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/enhancers_types/checkpoint-800/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/enhancers_types/checkpoint-800/tokenizer_config.json -100%|██████████| 828/828 [00:40<00:00, 21.66it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/enhancers_types/checkpoint-828 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/enhancers_types/checkpoint-828/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.83it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/enhancers_types/checkpoint-828/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/enhancers_types/checkpoint-828/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 828/828 [00:41<00:00, 20.15it/s] -{'train_runtime': '41.1', 'train_samples_per_second': '2569', 'train_steps_per_second': '20.15', 'train_loss': '0.6311', 'epoch': '4'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 82.31it/s] diff --git a/wandb/run-20260305_051703-krihcn6o/files/requirements.txt b/wandb/run-20260305_051703-krihcn6o/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_051703-krihcn6o/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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/home/n5huang/dna_token/pretrain/models/model_len_reg/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -bert.pooler.dense.bias | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 25,267 - Num Epochs = 2 - Num update steps per epoch = 198 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 396 - Number of trainable parameters = 45,088,514 - 51%|█████ | 200/396 [00:07<00:06, 29.58it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/promoter_all/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/promoter_all/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.02it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/promoter_all/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/promoter_all/checkpoint-200/tokenizer_config.json -100%|█████████▉| 395/396 [00:15<00:00, 27.93it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/promoter_all/checkpoint-396 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/promoter_all/checkpoint-396/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.43it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/promoter_all/checkpoint-396/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/promoter_all/checkpoint-396/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 396/396 [00:16<00:00, 24.08it/s] -{'train_runtime': '16.44', 'train_samples_per_second': '3073', 'train_steps_per_second': '24.08', 'train_loss': '0.3299', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3159 - Batch size = 128 -100%|██████████| 25/25 [00:00<00:00, 97.15it/s] diff --git a/wandb/run-20260305_051800-xniqag9u/files/requirements.txt b/wandb/run-20260305_051800-xniqag9u/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_051800-xniqag9u/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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/data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T05:18:30.374641Z" - writerId: s8zfecfo0vgcax960qpc5tgmcvqvb3ml - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_051830-ttiauor3/files/output.log b/wandb/run-20260305_051830-ttiauor3/files/output.log deleted file mode 100644 index 701f06c54b4c5fee4eb7c0664315ebd5a741698f..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_051830-ttiauor3/files/output.log +++ /dev/null @@ -1,55 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 22749.84it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_reg/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -classifier.weight | MISSING | -classifier.bias | MISSING | -bert.pooler.dense.weight | MISSING | -bert.pooler.dense.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 25,097 - Num Epochs = 2 - Num update steps per epoch = 197 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 394 - Number of trainable parameters = 45,088,514 - 51%|█████ | 199/394 [00:07<00:06, 28.34it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/promoter_no_tata/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/promoter_no_tata/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.61it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/promoter_no_tata/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/promoter_no_tata/checkpoint-200/tokenizer_config.json - 99%|█████████▉| 391/394 [00:15<00:00, 28.18it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/promoter_no_tata/checkpoint-394 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/promoter_no_tata/checkpoint-394/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.09it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/promoter_no_tata/checkpoint-394/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/promoter_no_tata/checkpoint-394/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 394/394 [00:16<00:00, 24.44it/s] -{'train_runtime': '16.12', 'train_samples_per_second': '3114', 'train_steps_per_second': '24.45', 'train_loss': '0.313', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3138 - Batch size = 128 -100%|██████████| 25/25 [00:00<00:00, 100.76it/s] diff --git a/wandb/run-20260305_051830-ttiauor3/files/requirements.txt b/wandb/run-20260305_051830-ttiauor3/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_051830-ttiauor3/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T05:18:59.491616Z" - writerId: r5rfykfmy9qohjt4qff7m6v2f2p1j59h - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_051859-jc8o03qu/files/output.log b/wandb/run-20260305_051859-jc8o03qu/files/output.log deleted file mode 100644 index a445214eb7b4656ae0755ce7f593d64742c2996c..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_051859-jc8o03qu/files/output.log +++ /dev/null @@ -1,50 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 24276.49it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_reg/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -bert.pooler.dense.weight | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.bias | MISSING | -classifier.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 4,219 - Num Epochs = 2 - Num update steps per epoch = 33 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 66 - Number of trainable parameters = 45,088,514 - 97%|█████████▋| 64/66 [00:02<00:00, 28.14it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/promoter_tata/checkpoint-66 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/promoter_tata/checkpoint-66/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.12it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/promoter_tata/checkpoint-66/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/promoter_tata/checkpoint-66/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 66/66 [00:03<00:00, 18.17it/s] -{'train_runtime': '3.633', 'train_samples_per_second': '2323', 'train_steps_per_second': '18.17', 'train_loss': '0.4455', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 528 - Batch size = 128 -100%|██████████| 5/5 [00:00<00:00, 103.64it/s] diff --git a/wandb/run-20260305_051859-jc8o03qu/files/requirements.txt b/wandb/run-20260305_051859-jc8o03qu/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_051859-jc8o03qu/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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- genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "547101941760" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T05:19:14.187893Z" - writerId: dbrdi9p2an6l3lrhjhq75gjfed3oeitw - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_051914-wt4t29ev/files/output.log b/wandb/run-20260305_051914-wt4t29ev/files/output.log deleted file mode 100644 index 886e72dfb5fb816118efad7d9579b837b022fee5..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_051914-wt4t29ev/files/output.log +++ /dev/null @@ -1,70 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 24846.02it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_reg/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -classifier.weight | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.bias | MISSING | -bert.pooler.dense.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 4 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 828 - Number of trainable parameters = 45,088,514 - 24%|██▍ | 199/828 [00:11<00:35, 17.92it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/splice_sites_acceptors/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/splice_sites_acceptors/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 5.03it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/splice_sites_acceptors/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/splice_sites_acceptors/checkpoint-200/tokenizer_config.json - 48%|████▊ | 400/828 [00:23<00:24, 17.78it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/splice_sites_acceptors/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/splice_sites_acceptors/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.75it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/splice_sites_acceptors/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/splice_sites_acceptors/checkpoint-400/tokenizer_config.json - 72%|███████▏ | 599/828 [00:36<00:13, 17.27it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/splice_sites_acceptors/checkpoint-600 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/splice_sites_acceptors/checkpoint-600/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.16it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/splice_sites_acceptors/checkpoint-600/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/splice_sites_acceptors/checkpoint-600/tokenizer_config.json - 97%|█████████▋| 800/828 [00:48<00:01, 17.63it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/splice_sites_acceptors/checkpoint-800 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/splice_sites_acceptors/checkpoint-800/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 5.27it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/splice_sites_acceptors/checkpoint-800/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/splice_sites_acceptors/checkpoint-800/tokenizer_config.json -100%|█████████▉| 826/828 [00:50<00:00, 17.15it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/splice_sites_acceptors/checkpoint-828 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/splice_sites_acceptors/checkpoint-828/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.46it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/splice_sites_acceptors/checkpoint-828/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/splice_sites_acceptors/checkpoint-828/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 828/828 [00:50<00:00, 16.25it/s] -{'train_runtime': '50.94', 'train_samples_per_second': '2073', 'train_steps_per_second': '16.25', 'train_loss': '0.4405', 'epoch': '4'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 60.14it/s] diff --git a/wandb/run-20260305_051914-wt4t29ev/files/requirements.txt b/wandb/run-20260305_051914-wt4t29ev/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_051914-wt4t29ev/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T05:20:20.480333Z" - writerId: qmfmlcemkfkfjwlia0g2jp3dwqciq4z2 - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_052020-l30jcvpy/files/output.log b/wandb/run-20260305_052020-l30jcvpy/files/output.log deleted file mode 100644 index 893b604130e7961d32a7616e8fd19229a2cbf9d7..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_052020-l30jcvpy/files/output.log +++ /dev/null @@ -1,70 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 22145.68it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_reg/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -classifier.bias | MISSING | -bert.pooler.dense.weight | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 4 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 828 - Number of trainable parameters = 45,089,283 - 24%|██▍ | 199/828 [00:11<00:36, 17.39it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/splice_sites_all/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/splice_sites_all/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.83it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/splice_sites_all/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/splice_sites_all/checkpoint-200/tokenizer_config.json - 48%|████▊ | 400/828 [00:24<00:24, 17.60it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/splice_sites_all/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/splice_sites_all/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 5.08it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/splice_sites_all/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/splice_sites_all/checkpoint-400/tokenizer_config.json - 72%|███████▏ | 599/828 [00:36<00:13, 17.60it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/splice_sites_all/checkpoint-600 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/splice_sites_all/checkpoint-600/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.21it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/splice_sites_all/checkpoint-600/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/splice_sites_all/checkpoint-600/tokenizer_config.json - 97%|█████████▋| 800/828 [00:48<00:01, 17.87it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/splice_sites_all/checkpoint-800 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/splice_sites_all/checkpoint-800/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.22it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/splice_sites_all/checkpoint-800/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/splice_sites_all/checkpoint-800/tokenizer_config.json -100%|█████████▉| 826/828 [00:50<00:00, 17.19it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/splice_sites_all/checkpoint-828 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/splice_sites_all/checkpoint-828/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.59it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/splice_sites_all/checkpoint-828/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/splice_sites_all/checkpoint-828/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 828/828 [00:51<00:00, 16.03it/s] -{'train_runtime': '51.65', 'train_samples_per_second': '2044', 'train_steps_per_second': '16.03', 'train_loss': '0.7719', 'epoch': '4'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 61.22it/s] diff --git a/wandb/run-20260305_052020-l30jcvpy/files/requirements.txt b/wandb/run-20260305_052020-l30jcvpy/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_052020-l30jcvpy/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 -accelerate==1.13.0 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -triton==3.6.0 -nvidia-nccl-cu12==2.27.5 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -cuda-pathfinder==1.4.0 -shellingham==1.5.4 -torchaudio==2.5.1 -nvidia-cufile-cu12==1.13.1.3 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -nvidia-nvjitlink-cu12==12.8.93 -click==8.3.1 -MarkupSafe==3.0.2 -nvidia-nvshmem-cu12==3.4.5 -urllib3==2.6.3 -cuda-bindings==12.9.4 -propcache==0.4.1 -nvidia-cusolver-cu12==11.7.3.90 -sympy==1.14.0 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -nvidia-cuda-runtime-cu12==12.8.90 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_052020-l30jcvpy/files/wandb-metadata.json b/wandb/run-20260305_052020-l30jcvpy/files/wandb-metadata.json deleted file mode 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/home/n5huang/dna_token/tokenizer_evaluation/merge_bpe/merge_tokenizer_unigram_len.json - - --trust_remote_code - - "True" - - --data_path - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/splice_sites_donors/split - - --kmer - - "-1" - - --run_name - - hg38_BPE_len_reg__merge_bpe_merge_tokenizer_unigram_len_3e-5_splice_sites_donors_seed42 - - --model_max_length - - "140" - - --per_device_train_batch_size - - "128" - - --per_device_eval_batch_size - - "128" - - --gradient_accumulation_steps - - "1" - - --learning_rate - - "3e-5" - - --num_train_epochs - - "4" - - --fp16 - - --save_steps - - "200" - - --output_dir - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/splice_sites_donors - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "547106910208" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T05:21:28.612792Z" - writerId: yp353a4r3p8gefvdxw90y9k7r8n72ayt - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_052128-ggwtisfb/files/output.log b/wandb/run-20260305_052128-ggwtisfb/files/output.log deleted file mode 100644 index a502598d041e824223ec1b8f9fafa44cf856c224..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_052128-ggwtisfb/files/output.log +++ /dev/null @@ -1,70 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 24175.35it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_reg/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -bert.pooler.dense.bias | MISSING | -classifier.bias | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 4 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 828 - Number of trainable parameters = 45,088,514 - 24%|██▍ | 199/828 [00:12<00:35, 17.55it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/splice_sites_donors/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/splice_sites_donors/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 2.87it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/splice_sites_donors/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/splice_sites_donors/checkpoint-200/tokenizer_config.json - 48%|████▊ | 400/828 [00:24<00:25, 16.98it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/splice_sites_donors/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/splice_sites_donors/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.13it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/splice_sites_donors/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/splice_sites_donors/checkpoint-400/tokenizer_config.json - 72%|███████▏ | 599/828 [00:37<00:13, 17.50it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/splice_sites_donors/checkpoint-600 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/splice_sites_donors/checkpoint-600/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.33it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/splice_sites_donors/checkpoint-600/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/splice_sites_donors/checkpoint-600/tokenizer_config.json - 97%|█████████▋| 800/828 [00:49<00:01, 17.16it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/splice_sites_donors/checkpoint-800 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/splice_sites_donors/checkpoint-800/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 2.96it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/splice_sites_donors/checkpoint-800/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/splice_sites_donors/checkpoint-800/tokenizer_config.json -100%|█████████▉| 826/828 [00:52<00:00, 16.45it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/splice_sites_donors/checkpoint-828 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/splice_sites_donors/checkpoint-828/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.00it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/splice_sites_donors/checkpoint-828/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/splice_sites_donors/checkpoint-828/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 828/828 [00:53<00:00, 15.58it/s] -{'train_runtime': '53.13', 'train_samples_per_second': '1988', 'train_steps_per_second': '15.59', 'train_loss': '0.4474', 'epoch': '4'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 61.47it/s] diff --git a/wandb/run-20260305_052128-ggwtisfb/files/requirements.txt b/wandb/run-20260305_052128-ggwtisfb/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_052128-ggwtisfb/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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/data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T05:22:37.283447Z" - writerId: bglq5iq9bqfvf6o5ser0d04v8ij11jry - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_052237-foe7ed2z/files/output.log b/wandb/run-20260305_052237-foe7ed2z/files/output.log deleted file mode 100644 index 943b9203b8881d67721d713533fb2a73b83fecbd..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_052237-foe7ed2z/files/output.log +++ /dev/null @@ -1,60 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 17065.81it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_reg/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -bert.pooler.dense.bias | MISSING | -classifier.bias | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 2 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 414 - Number of trainable parameters = 45,088,514 - 48%|████▊ | 199/414 [00:15<00:16, 12.84it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H2AFZ/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H2AFZ/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.37it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H2AFZ/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H2AFZ/checkpoint-200/tokenizer_config.json - 96%|█████████▋| 399/414 [00:31<00:01, 12.85it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H2AFZ/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H2AFZ/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.39it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H2AFZ/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H2AFZ/checkpoint-400/tokenizer_config.json -100%|█████████▉| 413/414 [00:33<00:00, 10.68it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H2AFZ/checkpoint-414 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H2AFZ/checkpoint-414/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.10it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H2AFZ/checkpoint-414/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H2AFZ/checkpoint-414/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 414/414 [00:34<00:00, 11.87it/s] -{'train_runtime': '34.87', 'train_samples_per_second': '1514', 'train_steps_per_second': '11.87', 'train_loss': '0.5245', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 43.96it/s] diff --git a/wandb/run-20260305_052237-foe7ed2z/files/requirements.txt b/wandb/run-20260305_052237-foe7ed2z/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_052237-foe7ed2z/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 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cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T05:23:30.530968Z" - writerId: axbgm24aimdt3z9667aeknud8huzopse - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_052330-7wyqfcft/files/output.log b/wandb/run-20260305_052330-7wyqfcft/files/output.log deleted file mode 100644 index 0863775be47aff9310d65779a7021044234f8f33..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_052330-7wyqfcft/files/output.log +++ /dev/null @@ -1,55 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 19450.17it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_reg/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.decoder.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -bert.pooler.dense.bias | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.weight | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 25,292 - Num Epochs = 2 - Num update steps per epoch = 198 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 396 - Number of trainable parameters = 45,088,514 - 50%|█████ | 199/396 [00:15<00:14, 13.85it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H3K27ac/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H3K27ac/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.93it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H3K27ac/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H3K27ac/checkpoint-200/tokenizer_config.json -100%|█████████▉| 395/396 [00:31<00:00, 12.81it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H3K27ac/checkpoint-396 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H3K27ac/checkpoint-396/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.30it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H3K27ac/checkpoint-396/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H3K27ac/checkpoint-396/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 396/396 [00:32<00:00, 12.15it/s] -{'train_runtime': '32.6', 'train_samples_per_second': '1552', 'train_steps_per_second': '12.15', 'train_loss': '0.5483', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3163 - Batch size = 128 -100%|██████████| 25/25 [00:00<00:00, 43.28it/s] diff --git a/wandb/run-20260305_052330-7wyqfcft/files/requirements.txt b/wandb/run-20260305_052330-7wyqfcft/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_052330-7wyqfcft/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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/home/n5huang/dna_token/tokenizer_evaluation/merge_bpe/merge_tokenizer_unigram_len.json - - --trust_remote_code - - "True" - - --data_path - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/H3K27me3/split - - --kmer - - "-1" - - --run_name - - hg38_BPE_len_reg__merge_bpe_merge_tokenizer_unigram_len_3e-5_H3K27me3_seed42 - - --model_max_length - - "220" - - --per_device_train_batch_size - - "128" - - --per_device_eval_batch_size - - "128" - - --gradient_accumulation_steps - - "1" - - --learning_rate - - "3e-5" - - --num_train_epochs - - "2" - - --fp16 - - --save_steps - - "200" - - --output_dir - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H3K27me3 - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "547114090496" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T05:24:20.767985Z" - writerId: bukdpbwrprir8qrvs0ikwhaw5jtgfnq4 - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_052420-5ch97dnd/files/output.log b/wandb/run-20260305_052420-5ch97dnd/files/output.log deleted file mode 100644 index 954f0371383137ffc7d461d241ed9bdf1b34aef6..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_052420-5ch97dnd/files/output.log +++ /dev/null @@ -1,60 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 24539.46it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_reg/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -bert.pooler.dense.bias | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.weight | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 2 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 414 - Number of trainable parameters = 45,088,514 - 48%|████▊ | 199/414 [00:16<00:16, 13.01it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H3K27me3/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H3K27me3/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 2.83it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H3K27me3/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H3K27me3/checkpoint-200/tokenizer_config.json - 96%|█████████▋| 399/414 [00:32<00:01, 12.85it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H3K27me3/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H3K27me3/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 2.84it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H3K27me3/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H3K27me3/checkpoint-400/tokenizer_config.json -100%|█████████▉| 413/414 [00:34<00:00, 10.66it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H3K27me3/checkpoint-414 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H3K27me3/checkpoint-414/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 2.79it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H3K27me3/checkpoint-414/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H3K27me3/checkpoint-414/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 414/414 [00:35<00:00, 11.59it/s] -{'train_runtime': '35.73', 'train_samples_per_second': '1478', 'train_steps_per_second': '11.59', 'train_loss': '0.4643', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 43.63it/s] diff --git a/wandb/run-20260305_052420-5ch97dnd/files/requirements.txt b/wandb/run-20260305_052420-5ch97dnd/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_052420-5ch97dnd/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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/data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T05:25:15.618276Z" - writerId: 4dyznfi42g8cajsh28ge2i9rtq8h0jxg - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_052515-mx5radu6/files/output.log b/wandb/run-20260305_052515-mx5radu6/files/output.log deleted file mode 100644 index e1f40395070fb4552538e2c5e66f7275127ad81b..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_052515-mx5radu6/files/output.log +++ /dev/null @@ -1,60 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 22050.01it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_reg/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -bert.pooler.dense.weight | MISSING | -classifier.bias | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 2 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 414 - Number of trainable parameters = 45,088,514 - 48%|████▊ | 199/414 [00:15<00:16, 13.14it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H3K36me3/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H3K36me3/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.36it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H3K36me3/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H3K36me3/checkpoint-200/tokenizer_config.json - 96%|█████████▋| 399/414 [00:32<00:01, 13.03it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H3K36me3/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H3K36me3/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.38it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H3K36me3/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H3K36me3/checkpoint-400/tokenizer_config.json -100%|█████████▉| 413/414 [00:33<00:00, 11.02it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H3K36me3/checkpoint-414 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H3K36me3/checkpoint-414/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.96it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H3K36me3/checkpoint-414/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H3K36me3/checkpoint-414/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 414/414 [00:34<00:00, 11.97it/s] -{'train_runtime': '34.6', 'train_samples_per_second': '1526', 'train_steps_per_second': '11.97', 'train_loss': '0.4662', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 42.07it/s] diff --git a/wandb/run-20260305_052515-mx5radu6/files/requirements.txt b/wandb/run-20260305_052515-mx5radu6/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_052515-mx5radu6/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 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cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T05:26:07.878433Z" - writerId: w5cc96ggvxyqwcuvoxwch0pw50zjxeaa - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_052607-onpgnnnp/files/output.log b/wandb/run-20260305_052607-onpgnnnp/files/output.log deleted file mode 100644 index a4b32b58cb0ea3540416d53c1778cc958263558b..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_052607-onpgnnnp/files/output.log +++ /dev/null @@ -1,60 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 20969.44it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_reg/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -classifier.weight | MISSING | -bert.pooler.dense.weight | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 2 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 414 - Number of trainable parameters = 45,088,514 - 48%|████▊ | 199/414 [00:15<00:16, 13.03it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H3K4me1/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H3K4me1/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.96it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H3K4me1/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H3K4me1/checkpoint-200/tokenizer_config.json - 96%|█████████▋| 399/414 [00:31<00:01, 13.02it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H3K4me1/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H3K4me1/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.99it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H3K4me1/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H3K4me1/checkpoint-400/tokenizer_config.json -100%|█████████▉| 413/414 [00:33<00:00, 11.42it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H3K4me1/checkpoint-414 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H3K4me1/checkpoint-414/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.76it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H3K4me1/checkpoint-414/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H3K4me1/checkpoint-414/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 414/414 [00:34<00:00, 12.04it/s] -{'train_runtime': '34.37', 'train_samples_per_second': '1536', 'train_steps_per_second': '12.04', 'train_loss': '0.5507', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 43.87it/s] diff --git a/wandb/run-20260305_052607-onpgnnnp/files/requirements.txt b/wandb/run-20260305_052607-onpgnnnp/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_052607-onpgnnnp/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 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cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T05:27:00.195522Z" - writerId: 78eo19mywry34figyp5i8xc6xl9rso2c - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_052700-9pq8jqjf/files/output.log b/wandb/run-20260305_052700-9pq8jqjf/files/output.log deleted file mode 100644 index 0fe8433a980513bb40d355b9ca30958276aa7137..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_052700-9pq8jqjf/files/output.log +++ /dev/null @@ -1,60 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 16244.52it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_reg/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -classifier.weight | MISSING | -bert.pooler.dense.bias | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 25,710 - Num Epochs = 2 - Num update steps per epoch = 201 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 402 - Number of trainable parameters = 45,088,514 - 50%|████▉ | 199/402 [00:15<00:15, 13.01it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H3K4me2/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H3K4me2/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.69it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H3K4me2/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H3K4me2/checkpoint-200/tokenizer_config.json - 99%|█████████▉| 399/402 [00:31<00:00, 13.02it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H3K4me2/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H3K4me2/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.47it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H3K4me2/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H3K4me2/checkpoint-400/tokenizer_config.json -100%|█████████▉| 401/402 [00:32<00:00, 5.40it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H3K4me2/checkpoint-402 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H3K4me2/checkpoint-402/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 5.14it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H3K4me2/checkpoint-402/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H3K4me2/checkpoint-402/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 402/402 [00:33<00:00, 12.06it/s] -{'train_runtime': '33.33', 'train_samples_per_second': '1543', 'train_steps_per_second': '12.06', 'train_loss': '0.4944', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3215 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 44.64it/s] diff --git a/wandb/run-20260305_052700-9pq8jqjf/files/requirements.txt b/wandb/run-20260305_052700-9pq8jqjf/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_052700-9pq8jqjf/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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--seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "547123486720" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T05:27:51.875085Z" - writerId: 6p0sjkvu06aipj558ubcslvy4m5pzyub - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_052751-k3xu93ac/files/output.log b/wandb/run-20260305_052751-k3xu93ac/files/output.log deleted file mode 100644 index 46181fe85bfbee1fa98803c347c8738aa4f3ec39..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_052751-k3xu93ac/files/output.log +++ /dev/null @@ -1,55 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 22755.95it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_reg/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -bert.pooler.dense.weight | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.bias | MISSING | -classifier.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 14,595 - Num Epochs = 2 - Num update steps per epoch = 115 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 230 - Number of trainable parameters = 45,088,514 - 87%|████████▋ | 199/230 [00:15<00:02, 12.90it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H3K4me3/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H3K4me3/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.40it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H3K4me3/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H3K4me3/checkpoint-200/tokenizer_config.json -100%|█████████▉| 229/230 [00:18<00:00, 13.00it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H3K4me3/checkpoint-230 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H3K4me3/checkpoint-230/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.50it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H3K4me3/checkpoint-230/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H3K4me3/checkpoint-230/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 230/230 [00:19<00:00, 11.78it/s] -{'train_runtime': '19.52', 'train_samples_per_second': '1495', 'train_steps_per_second': '11.78', 'train_loss': '0.412', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 1825 - Batch size = 128 -100%|██████████| 15/15 [00:00<00:00, 46.52it/s] diff --git a/wandb/run-20260305_052751-k3xu93ac/files/requirements.txt b/wandb/run-20260305_052751-k3xu93ac/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_052751-k3xu93ac/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 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/data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T05:28:25.658223Z" - writerId: 4464hfavese07taj6c9wcaluj89pk33f - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_052825-9i48duza/files/output.log b/wandb/run-20260305_052825-9i48duza/files/output.log deleted file mode 100644 index 4916d7838c7e4635b7e195498933f2ba50d7952f..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_052825-9i48duza/files/output.log +++ /dev/null @@ -1,55 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 23183.10it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_reg/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -classifier.bias | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.weight | MISSING | -bert.pooler.dense.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 19,422 - Num Epochs = 2 - Num update steps per epoch = 152 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 304 - Number of trainable parameters = 45,088,514 - 65%|██████▌ | 199/304 [00:15<00:08, 12.96it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H3K9ac/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H3K9ac/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.51it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H3K9ac/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H3K9ac/checkpoint-200/tokenizer_config.json -100%|█████████▉| 303/304 [00:24<00:00, 13.12it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H3K9ac/checkpoint-304 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H3K9ac/checkpoint-304/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.92it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H3K9ac/checkpoint-304/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H3K9ac/checkpoint-304/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 304/304 [00:25<00:00, 12.01it/s] -{'train_runtime': '25.31', 'train_samples_per_second': '1535', 'train_steps_per_second': '12.01', 'train_loss': '0.5199', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 2429 - Batch size = 128 -100%|██████████| 19/19 [00:00<00:00, 43.74it/s] diff --git a/wandb/run-20260305_052825-9i48duza/files/requirements.txt b/wandb/run-20260305_052825-9i48duza/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_052825-9i48duza/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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/data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T05:29:06.301002Z" - writerId: j9xar4027wfow1d78rtlxuayokajeouo - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_052906-ncuf9bth/files/output.log b/wandb/run-20260305_052906-ncuf9bth/files/output.log deleted file mode 100644 index f0fe923ac1da2572ac3696984541069b45c382b8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_052906-ncuf9bth/files/output.log +++ /dev/null @@ -1,55 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 23100.92it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_reg/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.decoder.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -classifier.weight | MISSING | -bert.pooler.dense.bias | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 22,630 - Num Epochs = 2 - Num update steps per epoch = 177 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 354 - Number of trainable parameters = 45,088,514 - 56%|█████▌ | 199/354 [00:15<00:12, 12.89it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H3K9me3/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H3K9me3/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.15it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H3K9me3/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H3K9me3/checkpoint-200/tokenizer_config.json -100%|█████████▉| 353/354 [00:28<00:00, 12.84it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H3K9me3/checkpoint-354 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H3K9me3/checkpoint-354/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.71it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H3K9me3/checkpoint-354/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H3K9me3/checkpoint-354/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 354/354 [00:29<00:00, 12.01it/s] -{'train_runtime': '29.47', 'train_samples_per_second': '1536', 'train_steps_per_second': '12.01', 'train_loss': '0.594', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 2830 - Batch size = 128 -100%|██████████| 23/23 [00:00<00:00, 44.74it/s] diff --git a/wandb/run-20260305_052906-ncuf9bth/files/requirements.txt b/wandb/run-20260305_052906-ncuf9bth/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_052906-ncuf9bth/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T05:29:53.635417Z" - writerId: dtyi2606z5f3h0cltxn53c5rh716na2r - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_052953-ghny7l3p/files/output.log b/wandb/run-20260305_052953-ghny7l3p/files/output.log deleted file mode 100644 index 4cdf75716e728a4524dda99fc0fefbe4fe4a4221..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_052953-ghny7l3p/files/output.log +++ /dev/null @@ -1,60 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 19782.61it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_reg/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -bert.pooler.dense.weight | MISSING | -classifier.weight | MISSING | -classifier.bias | MISSING | -bert.pooler.dense.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 25,816 - Num Epochs = 2 - Num update steps per epoch = 202 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 404 - Number of trainable parameters = 45,088,514 - 49%|████▉ | 199/404 [00:15<00:15, 13.09it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H4K20me1/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H4K20me1/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.99it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H4K20me1/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H4K20me1/checkpoint-200/tokenizer_config.json - 99%|█████████▉| 399/404 [00:31<00:00, 12.98it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H4K20me1/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H4K20me1/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.86it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H4K20me1/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H4K20me1/checkpoint-400/tokenizer_config.json -100%|█████████▉| 403/404 [00:32<00:00, 7.06it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H4K20me1/checkpoint-404 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H4K20me1/checkpoint-404/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 2.89it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H4K20me1/checkpoint-404/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len/H4K20me1/checkpoint-404/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 404/404 [00:33<00:00, 11.99it/s] -{'train_runtime': '33.7', 'train_samples_per_second': '1532', 'train_steps_per_second': '11.99', 'train_loss': '0.4431', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3227 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 44.75it/s] diff --git a/wandb/run-20260305_052953-ghny7l3p/files/requirements.txt b/wandb/run-20260305_052953-ghny7l3p/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_052953-ghny7l3p/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 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info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "547130646528" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T05:30:44.504154Z" - writerId: c2q6ra9etty7ydpl9nrx3rok9543qn81 - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_053044-pytq47g5/files/output.log b/wandb/run-20260305_053044-pytq47g5/files/output.log deleted file mode 100644 index a06cae87ace3bc12b25ad4f56d70aa2d2ce740fd..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_053044-pytq47g5/files/output.log +++ /dev/null @@ -1,70 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 19968.17it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_reg/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -bert.pooler.dense.bias | MISSING | -classifier.bias | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 4 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 828 - Number of trainable parameters = 45,088,514 - 24%|██▍ | 199/828 [00:08<00:27, 22.75it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/enhancers/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/enhancers/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.85it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/enhancers/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/enhancers/checkpoint-200/tokenizer_config.json - 48%|████▊ | 400/828 [00:17<00:18, 23.54it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/enhancers/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/enhancers/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.33it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/enhancers/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/enhancers/checkpoint-400/tokenizer_config.json - 72%|███████▏ | 598/828 [00:26<00:09, 24.33it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/enhancers/checkpoint-600 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/enhancers/checkpoint-600/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 2.98it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/enhancers/checkpoint-600/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/enhancers/checkpoint-600/tokenizer_config.json - 96%|█████████▋| 799/828 [00:35<00:01, 24.58it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/enhancers/checkpoint-800 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/enhancers/checkpoint-800/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.25it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/enhancers/checkpoint-800/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/enhancers/checkpoint-800/tokenizer_config.json -100%|█████████▉| 826/828 [00:37<00:00, 21.56it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/enhancers/checkpoint-828 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/enhancers/checkpoint-828/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.95it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/enhancers/checkpoint-828/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/enhancers/checkpoint-828/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 828/828 [00:38<00:00, 21.35it/s] -{'train_runtime': '38.77', 'train_samples_per_second': '2723', 'train_steps_per_second': '21.35', 'train_loss': '0.5044', 'epoch': '4'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 79.96it/s] diff --git a/wandb/run-20260305_053044-pytq47g5/files/requirements.txt b/wandb/run-20260305_053044-pytq47g5/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_053044-pytq47g5/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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/home/n5huang/dna_token/pretrain/models/model_len_reg/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -classifier.weight | MISSING | -bert.pooler.dense.bias | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 4 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 828 - Number of trainable parameters = 45,089,283 - 24%|██▍ | 199/828 [00:08<00:26, 23.59it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/enhancers_types/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/enhancers_types/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.05it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/enhancers_types/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/enhancers_types/checkpoint-200/tokenizer_config.json - 48%|████▊ | 400/828 [00:17<00:18, 23.01it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/enhancers_types/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/enhancers_types/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.16it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/enhancers_types/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/enhancers_types/checkpoint-400/tokenizer_config.json - 72%|███████▏ | 598/828 [00:26<00:09, 23.83it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/enhancers_types/checkpoint-600 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/enhancers_types/checkpoint-600/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.56it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/enhancers_types/checkpoint-600/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/enhancers_types/checkpoint-600/tokenizer_config.json - 96%|█████████▋| 799/828 [00:36<00:01, 24.49it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/enhancers_types/checkpoint-800 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/enhancers_types/checkpoint-800/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.25it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/enhancers_types/checkpoint-800/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/enhancers_types/checkpoint-800/tokenizer_config.json -100%|█████████▉| 826/828 [00:38<00:00, 20.94it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/enhancers_types/checkpoint-828 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/enhancers_types/checkpoint-828/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 2.90it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/enhancers_types/checkpoint-828/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/enhancers_types/checkpoint-828/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 828/828 [00:39<00:00, 21.03it/s] -{'train_runtime': '39.37', 'train_samples_per_second': '2682', 'train_steps_per_second': '21.03', 'train_loss': '0.6353', 'epoch': '4'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 82.24it/s] diff --git a/wandb/run-20260305_053137-q3y543gi/files/requirements.txt b/wandb/run-20260305_053137-q3y543gi/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_053137-q3y543gi/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 -accelerate==1.13.0 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -triton==3.6.0 -nvidia-nccl-cu12==2.27.5 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -cuda-pathfinder==1.4.0 -shellingham==1.5.4 -torchaudio==2.5.1 -nvidia-cufile-cu12==1.13.1.3 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -nvidia-nvjitlink-cu12==12.8.93 -click==8.3.1 -MarkupSafe==3.0.2 -nvidia-nvshmem-cu12==3.4.5 -urllib3==2.6.3 -cuda-bindings==12.9.4 -propcache==0.4.1 -nvidia-cusolver-cu12==11.7.3.90 -sympy==1.14.0 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -nvidia-cuda-runtime-cu12==12.8.90 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_053137-q3y543gi/files/wandb-metadata.json b/wandb/run-20260305_053137-q3y543gi/files/wandb-metadata.json deleted file mode 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--log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "547133259776" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T05:32:30.762589Z" - writerId: fb8dbx9h5sca9a8uv2zsbfu12x3davjw - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_053230-1eh29rxn/files/output.log b/wandb/run-20260305_053230-1eh29rxn/files/output.log deleted file mode 100644 index 90685744922790677c6a530cd98cfa262b493040..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_053230-1eh29rxn/files/output.log +++ /dev/null @@ -1,55 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 18856.26it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_reg/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -classifier.bias | MISSING | -bert.pooler.dense.bias | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 25,267 - Num Epochs = 2 - Num update steps per epoch = 198 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 396 - Number of trainable parameters = 45,088,514 - 51%|█████ | 200/396 [00:08<00:06, 29.01it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/promoter_all/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/promoter_all/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.09it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/promoter_all/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/promoter_all/checkpoint-200/tokenizer_config.json -100%|█████████▉| 395/396 [00:16<00:00, 24.61it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/promoter_all/checkpoint-396 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/promoter_all/checkpoint-396/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.20it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/promoter_all/checkpoint-396/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/promoter_all/checkpoint-396/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 396/396 [00:17<00:00, 23.17it/s] -{'train_runtime': '17.09', 'train_samples_per_second': '2957', 'train_steps_per_second': '23.17', 'train_loss': '0.3338', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3159 - Batch size = 128 -100%|██████████| 25/25 [00:00<00:00, 98.26it/s] diff --git a/wandb/run-20260305_053230-1eh29rxn/files/requirements.txt b/wandb/run-20260305_053230-1eh29rxn/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_053230-1eh29rxn/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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/home/n5huang/dna_token/tokenizer_evaluation/merge_bpe/merge_tokenizer_unigram_len2.json - - --trust_remote_code - - "True" - - --data_path - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/promoter_no_tata/split - - --kmer - - "-1" - - --run_name - - hg38_BPE_len_reg__merge_bpe_merge_tokenizer_unigram_len2_3e-5_promoter_no_tata_seed42 - - --model_max_length - - "80" - - --per_device_train_batch_size - - "128" - - --per_device_eval_batch_size - - "128" - - --gradient_accumulation_steps - - "1" - - --learning_rate - - "3e-5" - - --num_train_epochs - - "2" - - --fp16 - - --save_steps - - "200" - - --output_dir - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/promoter_no_tata - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "547135332352" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T05:33:01.448114Z" - writerId: llyad4n7p0f032k21h2hndfxk7pdzbfs - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_053301-jxq6iqv8/files/output.log b/wandb/run-20260305_053301-jxq6iqv8/files/output.log deleted file mode 100644 index 621eee684de2e064299e0624fc708da7292151fc..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_053301-jxq6iqv8/files/output.log +++ /dev/null @@ -1,55 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 12968.37it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_reg/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -bert.pooler.dense.weight | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 25,097 - Num Epochs = 2 - Num update steps per epoch = 197 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 394 - Number of trainable parameters = 45,088,514 - 51%|█████ | 199/394 [00:08<00:07, 27.85it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/promoter_no_tata/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/promoter_no_tata/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.28it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/promoter_no_tata/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/promoter_no_tata/checkpoint-200/tokenizer_config.json -100%|██████████| 394/394 [00:16<00:00, 28.39it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/promoter_no_tata/checkpoint-394 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/promoter_no_tata/checkpoint-394/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.35it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/promoter_no_tata/checkpoint-394/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/promoter_no_tata/checkpoint-394/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 394/394 [00:16<00:00, 23.25it/s] -{'train_runtime': '16.94', 'train_samples_per_second': '2962', 'train_steps_per_second': '23.25', 'train_loss': '0.3162', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3138 - Batch size = 128 -100%|██████████| 25/25 [00:00<00:00, 99.74it/s] diff --git a/wandb/run-20260305_053301-jxq6iqv8/files/requirements.txt b/wandb/run-20260305_053301-jxq6iqv8/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_053301-jxq6iqv8/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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/home/n5huang/dna_token/pretrain/models/model_len_reg/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -bert.pooler.dense.bias | MISSING | -classifier.weight | MISSING | -classifier.bias | MISSING | -bert.pooler.dense.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 4,219 - Num Epochs = 2 - Num update steps per epoch = 33 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 66 - Number of trainable parameters = 45,088,514 - 97%|█████████▋| 64/66 [00:02<00:00, 28.19it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/promoter_tata/checkpoint-66 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/promoter_tata/checkpoint-66/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.81it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/promoter_tata/checkpoint-66/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/promoter_tata/checkpoint-66/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 66/66 [00:03<00:00, 18.63it/s] -{'train_runtime': '3.541', 'train_samples_per_second': '2383', 'train_steps_per_second': '18.64', 'train_loss': '0.4727', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 528 - Batch size = 128 -100%|██████████| 5/5 [00:00<00:00, 101.19it/s] diff --git a/wandb/run-20260305_053331-69jmd1gq/files/requirements.txt b/wandb/run-20260305_053331-69jmd1gq/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_053331-69jmd1gq/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T05:33:46.140096Z" - writerId: 2grnizam4jri4eg42h83zla6ce7daqmb - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_053346-jcywxbyq/files/output.log b/wandb/run-20260305_053346-jcywxbyq/files/output.log deleted file mode 100644 index f0b5cef1bb3c9e2bdb60e8718e4fb3fbf68d507f..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_053346-jcywxbyq/files/output.log +++ /dev/null @@ -1,70 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 19508.39it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_reg/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -bert.pooler.dense.weight | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 4 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 828 - Number of trainable parameters = 45,088,514 - 24%|██▍ | 199/828 [00:12<00:35, 17.66it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_acceptors/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_acceptors/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.34it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_acceptors/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_acceptors/checkpoint-200/tokenizer_config.json - 48%|████▊ | 400/828 [00:24<00:25, 16.82it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_acceptors/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_acceptors/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.71it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_acceptors/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_acceptors/checkpoint-400/tokenizer_config.json - 72%|███████▏ | 599/828 [00:36<00:13, 17.38it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_acceptors/checkpoint-600 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_acceptors/checkpoint-600/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.15it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_acceptors/checkpoint-600/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_acceptors/checkpoint-600/tokenizer_config.json - 97%|█████████▋| 800/828 [00:48<00:01, 17.46it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_acceptors/checkpoint-800 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_acceptors/checkpoint-800/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.33it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_acceptors/checkpoint-800/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_acceptors/checkpoint-800/tokenizer_config.json -100%|█████████▉| 826/828 [00:51<00:00, 17.07it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_acceptors/checkpoint-828 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_acceptors/checkpoint-828/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.14it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_acceptors/checkpoint-828/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_acceptors/checkpoint-828/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 828/828 [00:51<00:00, 15.94it/s] -{'train_runtime': '51.93', 'train_samples_per_second': '2034', 'train_steps_per_second': '15.95', 'train_loss': '0.4471', 'epoch': '4'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 59.66it/s] diff --git a/wandb/run-20260305_053346-jcywxbyq/files/requirements.txt b/wandb/run-20260305_053346-jcywxbyq/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_053346-jcywxbyq/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 -accelerate==1.13.0 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -triton==3.6.0 -nvidia-nccl-cu12==2.27.5 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -cuda-pathfinder==1.4.0 -shellingham==1.5.4 -torchaudio==2.5.1 -nvidia-cufile-cu12==1.13.1.3 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -nvidia-nvjitlink-cu12==12.8.93 -click==8.3.1 -MarkupSafe==3.0.2 -nvidia-nvshmem-cu12==3.4.5 -urllib3==2.6.3 -cuda-bindings==12.9.4 -propcache==0.4.1 -nvidia-cusolver-cu12==11.7.3.90 -sympy==1.14.0 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -nvidia-cuda-runtime-cu12==12.8.90 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_053346-jcywxbyq/files/wandb-metadata.json b/wandb/run-20260305_053346-jcywxbyq/files/wandb-metadata.json deleted file mode 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- - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "547139940352" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T05:34:54.269038Z" - writerId: ixybouv9ukejpuf6c4ci0hk0jzxd1sh3 - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_053454-zv672fmj/files/output.log b/wandb/run-20260305_053454-zv672fmj/files/output.log deleted file mode 100644 index 497b1efb00eb7534a4dd12256279f27188b2b41c..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_053454-zv672fmj/files/output.log +++ /dev/null @@ -1,70 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 23444.83it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_reg/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -bert.pooler.dense.bias | MISSING | -classifier.bias | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 4 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 828 - Number of trainable parameters = 45,089,283 - 24%|██▍ | 199/828 [00:11<00:35, 17.60it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_all/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_all/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.77it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_all/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_all/checkpoint-200/tokenizer_config.json - 48%|████▊ | 400/828 [00:24<00:24, 17.65it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_all/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_all/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.99it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_all/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_all/checkpoint-400/tokenizer_config.json - 72%|███████▏ | 599/828 [00:36<00:13, 17.16it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_all/checkpoint-600 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_all/checkpoint-600/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.31it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_all/checkpoint-600/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_all/checkpoint-600/tokenizer_config.json - 97%|█████████▋| 800/828 [00:48<00:01, 17.35it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_all/checkpoint-800 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_all/checkpoint-800/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.61it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_all/checkpoint-800/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_all/checkpoint-800/tokenizer_config.json -100%|█████████▉| 826/828 [00:50<00:00, 16.47it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_all/checkpoint-828 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_all/checkpoint-828/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.12it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_all/checkpoint-828/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_all/checkpoint-828/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 828/828 [00:51<00:00, 16.05it/s] -{'train_runtime': '51.58', 'train_samples_per_second': '2047', 'train_steps_per_second': '16.05', 'train_loss': '0.7787', 'epoch': '4'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 61.50it/s] diff --git a/wandb/run-20260305_053454-zv672fmj/files/requirements.txt b/wandb/run-20260305_053454-zv672fmj/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_053454-zv672fmj/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T05:36:01.160990Z" - writerId: x7alrsbo07fi7qtp6mcxduhztub9i0fg - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_053601-325h5jfv/files/output.log b/wandb/run-20260305_053601-325h5jfv/files/output.log deleted file mode 100644 index bf655a23ffbc57ae21caa6398ecb72e2ba1d72c5..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_053601-325h5jfv/files/output.log +++ /dev/null @@ -1,70 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 22241.02it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_reg/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -classifier.weight | MISSING | -bert.pooler.dense.bias | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 4 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 828 - Number of trainable parameters = 45,088,514 - 24%|██▍ | 199/828 [00:12<00:36, 17.25it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_donors/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_donors/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.58it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_donors/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_donors/checkpoint-200/tokenizer_config.json - 48%|████▊ | 400/828 [00:24<00:25, 17.03it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_donors/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_donors/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 5.24it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_donors/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_donors/checkpoint-400/tokenizer_config.json - 72%|███████▏ | 599/828 [00:36<00:13, 17.45it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_donors/checkpoint-600 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_donors/checkpoint-600/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.98it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_donors/checkpoint-600/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_donors/checkpoint-600/tokenizer_config.json - 97%|█████████▋| 800/828 [00:48<00:01, 17.34it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_donors/checkpoint-800 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_donors/checkpoint-800/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.49it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_donors/checkpoint-800/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_donors/checkpoint-800/tokenizer_config.json -100%|█████████▉| 826/828 [00:50<00:00, 17.09it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_donors/checkpoint-828 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_donors/checkpoint-828/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.28it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_donors/checkpoint-828/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_donors/checkpoint-828/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 828/828 [00:51<00:00, 15.93it/s] -{'train_runtime': '51.97', 'train_samples_per_second': '2032', 'train_steps_per_second': '15.93', 'train_loss': '0.446', 'epoch': '4'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 61.15it/s] diff --git a/wandb/run-20260305_053601-325h5jfv/files/requirements.txt b/wandb/run-20260305_053601-325h5jfv/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_053601-325h5jfv/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 -accelerate==1.13.0 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -triton==3.6.0 -nvidia-nccl-cu12==2.27.5 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -cuda-pathfinder==1.4.0 -shellingham==1.5.4 -torchaudio==2.5.1 -nvidia-cufile-cu12==1.13.1.3 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -nvidia-nvjitlink-cu12==12.8.93 -click==8.3.1 -MarkupSafe==3.0.2 -nvidia-nvshmem-cu12==3.4.5 -urllib3==2.6.3 -cuda-bindings==12.9.4 -propcache==0.4.1 -nvidia-cusolver-cu12==11.7.3.90 -sympy==1.14.0 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -nvidia-cuda-runtime-cu12==12.8.90 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_053601-325h5jfv/files/wandb-metadata.json b/wandb/run-20260305_053601-325h5jfv/files/wandb-metadata.json deleted file mode 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cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T05:37:08.492241Z" - writerId: 9w2du2yclbuzir8ao10s7zrlzx9jhwu4 - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_053708-a833wkdd/files/output.log b/wandb/run-20260305_053708-a833wkdd/files/output.log deleted file mode 100644 index 994e660608ac4b1967230722c11200d21085d6c8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_053708-a833wkdd/files/output.log +++ /dev/null @@ -1,60 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 20847.67it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_reg/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -bert.pooler.dense.bias | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.weight | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 2 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 414 - Number of trainable parameters = 45,088,514 - 48%|████▊ | 199/414 [00:16<00:17, 12.20it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H2AFZ/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H2AFZ/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.25it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H2AFZ/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H2AFZ/checkpoint-200/tokenizer_config.json - 96%|█████████▋| 399/414 [00:33<00:01, 12.07it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H2AFZ/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H2AFZ/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.82it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H2AFZ/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H2AFZ/checkpoint-400/tokenizer_config.json -100%|█████████▉| 413/414 [00:35<00:00, 10.80it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H2AFZ/checkpoint-414 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H2AFZ/checkpoint-414/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.30it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H2AFZ/checkpoint-414/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H2AFZ/checkpoint-414/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 414/414 [00:35<00:00, 11.50it/s] -{'train_runtime': '35.98', 'train_samples_per_second': '1467', 'train_steps_per_second': '11.51', 'train_loss': '0.5269', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 42.49it/s] diff --git a/wandb/run-20260305_053708-a833wkdd/files/requirements.txt b/wandb/run-20260305_053708-a833wkdd/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_053708-a833wkdd/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 -accelerate==1.13.0 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -triton==3.6.0 -nvidia-nccl-cu12==2.27.5 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -cuda-pathfinder==1.4.0 -shellingham==1.5.4 -torchaudio==2.5.1 -nvidia-cufile-cu12==1.13.1.3 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -nvidia-nvjitlink-cu12==12.8.93 -click==8.3.1 -MarkupSafe==3.0.2 -nvidia-nvshmem-cu12==3.4.5 -urllib3==2.6.3 -cuda-bindings==12.9.4 -propcache==0.4.1 -nvidia-cusolver-cu12==11.7.3.90 -sympy==1.14.0 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -nvidia-cuda-runtime-cu12==12.8.90 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_053708-a833wkdd/files/wandb-metadata.json b/wandb/run-20260305_053708-a833wkdd/files/wandb-metadata.json deleted file mode 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- --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "547146883072" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - 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/data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T05:38:02.861208Z" - writerId: vi7h717wkcc1grppr4mwc67daxaibngk - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_053802-i7xrmj1i/files/output.log b/wandb/run-20260305_053802-i7xrmj1i/files/output.log deleted file mode 100644 index 24021c31b0f0edd0273c8081c4633c0832d8b524..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_053802-i7xrmj1i/files/output.log +++ /dev/null @@ -1,55 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 22474.65it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_reg/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -bert.pooler.dense.weight | MISSING | -classifier.bias | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 25,292 - Num Epochs = 2 - Num update steps per epoch = 198 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 396 - Number of trainable parameters = 45,088,514 - 50%|█████ | 199/396 [00:16<00:15, 12.76it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H3K27ac/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H3K27ac/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.96it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H3K27ac/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H3K27ac/checkpoint-200/tokenizer_config.json -100%|█████████▉| 395/396 [00:33<00:00, 12.35it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H3K27ac/checkpoint-396 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H3K27ac/checkpoint-396/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.32it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H3K27ac/checkpoint-396/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H3K27ac/checkpoint-396/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 396/396 [00:34<00:00, 11.64it/s] -{'train_runtime': '34.02', 'train_samples_per_second': '1487', 'train_steps_per_second': '11.64', 'train_loss': '0.5533', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3163 - Batch size = 128 -100%|██████████| 25/25 [00:00<00:00, 42.21it/s] diff --git a/wandb/run-20260305_053802-i7xrmj1i/files/requirements.txt b/wandb/run-20260305_053802-i7xrmj1i/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_053802-i7xrmj1i/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T05:38:55.355099Z" - writerId: ufn9ke1paxzhkxsuizsqewq8mdtm4adw - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_053855-u71qtui7/files/output.log b/wandb/run-20260305_053855-u71qtui7/files/output.log deleted file mode 100644 index eedb6beca885a3f7b84491a3e2b7ff31dbfa9256..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_053855-u71qtui7/files/output.log +++ /dev/null @@ -1,60 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 21067.47it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_reg/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -bert.pooler.dense.bias | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.bias | MISSING | -classifier.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 2 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 414 - Number of trainable parameters = 45,088,514 - 48%|████▊ | 200/414 [00:16<00:17, 12.37it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H3K27me3/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H3K27me3/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.18it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H3K27me3/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H3K27me3/checkpoint-200/tokenizer_config.json - 97%|█████████▋| 400/414 [00:33<00:01, 12.46it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H3K27me3/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H3K27me3/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.77it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H3K27me3/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H3K27me3/checkpoint-400/tokenizer_config.json -100%|██████████| 414/414 [00:35<00:00, 12.24it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H3K27me3/checkpoint-414 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H3K27me3/checkpoint-414/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.30it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H3K27me3/checkpoint-414/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H3K27me3/checkpoint-414/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 414/414 [00:35<00:00, 11.58it/s] -{'train_runtime': '35.74', 'train_samples_per_second': '1477', 'train_steps_per_second': '11.58', 'train_loss': '0.4725', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 42.28it/s] diff --git a/wandb/run-20260305_053855-u71qtui7/files/requirements.txt b/wandb/run-20260305_053855-u71qtui7/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_053855-u71qtui7/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 -accelerate==1.13.0 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -triton==3.6.0 -nvidia-nccl-cu12==2.27.5 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -cuda-pathfinder==1.4.0 -shellingham==1.5.4 -torchaudio==2.5.1 -nvidia-cufile-cu12==1.13.1.3 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -nvidia-nvjitlink-cu12==12.8.93 -click==8.3.1 -MarkupSafe==3.0.2 -nvidia-nvshmem-cu12==3.4.5 -urllib3==2.6.3 -cuda-bindings==12.9.4 -propcache==0.4.1 -nvidia-cusolver-cu12==11.7.3.90 -sympy==1.14.0 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -nvidia-cuda-runtime-cu12==12.8.90 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_053855-u71qtui7/files/wandb-metadata.json b/wandb/run-20260305_053855-u71qtui7/files/wandb-metadata.json deleted file mode 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Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T05:39:48.997698Z" - writerId: 6g3piyr2d7ma55r6ce2i6b14edv9782l - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_053948-71lnzx7g/files/output.log b/wandb/run-20260305_053948-71lnzx7g/files/output.log deleted file mode 100644 index 2e7faf17d9217a8b9d16ef08883948c10c84b414..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_053948-71lnzx7g/files/output.log +++ /dev/null @@ -1,60 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 20997.51it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_reg/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -classifier.bias | MISSING | -bert.pooler.dense.weight | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 2 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 414 - Number of trainable parameters = 45,088,514 - 48%|████▊ | 200/414 [00:16<00:17, 12.19it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H3K36me3/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H3K36me3/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 2.95it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H3K36me3/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H3K36me3/checkpoint-200/tokenizer_config.json - 97%|█████████▋| 400/414 [00:33<00:01, 11.82it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H3K36me3/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H3K36me3/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.75it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H3K36me3/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H3K36me3/checkpoint-400/tokenizer_config.json -100%|██████████| 414/414 [00:35<00:00, 11.30it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H3K36me3/checkpoint-414 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H3K36me3/checkpoint-414/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.36it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H3K36me3/checkpoint-414/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H3K36me3/checkpoint-414/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 414/414 [00:36<00:00, 11.39it/s] -{'train_runtime': '36.35', 'train_samples_per_second': '1452', 'train_steps_per_second': '11.39', 'train_loss': '0.465', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 42.45it/s] diff --git a/wandb/run-20260305_053948-71lnzx7g/files/requirements.txt b/wandb/run-20260305_053948-71lnzx7g/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_053948-71lnzx7g/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 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/data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T05:40:44.172171Z" - writerId: tvdnn4syfor5l1qmnus75ayjxn8oh5gu - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_054044-05qyz808/files/output.log b/wandb/run-20260305_054044-05qyz808/files/output.log deleted file mode 100644 index c33d15930bf9a34cac538e339f5b228cc4347b41..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_054044-05qyz808/files/output.log +++ /dev/null @@ -1,60 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 18254.96it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_reg/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -bert.pooler.dense.bias | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.bias | MISSING | -classifier.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 2 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 414 - Number of trainable parameters = 45,088,514 - 48%|████▊ | 199/414 [00:16<00:17, 12.27it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H3K4me1/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H3K4me1/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.65it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H3K4me1/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H3K4me1/checkpoint-200/tokenizer_config.json - 96%|█████████▋| 399/414 [00:34<00:01, 12.42it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H3K4me1/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H3K4me1/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 2.99it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H3K4me1/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H3K4me1/checkpoint-400/tokenizer_config.json -100%|█████████▉| 413/414 [00:36<00:00, 10.23it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H3K4me1/checkpoint-414 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H3K4me1/checkpoint-414/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 2.91it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H3K4me1/checkpoint-414/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H3K4me1/checkpoint-414/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 414/414 [00:37<00:00, 11.13it/s] -{'train_runtime': '37.18', 'train_samples_per_second': '1420', 'train_steps_per_second': '11.13', 'train_loss': '0.5525', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 42.21it/s] diff --git a/wandb/run-20260305_054044-05qyz808/files/requirements.txt b/wandb/run-20260305_054044-05qyz808/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_054044-05qyz808/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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- --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "547155959808" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T05:41:40.157993Z" - writerId: w4h6s46f3fvdl86zxa5058mja5kegtle - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_054140-l43j52i0/files/output.log b/wandb/run-20260305_054140-l43j52i0/files/output.log deleted file mode 100644 index b5801b09b4f7c1dc580d110b889592f9c9cfc7cf..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_054140-l43j52i0/files/output.log +++ /dev/null @@ -1,60 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 21295.16it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_reg/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -classifier.bias | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 25,710 - Num Epochs = 2 - Num update steps per epoch = 201 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 402 - Number of trainable parameters = 45,088,514 - 50%|████▉ | 200/402 [00:16<00:16, 12.04it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H3K4me2/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H3K4me2/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.96it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H3K4me2/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H3K4me2/checkpoint-200/tokenizer_config.json -100%|█████████▉| 400/402 [00:33<00:00, 12.43it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H3K4me2/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H3K4me2/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.53it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H3K4me2/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H3K4me2/checkpoint-400/tokenizer_config.json -100%|██████████| 402/402 [00:34<00:00, 5.72it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H3K4me2/checkpoint-402 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H3K4me2/checkpoint-402/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.42it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H3K4me2/checkpoint-402/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H3K4me2/checkpoint-402/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 402/402 [00:35<00:00, 11.46it/s] -{'train_runtime': '35.07', 'train_samples_per_second': '1466', 'train_steps_per_second': '11.46', 'train_loss': '0.5029', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3215 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 43.65it/s] diff --git a/wandb/run-20260305_054140-l43j52i0/files/requirements.txt b/wandb/run-20260305_054140-l43j52i0/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_054140-l43j52i0/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 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/data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T05:42:32.731180Z" - writerId: ohcatx4yv6yurg2j5hcmegwzobesq2bl - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_054232-hvymwzao/files/output.log b/wandb/run-20260305_054232-hvymwzao/files/output.log deleted file mode 100644 index 1c603de0f5cc774a4d68a36870ecb9e14df27061..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_054232-hvymwzao/files/output.log +++ /dev/null @@ -1,55 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 21613.51it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_reg/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -bert.pooler.dense.weight | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.weight | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 14,595 - Num Epochs = 2 - Num update steps per epoch = 115 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 230 - Number of trainable parameters = 45,088,514 - 87%|████████▋ | 200/230 [00:16<00:02, 12.57it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H3K4me3/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H3K4me3/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.94it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H3K4me3/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H3K4me3/checkpoint-200/tokenizer_config.json - 99%|█████████▉| 228/230 [00:19<00:00, 12.34it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H3K4me3/checkpoint-230 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H3K4me3/checkpoint-230/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.77it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H3K4me3/checkpoint-230/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H3K4me3/checkpoint-230/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 230/230 [00:20<00:00, 11.32it/s] -{'train_runtime': '20.32', 'train_samples_per_second': '1437', 'train_steps_per_second': '11.32', 'train_loss': '0.4201', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 1825 - Batch size = 128 -100%|██████████| 15/15 [00:00<00:00, 45.48it/s] diff --git a/wandb/run-20260305_054232-hvymwzao/files/requirements.txt b/wandb/run-20260305_054232-hvymwzao/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_054232-hvymwzao/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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/data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T05:43:07.860297Z" - writerId: jo2xhyckwvwigzbqz7z3m5q32qk9r5mc - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_054307-1s6wdza2/files/output.log b/wandb/run-20260305_054307-1s6wdza2/files/output.log deleted file mode 100644 index 00ed9f3359808dc920f6b2d62d2b2d9c6dbdb761..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_054307-1s6wdza2/files/output.log +++ /dev/null @@ -1,55 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 25539.56it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_reg/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -classifier.bias | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.weight | MISSING | -bert.pooler.dense.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 19,422 - Num Epochs = 2 - Num update steps per epoch = 152 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 304 - Number of trainable parameters = 45,088,514 - 65%|██████▌ | 199/304 [00:16<00:08, 12.40it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H3K9ac/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H3K9ac/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.29it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H3K9ac/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H3K9ac/checkpoint-200/tokenizer_config.json -100%|█████████▉| 303/304 [00:25<00:00, 12.27it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H3K9ac/checkpoint-304 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H3K9ac/checkpoint-304/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.15it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H3K9ac/checkpoint-304/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H3K9ac/checkpoint-304/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 304/304 [00:26<00:00, 11.40it/s] -{'train_runtime': '26.66', 'train_samples_per_second': '1457', 'train_steps_per_second': '11.4', 'train_loss': '0.5228', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 2429 - Batch size = 128 -100%|██████████| 19/19 [00:00<00:00, 42.30it/s] diff --git a/wandb/run-20260305_054307-1s6wdza2/files/requirements.txt b/wandb/run-20260305_054307-1s6wdza2/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_054307-1s6wdza2/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T05:43:50.291901Z" - writerId: 7nzsy5to3x0mz0tygvzjav5hsltb3pkg - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_054350-rvmw3zwj/files/output.log b/wandb/run-20260305_054350-rvmw3zwj/files/output.log deleted file mode 100644 index 6d65d78460566ba822bbb7a9ba1436569a13a367..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_054350-rvmw3zwj/files/output.log +++ /dev/null @@ -1,55 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 20780.18it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_reg/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -classifier.bias | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.bias | MISSING | -bert.pooler.dense.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 22,630 - Num Epochs = 2 - Num update steps per epoch = 177 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 354 - Number of trainable parameters = 45,088,514 - 56%|█████▋ | 200/354 [00:17<00:12, 12.37it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H3K9me3/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H3K9me3/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.27it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H3K9me3/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H3K9me3/checkpoint-200/tokenizer_config.json -100%|██████████| 354/354 [00:30<00:00, 12.74it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H3K9me3/checkpoint-354 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H3K9me3/checkpoint-354/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.33it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H3K9me3/checkpoint-354/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H3K9me3/checkpoint-354/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 354/354 [00:31<00:00, 11.17it/s] -{'train_runtime': '31.68', 'train_samples_per_second': '1429', 'train_steps_per_second': '11.18', 'train_loss': '0.5945', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 2830 - Batch size = 128 -100%|██████████| 23/23 [00:00<00:00, 42.34it/s] diff --git a/wandb/run-20260305_054350-rvmw3zwj/files/requirements.txt b/wandb/run-20260305_054350-rvmw3zwj/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_054350-rvmw3zwj/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 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/data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T05:44:39.169432Z" - writerId: cayamva9gfhv3bwgs5x80hl640zdokge - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_054439-nn1nihbk/files/output.log b/wandb/run-20260305_054439-nn1nihbk/files/output.log deleted file mode 100644 index 676232c2d4fccfe7600f5a850225663e316bec4b..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_054439-nn1nihbk/files/output.log +++ /dev/null @@ -1,60 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 23036.85it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_reg/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.dense.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -bert.pooler.dense.bias | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.bias | MISSING | -classifier.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 25,816 - Num Epochs = 2 - Num update steps per epoch = 202 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 404 - Number of trainable parameters = 45,088,514 - 50%|████▉ | 200/404 [00:16<00:16, 12.65it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H4K20me1/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H4K20me1/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.83it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H4K20me1/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H4K20me1/checkpoint-200/tokenizer_config.json - 99%|█████████▉| 400/404 [00:33<00:00, 12.39it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H4K20me1/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H4K20me1/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.58it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H4K20me1/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H4K20me1/checkpoint-400/tokenizer_config.json -100%|██████████| 404/404 [00:34<00:00, 5.84it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H4K20me1/checkpoint-404 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H4K20me1/checkpoint-404/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.29it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H4K20me1/checkpoint-404/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_len2/H4K20me1/checkpoint-404/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 404/404 [00:35<00:00, 11.52it/s] -{'train_runtime': '35.07', 'train_samples_per_second': '1472', 'train_steps_per_second': '11.52', 'train_loss': '0.4474', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3227 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 42.99it/s] diff --git a/wandb/run-20260305_054439-nn1nihbk/files/requirements.txt b/wandb/run-20260305_054439-nn1nihbk/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_054439-nn1nihbk/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 -accelerate==1.13.0 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -triton==3.6.0 -nvidia-nccl-cu12==2.27.5 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -cuda-pathfinder==1.4.0 -shellingham==1.5.4 -torchaudio==2.5.1 -nvidia-cufile-cu12==1.13.1.3 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -nvidia-nvjitlink-cu12==12.8.93 -click==8.3.1 -MarkupSafe==3.0.2 -nvidia-nvshmem-cu12==3.4.5 -urllib3==2.6.3 -cuda-bindings==12.9.4 -propcache==0.4.1 -nvidia-cusolver-cu12==11.7.3.90 -sympy==1.14.0 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -nvidia-cuda-runtime-cu12==12.8.90 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_054439-nn1nihbk/files/wandb-metadata.json b/wandb/run-20260305_054439-nn1nihbk/files/wandb-metadata.json deleted file mode 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/home/n5huang/dna_token/pretrain/models/model_len_reg/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -bert.pooler.dense.bias | MISSING | -classifier.weight | MISSING | -classifier.bias | MISSING | -bert.pooler.dense.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 755}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 4 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 828 - Number of trainable parameters = 45,088,514 - 24%|██▍ | 199/828 [00:08<00:26, 24.13it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.57it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers/checkpoint-200/tokenizer_config.json - 48%|████▊ | 400/828 [00:17<00:17, 24.25it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.75it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers/checkpoint-400/tokenizer_config.json - 72%|███████▏ | 598/828 [00:27<00:09, 24.65it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers/checkpoint-600 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers/checkpoint-600/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.60it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers/checkpoint-600/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers/checkpoint-600/tokenizer_config.json - 96%|█████████▋| 799/828 [00:36<00:01, 24.64it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers/checkpoint-800 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers/checkpoint-800/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 2.98it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers/checkpoint-800/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers/checkpoint-800/tokenizer_config.json -100%|█████████▉| 826/828 [00:38<00:00, 21.67it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers/checkpoint-828 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers/checkpoint-828/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.87it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers/checkpoint-828/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers/checkpoint-828/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 828/828 [00:39<00:00, 21.16it/s] -{'train_runtime': '39.13', 'train_samples_per_second': '2699', 'train_steps_per_second': '21.16', 'train_loss': '0.5811', 'epoch': '4'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 82.32it/s] diff --git a/wandb/run-20260305_054533-ukwbyz4p/files/requirements.txt b/wandb/run-20260305_054533-ukwbyz4p/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_054533-ukwbyz4p/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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wandb-AsyncioManager-main:4124787 [mailbox.py:close():155] Closing mailbox, abandoning 1 handles. diff --git a/wandb/run-20260305_054533-ukwbyz4p/run-ukwbyz4p.wandb b/wandb/run-20260305_054533-ukwbyz4p/run-ukwbyz4p.wandb deleted file mode 100644 index 19b297f1f908c4c73a937ee769eadc44ed50071a..0000000000000000000000000000000000000000 Binary files a/wandb/run-20260305_054533-ukwbyz4p/run-ukwbyz4p.wandb and /dev/null differ diff --git a/wandb/run-20260305_054626-wj8grywx/files/config.yaml b/wandb/run-20260305_054626-wj8grywx/files/config.yaml deleted file mode 100644 index a58d4d62299c6263cb760d91db9dcec7fe972cfb..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_054626-wj8grywx/files/config.yaml +++ /dev/null @@ -1,139 +0,0 @@ -_wandb: - value: - cli_version: 0.25.0 - e: - iixyl2il8q2hcdnbjqse580mcn0rgsmc: - args: - - --model_name_or_path - - /home/n5huang/dna_token/pretrain/models/model_len_reg/checkpoint-100000 - - --tokenizer_path - - /home/n5huang/dna_token/tokenizer_evaluation/merge_bpe/merge_tokenizer_unigram_tf_idf.json - - --trust_remote_code - - "True" - - --data_path - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/enhancers_types/split - - --kmer - - "-1" - - --run_name - - hg38_BPE_len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf_3e-5_enhancers_types_seed42 - - --model_max_length - - "100" - - --per_device_train_batch_size - - "128" - - --per_device_eval_batch_size - - "128" - - --gradient_accumulation_steps - - "1" - - --learning_rate - - "3e-5" - - --num_train_epochs - - "4" - - --fp16 - - --save_steps - - "200" - - --output_dir - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers_types - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "547165474816" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T05:46:26.477851Z" - writerId: iixyl2il8q2hcdnbjqse580mcn0rgsmc - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_054626-wj8grywx/files/output.log b/wandb/run-20260305_054626-wj8grywx/files/output.log deleted file mode 100644 index 4b73f96490add4e9ce7c9296f2b8b32d2700374f..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_054626-wj8grywx/files/output.log +++ /dev/null @@ -1,70 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 20814.89it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_reg/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -bert.pooler.dense.weight | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.bias | MISSING | -classifier.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 755}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 4 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 828 - Number of trainable parameters = 45,089,283 - 24%|██▍ | 199/828 [00:08<00:26, 23.90it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers_types/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers_types/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.07it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers_types/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers_types/checkpoint-200/tokenizer_config.json - 48%|████▊ | 400/828 [00:18<00:18, 22.93it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers_types/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers_types/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.38it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers_types/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers_types/checkpoint-400/tokenizer_config.json - 72%|███████▏ | 598/828 [00:26<00:10, 22.90it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers_types/checkpoint-600 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers_types/checkpoint-600/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.87it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers_types/checkpoint-600/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers_types/checkpoint-600/tokenizer_config.json - 96%|█████████▋| 799/828 [00:36<00:01, 24.19it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers_types/checkpoint-800 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers_types/checkpoint-800/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.31it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers_types/checkpoint-800/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers_types/checkpoint-800/tokenizer_config.json -100%|█████████▉| 826/828 [00:38<00:00, 21.17it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers_types/checkpoint-828 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers_types/checkpoint-828/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.39it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers_types/checkpoint-828/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers_types/checkpoint-828/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 828/828 [00:39<00:00, 21.10it/s] -{'train_runtime': '39.24', 'train_samples_per_second': '2691', 'train_steps_per_second': '21.1', 'train_loss': '0.7132', 'epoch': '4'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 82.27it/s] diff --git a/wandb/run-20260305_054626-wj8grywx/files/requirements.txt b/wandb/run-20260305_054626-wj8grywx/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_054626-wj8grywx/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 -accelerate==1.13.0 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -triton==3.6.0 -nvidia-nccl-cu12==2.27.5 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -cuda-pathfinder==1.4.0 -shellingham==1.5.4 -torchaudio==2.5.1 -nvidia-cufile-cu12==1.13.1.3 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -nvidia-nvjitlink-cu12==12.8.93 -click==8.3.1 -MarkupSafe==3.0.2 -nvidia-nvshmem-cu12==3.4.5 -urllib3==2.6.3 -cuda-bindings==12.9.4 -propcache==0.4.1 -nvidia-cusolver-cu12==11.7.3.90 -sympy==1.14.0 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -nvidia-cuda-runtime-cu12==12.8.90 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_054626-wj8grywx/files/wandb-metadata.json b/wandb/run-20260305_054626-wj8grywx/files/wandb-metadata.json deleted file mode 100644 index c310c66645c59ae4983e58b65dbb4f68637f7dfc..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_054626-wj8grywx/files/wandb-metadata.json +++ /dev/null @@ -1,134 +0,0 @@ -{ - "os": "Linux-5.15.0-72-generic-x86_64-with-glibc2.35", - "python": "CPython 3.10.19", - "startedAt": "2026-03-05T05:46:26.477851Z", - "args": [ - "--model_name_or_path", - "/home/n5huang/dna_token/pretrain/models/model_len_reg/checkpoint-100000", - "--tokenizer_path", - "/home/n5huang/dna_token/tokenizer_evaluation/merge_bpe/merge_tokenizer_unigram_tf_idf.json", - "--trust_remote_code", - "True", - "--data_path", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/enhancers_types/split", - "--kmer", - "-1", - "--run_name", - "hg38_BPE_len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf_3e-5_enhancers_types_seed42", - "--model_max_length", - "100", - "--per_device_train_batch_size", - "128", - 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/data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T05:47:19.438096Z" - writerId: jbb4c5woc38lvm656241qvjnhwds3bly - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_054719-u5gidxzz/files/output.log b/wandb/run-20260305_054719-u5gidxzz/files/output.log deleted file mode 100644 index d1a63e47705f6b55de6f1ad72fa810ca0958d42d..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_054719-u5gidxzz/files/output.log +++ /dev/null @@ -1,55 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 21497.24it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_reg/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -classifier.weight | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.bias | MISSING | -bert.pooler.dense.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 755}. -***** Running training ***** - Num examples = 25,267 - Num Epochs = 2 - Num update steps per epoch = 198 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 396 - Number of trainable parameters = 45,088,514 - 50%|█████ | 199/396 [00:07<00:06, 29.12it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/promoter_all/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/promoter_all/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.01it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/promoter_all/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/promoter_all/checkpoint-200/tokenizer_config.json - 99%|█████████▉| 394/396 [00:15<00:00, 28.42it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/promoter_all/checkpoint-396 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/promoter_all/checkpoint-396/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.91it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/promoter_all/checkpoint-396/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/promoter_all/checkpoint-396/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 396/396 [00:16<00:00, 24.24it/s] -{'train_runtime': '16.34', 'train_samples_per_second': '3093', 'train_steps_per_second': '24.24', 'train_loss': '0.3939', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3159 - Batch size = 128 -100%|██████████| 25/25 [00:00<00:00, 88.69it/s] diff --git a/wandb/run-20260305_054719-u5gidxzz/files/requirements.txt b/wandb/run-20260305_054719-u5gidxzz/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_054719-u5gidxzz/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T05:47:49.748697Z" - writerId: hruxzeccdtao9a628ugg3m00v5ew6pq3 - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_054749-3jmoe0b8/files/output.log b/wandb/run-20260305_054749-3jmoe0b8/files/output.log deleted file mode 100644 index 582ddfbec9fd5e128f57832f0a1713d82e70e9b9..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_054749-3jmoe0b8/files/output.log +++ /dev/null @@ -1,55 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 22804.95it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_reg/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -bert.pooler.dense.weight | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.bias | MISSING | -classifier.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 755}. -***** Running training ***** - Num examples = 25,097 - Num Epochs = 2 - Num update steps per epoch = 197 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 394 - Number of trainable parameters = 45,088,514 - 51%|█████ | 200/394 [00:07<00:06, 28.77it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/promoter_no_tata/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/promoter_no_tata/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.82it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/promoter_no_tata/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/promoter_no_tata/checkpoint-200/tokenizer_config.json - 99%|█████████▉| 392/394 [00:15<00:00, 27.25it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/promoter_no_tata/checkpoint-394 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/promoter_no_tata/checkpoint-394/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.52it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/promoter_no_tata/checkpoint-394/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/promoter_no_tata/checkpoint-394/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 394/394 [00:16<00:00, 24.56it/s] -{'train_runtime': '16.04', 'train_samples_per_second': '3129', 'train_steps_per_second': '24.56', 'train_loss': '0.3779', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3138 - Batch size = 128 -100%|██████████| 25/25 [00:00<00:00, 99.17it/s] diff --git a/wandb/run-20260305_054749-3jmoe0b8/files/requirements.txt b/wandb/run-20260305_054749-3jmoe0b8/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_054749-3jmoe0b8/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 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/home/n5huang/dna_token/pretrain/models/model_len_reg/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -classifier.bias | MISSING | -bert.pooler.dense.weight | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 755}. -***** Running training ***** - Num examples = 4,219 - Num Epochs = 2 - Num update steps per epoch = 33 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 66 - Number of trainable parameters = 45,088,514 - 97%|█████████▋| 64/66 [00:02<00:00, 28.67it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/promoter_tata/checkpoint-66 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/promoter_tata/checkpoint-66/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.82it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/promoter_tata/checkpoint-66/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/promoter_tata/checkpoint-66/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 66/66 [00:03<00:00, 17.84it/s] -{'train_runtime': '3.691', 'train_samples_per_second': '2286', 'train_steps_per_second': '17.88', 'train_loss': '0.5486', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 528 - Batch size = 128 -100%|██████████| 5/5 [00:00<00:00, 102.56it/s] diff --git a/wandb/run-20260305_054819-ilfsm4th/files/requirements.txt b/wandb/run-20260305_054819-ilfsm4th/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_054819-ilfsm4th/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/splice_sites_acceptors/split - - --kmer - - "-1" - - --run_name - - hg38_BPE_len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf_3e-5_splice_sites_acceptors_seed42 - - --model_max_length - - "140" - - --per_device_train_batch_size - - "128" - - --per_device_eval_batch_size - - "128" - - --gradient_accumulation_steps - - "1" - - --learning_rate - - "3e-5" - - --num_train_epochs - - "4" - - --fp16 - - --save_steps - - "200" - - --output_dir - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_acceptors - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "547171999744" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T05:48:34.530045Z" - writerId: ggosqb21tmc1n1oxeiqvuz9n10vqcoa3 - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_054834-7aiwsb6p/files/output.log b/wandb/run-20260305_054834-7aiwsb6p/files/output.log deleted file mode 100644 index 74fcb514dafde1620fbda234fc830a263042b05d..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_054834-7aiwsb6p/files/output.log +++ /dev/null @@ -1,70 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 22576.46it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_reg/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -classifier.weight | MISSING | -classifier.bias | MISSING | -bert.pooler.dense.weight | MISSING | -bert.pooler.dense.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 755}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 4 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 828 - Number of trainable parameters = 45,088,514 - 24%|██▍ | 199/828 [00:11<00:36, 17.45it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_acceptors/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_acceptors/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.01it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_acceptors/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_acceptors/checkpoint-200/tokenizer_config.json - 48%|████▊ | 400/828 [00:24<00:24, 17.20it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_acceptors/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_acceptors/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.94it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_acceptors/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_acceptors/checkpoint-400/tokenizer_config.json - 72%|███████▏ | 599/828 [00:36<00:13, 17.27it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_acceptors/checkpoint-600 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_acceptors/checkpoint-600/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.53it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_acceptors/checkpoint-600/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_acceptors/checkpoint-600/tokenizer_config.json - 97%|█████████▋| 800/828 [00:48<00:01, 17.41it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_acceptors/checkpoint-800 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_acceptors/checkpoint-800/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.26it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_acceptors/checkpoint-800/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_acceptors/checkpoint-800/tokenizer_config.json -100%|█████████▉| 826/828 [00:50<00:00, 17.11it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_acceptors/checkpoint-828 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_acceptors/checkpoint-828/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.42it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_acceptors/checkpoint-828/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_acceptors/checkpoint-828/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 828/828 [00:51<00:00, 16.07it/s] -{'train_runtime': '51.52', 'train_samples_per_second': '2050', 'train_steps_per_second': '16.07', 'train_loss': '0.6191', 'epoch': '4'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 54.76it/s] diff --git a/wandb/run-20260305_054834-7aiwsb6p/files/requirements.txt b/wandb/run-20260305_054834-7aiwsb6p/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_054834-7aiwsb6p/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T05:49:41.987144Z" - writerId: s6f6ttp6m5hzd7lq4zyd839y2sr273dl - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_054941-8k63cppy/files/output.log b/wandb/run-20260305_054941-8k63cppy/files/output.log deleted file mode 100644 index b39d315a0fab11c2c78c207fcb60cea228d90587..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_054941-8k63cppy/files/output.log +++ /dev/null @@ -1,70 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 22897.39it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_reg/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -classifier.bias | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.weight | MISSING | -bert.pooler.dense.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 755}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 4 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 828 - Number of trainable parameters = 45,089,283 - 24%|██▍ | 199/828 [00:11<00:36, 17.07it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_all/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_all/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.25it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_all/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_all/checkpoint-200/tokenizer_config.json - 48%|████▊ | 400/828 [00:24<00:24, 17.67it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_all/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_all/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.25it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_all/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_all/checkpoint-400/tokenizer_config.json - 72%|███████▏ | 599/828 [00:36<00:13, 17.15it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_all/checkpoint-600 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_all/checkpoint-600/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.15it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_all/checkpoint-600/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_all/checkpoint-600/tokenizer_config.json - 97%|█████████▋| 800/828 [00:48<00:01, 17.34it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_all/checkpoint-800 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_all/checkpoint-800/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.60it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_all/checkpoint-800/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_all/checkpoint-800/tokenizer_config.json -100%|█████████▉| 826/828 [00:50<00:00, 16.99it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_all/checkpoint-828 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_all/checkpoint-828/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.35it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_all/checkpoint-828/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_all/checkpoint-828/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 828/828 [00:51<00:00, 16.11it/s] -{'train_runtime': '51.4', 'train_samples_per_second': '2054', 'train_steps_per_second': '16.11', 'train_loss': '1.017', 'epoch': '4'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 61.71it/s] diff --git a/wandb/run-20260305_054941-8k63cppy/files/requirements.txt b/wandb/run-20260305_054941-8k63cppy/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_054941-8k63cppy/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 -accelerate==1.13.0 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -triton==3.6.0 -nvidia-nccl-cu12==2.27.5 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -cuda-pathfinder==1.4.0 -shellingham==1.5.4 -torchaudio==2.5.1 -nvidia-cufile-cu12==1.13.1.3 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -nvidia-nvjitlink-cu12==12.8.93 -click==8.3.1 -MarkupSafe==3.0.2 -nvidia-nvshmem-cu12==3.4.5 -urllib3==2.6.3 -cuda-bindings==12.9.4 -propcache==0.4.1 -nvidia-cusolver-cu12==11.7.3.90 -sympy==1.14.0 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -nvidia-cuda-runtime-cu12==12.8.90 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_054941-8k63cppy/files/wandb-metadata.json b/wandb/run-20260305_054941-8k63cppy/files/wandb-metadata.json deleted file mode 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/home/n5huang/dna_token/tokenizer_evaluation/merge_bpe/merge_tokenizer_unigram_tf_idf.json - - --trust_remote_code - - "True" - - --data_path - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/splice_sites_donors/split - - --kmer - - "-1" - - --run_name - - hg38_BPE_len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf_3e-5_splice_sites_donors_seed42 - - --model_max_length - - "140" - - --per_device_train_batch_size - - "128" - - --per_device_eval_batch_size - - "128" - - --gradient_accumulation_steps - - "1" - - --learning_rate - - "3e-5" - - --num_train_epochs - - "4" - - --fp16 - - --save_steps - - "200" - - --output_dir - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_donors - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "547176775680" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T05:50:49.088358Z" - writerId: eq0lsxzb7bxpc7d0dx7tvebzrf1nzdtp - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_055049-w0flglxr/files/output.log b/wandb/run-20260305_055049-w0flglxr/files/output.log deleted file mode 100644 index 8a379daa7551cae837fd6e92538f88bb18ebb30e..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_055049-w0flglxr/files/output.log +++ /dev/null @@ -1,70 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 20673.70it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_reg/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -bert.pooler.dense.bias | MISSING | -classifier.bias | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 755}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 4 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 828 - Number of trainable parameters = 45,088,514 - 24%|██▍ | 199/828 [00:11<00:35, 17.62it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_donors/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_donors/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.96it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_donors/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_donors/checkpoint-200/tokenizer_config.json - 48%|████▊ | 400/828 [00:24<00:24, 17.50it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_donors/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_donors/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.75it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_donors/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_donors/checkpoint-400/tokenizer_config.json - 72%|███████▏ | 599/828 [00:36<00:13, 17.60it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_donors/checkpoint-600 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_donors/checkpoint-600/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.04it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_donors/checkpoint-600/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_donors/checkpoint-600/tokenizer_config.json - 97%|█████████▋| 800/828 [00:48<00:01, 17.50it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_donors/checkpoint-800 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_donors/checkpoint-800/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.59it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_donors/checkpoint-800/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_donors/checkpoint-800/tokenizer_config.json -100%|█████████▉| 826/828 [00:51<00:00, 16.91it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_donors/checkpoint-828 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_donors/checkpoint-828/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.22it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_donors/checkpoint-828/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_donors/checkpoint-828/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 828/828 [00:52<00:00, 15.86it/s] -{'train_runtime': '52.21', 'train_samples_per_second': '2022', 'train_steps_per_second': '15.86', 'train_loss': '0.5761', 'epoch': '4'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 61.40it/s] diff --git a/wandb/run-20260305_055049-w0flglxr/files/requirements.txt b/wandb/run-20260305_055049-w0flglxr/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_055049-w0flglxr/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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/home/n5huang/dna_token/pretrain/models/model_len_reg/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.decoder.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -bert.pooler.dense.weight | MISSING | -classifier.bias | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 755}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 2 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 414 - Number of trainable parameters = 45,088,514 - 48%|████▊ | 199/414 [00:23<00:16, 12.97it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H2AFZ/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H2AFZ/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.09it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H2AFZ/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H2AFZ/checkpoint-200/tokenizer_config.json - 96%|█████████▋| 399/414 [00:39<00:01, 13.06it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H2AFZ/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H2AFZ/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.22it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H2AFZ/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H2AFZ/checkpoint-400/tokenizer_config.json -100%|█████████▉| 413/414 [00:41<00:00, 11.05it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H2AFZ/checkpoint-414 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H2AFZ/checkpoint-414/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.63it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H2AFZ/checkpoint-414/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H2AFZ/checkpoint-414/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 414/414 [00:42<00:00, 9.84it/s] -{'train_runtime': '42.09', 'train_samples_per_second': '1255', 'train_steps_per_second': '9.837', 'train_loss': '0.605', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 43.72it/s] diff --git a/wandb/run-20260305_055157-opt91v37/files/requirements.txt b/wandb/run-20260305_055157-opt91v37/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_055157-opt91v37/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "547181477888" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T05:53:06.433125Z" - writerId: 7vyserff8d4umcumyul3bzd1u491ohlf - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_055306-rxerkliw/files/output.log b/wandb/run-20260305_055306-rxerkliw/files/output.log deleted file mode 100644 index 0e82be42ebc86ab8b320a5e787f72fddb7228cf5..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_055306-rxerkliw/files/output.log +++ /dev/null @@ -1,55 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 19262.67it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_reg/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -bert.pooler.dense.weight | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.bias | MISSING | -classifier.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 755}. -***** Running training ***** - Num examples = 25,292 - Num Epochs = 2 - Num update steps per epoch = 198 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 396 - Number of trainable parameters = 45,088,514 - 50%|█████ | 199/396 [00:15<00:14, 13.68it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K27ac/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K27ac/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.75it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K27ac/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K27ac/checkpoint-200/tokenizer_config.json -100%|█████████▉| 395/396 [00:32<00:00, 12.70it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K27ac/checkpoint-396 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K27ac/checkpoint-396/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.83it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K27ac/checkpoint-396/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K27ac/checkpoint-396/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 396/396 [00:32<00:00, 12.09it/s] -{'train_runtime': '32.76', 'train_samples_per_second': '1544', 'train_steps_per_second': '12.09', 'train_loss': '0.6164', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3163 - Batch size = 128 -100%|██████████| 25/25 [00:00<00:00, 43.92it/s] diff --git a/wandb/run-20260305_055306-rxerkliw/files/requirements.txt b/wandb/run-20260305_055306-rxerkliw/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_055306-rxerkliw/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 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/home/n5huang/dna_token/tokenizer_evaluation/merge_bpe/merge_tokenizer_unigram_tf_idf.json - - --trust_remote_code - - "True" - - --data_path - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/H3K27me3/split - - --kmer - - "-1" - - --run_name - - hg38_BPE_len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf_3e-5_H3K27me3_seed42 - - --model_max_length - - "220" - - --per_device_train_batch_size - - "128" - - --per_device_eval_batch_size - - "128" - - --gradient_accumulation_steps - - "1" - - --learning_rate - - "3e-5" - - --num_train_epochs - - "2" - - --fp16 - - --save_steps - - "200" - - --output_dir - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K27me3 - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "547216674816" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T05:53:58.581800Z" - writerId: nyhwa2rbo4l0ix8hb84mtt5mli1ql4ob - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_055358-4yntdz7l/files/output.log b/wandb/run-20260305_055358-4yntdz7l/files/output.log deleted file mode 100644 index 9c306d46f53ac95da2de12952adf81cc0653a581..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_055358-4yntdz7l/files/output.log +++ /dev/null @@ -1,60 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 15762.19it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_reg/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -bert.pooler.dense.bias | MISSING | -classifier.bias | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 755}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 2 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 414 - Number of trainable parameters = 45,088,514 - 48%|████▊ | 199/414 [00:15<00:16, 12.93it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K27me3/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K27me3/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.23it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K27me3/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K27me3/checkpoint-200/tokenizer_config.json - 96%|█████████▋| 399/414 [00:32<00:01, 12.76it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K27me3/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K27me3/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.61it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K27me3/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K27me3/checkpoint-400/tokenizer_config.json -100%|█████████▉| 413/414 [00:34<00:00, 10.99it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K27me3/checkpoint-414 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K27me3/checkpoint-414/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.61it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K27me3/checkpoint-414/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K27me3/checkpoint-414/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 414/414 [00:34<00:00, 11.85it/s] -{'train_runtime': '34.95', 'train_samples_per_second': '1511', 'train_steps_per_second': '11.85', 'train_loss': '0.5556', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 43.69it/s] diff --git a/wandb/run-20260305_055358-4yntdz7l/files/requirements.txt b/wandb/run-20260305_055358-4yntdz7l/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_055358-4yntdz7l/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 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/home/n5huang/dna_token/pretrain/models/model_len_reg/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -classifier.bias | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 755}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 2 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 414 - Number of trainable parameters = 45,088,514 - 48%|████▊ | 199/414 [00:15<00:16, 13.08it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K36me3/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K36me3/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.90it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K36me3/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K36me3/checkpoint-200/tokenizer_config.json - 96%|█████████▋| 399/414 [00:32<00:01, 13.04it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K36me3/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K36me3/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.15it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K36me3/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K36me3/checkpoint-400/tokenizer_config.json -100%|█████████▉| 413/414 [00:33<00:00, 10.89it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K36me3/checkpoint-414 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K36me3/checkpoint-414/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.13it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K36me3/checkpoint-414/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K36me3/checkpoint-414/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 414/414 [00:34<00:00, 11.96it/s] -{'train_runtime': '34.62', 'train_samples_per_second': '1525', 'train_steps_per_second': '11.96', 'train_loss': '0.5471', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 43.66it/s] diff --git a/wandb/run-20260305_055452-huj1ggo5/files/requirements.txt b/wandb/run-20260305_055452-huj1ggo5/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_055452-huj1ggo5/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "547223187456" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T05:55:44.653415Z" - writerId: laticm60hwb19pp0clgytunsvgrnkheo - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_055544-ggfysiha/files/output.log b/wandb/run-20260305_055544-ggfysiha/files/output.log deleted file mode 100644 index cff803398c5fba5f2a2bbb5365d46be31bd77532..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_055544-ggfysiha/files/output.log +++ /dev/null @@ -1,60 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 19687.91it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_reg/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -bert.pooler.dense.weight | MISSING | -classifier.bias | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 755}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 2 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 414 - Number of trainable parameters = 45,088,514 - 48%|████▊ | 199/414 [00:15<00:16, 13.11it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me1/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me1/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.43it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me1/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me1/checkpoint-200/tokenizer_config.json - 96%|█████████▋| 399/414 [00:32<00:01, 13.08it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me1/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me1/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.25it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me1/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me1/checkpoint-400/tokenizer_config.json -100%|█████████▉| 413/414 [00:34<00:00, 10.93it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me1/checkpoint-414 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me1/checkpoint-414/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.07it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me1/checkpoint-414/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me1/checkpoint-414/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 414/414 [00:34<00:00, 11.84it/s] -{'train_runtime': '34.96', 'train_samples_per_second': '1510', 'train_steps_per_second': '11.84', 'train_loss': '0.6256', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 43.08it/s] diff --git a/wandb/run-20260305_055544-ggfysiha/files/requirements.txt b/wandb/run-20260305_055544-ggfysiha/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_055544-ggfysiha/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 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/home/n5huang/dna_token/tokenizer_evaluation/merge_bpe/merge_tokenizer_unigram_tf_idf.json - - --trust_remote_code - - "True" - - --data_path - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/H3K4me2/split - - --kmer - - "-1" - - --run_name - - hg38_BPE_len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf_3e-5_H3K4me2_seed42 - - --model_max_length - - "220" - - --per_device_train_batch_size - - "128" - - --per_device_eval_batch_size - - "128" - - --gradient_accumulation_steps - - "1" - - --learning_rate - - "3e-5" - - --num_train_epochs - - "2" - - --fp16 - - --save_steps - - "200" - - --output_dir - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me2 - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "547225440256" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T05:56:37.363351Z" - writerId: zkw0euf9rsanx596w4myowh4ihkif7vq - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_055637-o3ysg40o/files/output.log b/wandb/run-20260305_055637-o3ysg40o/files/output.log deleted file mode 100644 index 5cc7499832578c6a7f1050ad074564704ea1efc7..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_055637-o3ysg40o/files/output.log +++ /dev/null @@ -1,60 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 20782.22it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_reg/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -classifier.weight | MISSING | -classifier.bias | MISSING | -bert.pooler.dense.bias | MISSING | -bert.pooler.dense.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 755}. -***** Running training ***** - Num examples = 25,710 - Num Epochs = 2 - Num update steps per epoch = 201 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 402 - Number of trainable parameters = 45,088,514 - 50%|████▉ | 199/402 [00:15<00:15, 12.89it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me2/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me2/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.47it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me2/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me2/checkpoint-200/tokenizer_config.json - 99%|█████████▉| 399/402 [00:32<00:00, 12.97it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me2/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me2/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.66it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me2/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me2/checkpoint-400/tokenizer_config.json -100%|█████████▉| 401/402 [00:33<00:00, 5.23it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me2/checkpoint-402 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me2/checkpoint-402/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.86it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me2/checkpoint-402/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me2/checkpoint-402/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 402/402 [00:34<00:00, 11.75it/s] -{'train_runtime': '34.21', 'train_samples_per_second': '1503', 'train_steps_per_second': '11.75', 'train_loss': '0.5692', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3215 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 44.36it/s] diff --git a/wandb/run-20260305_055637-o3ysg40o/files/requirements.txt b/wandb/run-20260305_055637-o3ysg40o/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_055637-o3ysg40o/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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/home/n5huang/dna_token/pretrain/models/model_len_reg/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -bert.pooler.dense.bias | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.weight | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 755}. -***** Running training ***** - Num examples = 14,595 - Num Epochs = 2 - Num update steps per epoch = 115 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 230 - Number of trainable parameters = 45,088,514 - 87%|████████▋ | 199/230 [00:16<00:02, 13.03it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me3/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me3/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.28it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me3/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me3/checkpoint-200/tokenizer_config.json -100%|█████████▉| 229/230 [00:19<00:00, 12.84it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me3/checkpoint-230 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me3/checkpoint-230/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.44it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me3/checkpoint-230/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me3/checkpoint-230/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 230/230 [00:19<00:00, 11.50it/s] -{'train_runtime': '19.99', 'train_samples_per_second': '1460', 'train_steps_per_second': '11.5', 'train_loss': '0.4927', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 1825 - Batch size = 128 -100%|██████████| 15/15 [00:00<00:00, 46.93it/s] diff --git a/wandb/run-20260305_055729-4f0f8cgt/files/requirements.txt b/wandb/run-20260305_055729-4f0f8cgt/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_055729-4f0f8cgt/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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/data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T05:58:04.970253Z" - writerId: 55tybrewuu0r3tntfiph2ie24ssu9ab3 - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_055804-6rojwoc7/files/output.log b/wandb/run-20260305_055804-6rojwoc7/files/output.log deleted file mode 100644 index a09f8599378e1fe4b1f0f43528474209fea2e209..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_055804-6rojwoc7/files/output.log +++ /dev/null @@ -1,55 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 7584.77it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_reg/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -classifier.bias | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 755}. -***** Running training ***** - Num examples = 19,422 - Num Epochs = 2 - Num update steps per epoch = 152 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 304 - Number of trainable parameters = 45,088,514 - 65%|██████▌ | 199/304 [00:21<00:08, 12.27it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K9ac/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K9ac/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 2.39it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K9ac/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K9ac/checkpoint-200/tokenizer_config.json -100%|█████████▉| 303/304 [00:32<00:00, 10.69it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K9ac/checkpoint-304 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K9ac/checkpoint-304/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 1.45it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K9ac/checkpoint-304/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K9ac/checkpoint-304/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 304/304 [00:34<00:00, 8.74it/s] -{'train_runtime': '34.79', 'train_samples_per_second': '1117', 'train_steps_per_second': '8.738', 'train_loss': '0.5901', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 2429 - Batch size = 128 -100%|██████████| 19/19 [00:00<00:00, 26.33it/s] diff --git a/wandb/run-20260305_055804-6rojwoc7/files/requirements.txt b/wandb/run-20260305_055804-6rojwoc7/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_055804-6rojwoc7/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T05:59:22.146724Z" - writerId: zuxa3qlnespduzf21llr1ftc9mzxwq9n - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_055922-85rszf73/files/output.log b/wandb/run-20260305_055922-85rszf73/files/output.log deleted file mode 100644 index 0774147fd3997b4b08291406edaf13327b34d7c9..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_055922-85rszf73/files/output.log +++ /dev/null @@ -1,55 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 7579.48it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_reg/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -classifier.weight | MISSING | -classifier.bias | MISSING | -bert.pooler.dense.weight | MISSING | -bert.pooler.dense.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 755}. -***** Running training ***** - Num examples = 22,630 - Num Epochs = 2 - Num update steps per epoch = 177 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 354 - Number of trainable parameters = 45,088,514 - 56%|█████▌ | 199/354 [00:21<00:17, 8.80it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K9me3/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K9me3/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 1.34it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K9me3/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K9me3/checkpoint-200/tokenizer_config.json -100%|█████████▉| 353/354 [00:41<00:00, 9.95it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K9me3/checkpoint-354 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K9me3/checkpoint-354/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 1.51it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K9me3/checkpoint-354/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K9me3/checkpoint-354/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 354/354 [00:43<00:00, 8.12it/s] -{'train_runtime': '43.62', 'train_samples_per_second': '1038', 'train_steps_per_second': '8.116', 'train_loss': '0.6717', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 2830 - Batch size = 128 -100%|██████████| 23/23 [00:01<00:00, 22.74it/s] diff --git a/wandb/run-20260305_055922-85rszf73/files/requirements.txt b/wandb/run-20260305_055922-85rszf73/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_055922-85rszf73/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 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/data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T06:00:56.861598Z" - writerId: l6dyc6h476t19alusbgijzcb9zf4pk61 - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_060056-1iyj30qn/files/output.log b/wandb/run-20260305_060056-1iyj30qn/files/output.log deleted file mode 100644 index 9825f4855f1eb36550038aad69bc9bc9b99b7e3d..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_060056-1iyj30qn/files/output.log +++ /dev/null @@ -1,60 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 20031.43it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_reg/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -bert.pooler.dense.weight | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.weight | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 755}. -***** Running training ***** - Num examples = 25,816 - Num Epochs = 2 - Num update steps per epoch = 202 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 404 - Number of trainable parameters = 45,088,514 - 49%|████▉ | 199/404 [00:15<00:15, 13.06it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H4K20me1/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H4K20me1/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.97it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H4K20me1/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H4K20me1/checkpoint-200/tokenizer_config.json - 99%|█████████▉| 399/404 [00:32<00:00, 12.72it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H4K20me1/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H4K20me1/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.62it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H4K20me1/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H4K20me1/checkpoint-400/tokenizer_config.json -100%|█████████▉| 403/404 [00:33<00:00, 6.28it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H4K20me1/checkpoint-404 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H4K20me1/checkpoint-404/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.48it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H4K20me1/checkpoint-404/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len_reg__merge_bpe_merge_tokenizer_unigram_tf_idf/H4K20me1/checkpoint-404/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 404/404 [00:34<00:00, 11.87it/s] -{'train_runtime': '34.05', 'train_samples_per_second': '1516', 'train_steps_per_second': '11.87', 'train_loss': '0.5131', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3227 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 45.01it/s] diff --git a/wandb/run-20260305_060056-1iyj30qn/files/requirements.txt b/wandb/run-20260305_060056-1iyj30qn/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_060056-1iyj30qn/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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- - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "547237130240" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T06:02:01.009521Z" - writerId: 7x6qtjiano51qp27zwh8cn8e9xxno1lp - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_060201-leeq2zek/files/output.log b/wandb/run-20260305_060201-leeq2zek/files/output.log deleted file mode 100644 index aea14131421236ab31cb9c615f1d0c1bbf56d76b..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_060201-leeq2zek/files/output.log +++ /dev/null @@ -1,69 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 20861.02it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_2/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -classifier.weight | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.bias | MISSING | -bert.pooler.dense.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 4 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 828 - Number of trainable parameters = 45,088,514 - 24%|██▍ | 199/828 [00:08<00:25, 24.59it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/enhancers/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/enhancers/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.69it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/enhancers/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/enhancers/checkpoint-200/tokenizer_config.json - 48%|████▊ | 400/828 [00:18<00:17, 24.34it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/enhancers/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/enhancers/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.15it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/enhancers/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/enhancers/checkpoint-400/tokenizer_config.json - 72%|███████▏ | 598/828 [00:26<00:09, 24.42it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/enhancers/checkpoint-600 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/enhancers/checkpoint-600/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.31it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/enhancers/checkpoint-600/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/enhancers/checkpoint-600/tokenizer_config.json - 96%|█████████▋| 799/828 [00:35<00:01, 24.17it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/enhancers/checkpoint-800 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/enhancers/checkpoint-800/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.95it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/enhancers/checkpoint-800/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/enhancers/checkpoint-800/tokenizer_config.json -100%|█████████▉| 826/828 [00:37<00:00, 21.22it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/enhancers/checkpoint-828 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/enhancers/checkpoint-828/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.37it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/enhancers/checkpoint-828/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/enhancers/checkpoint-828/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 828/828 [00:38<00:00, 21.47it/s] -{'train_runtime': '38.57', 'train_samples_per_second': '2738', 'train_steps_per_second': '21.47', 'train_loss': '0.5797', 'epoch': '4'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 82.40it/s] diff --git a/wandb/run-20260305_060201-leeq2zek/files/requirements.txt b/wandb/run-20260305_060201-leeq2zek/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_060201-leeq2zek/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 -accelerate==1.13.0 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -triton==3.6.0 -nvidia-nccl-cu12==2.27.5 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -cuda-pathfinder==1.4.0 -shellingham==1.5.4 -torchaudio==2.5.1 -nvidia-cufile-cu12==1.13.1.3 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -nvidia-nvjitlink-cu12==12.8.93 -click==8.3.1 -MarkupSafe==3.0.2 -nvidia-nvshmem-cu12==3.4.5 -urllib3==2.6.3 -cuda-bindings==12.9.4 -propcache==0.4.1 -nvidia-cusolver-cu12==11.7.3.90 -sympy==1.14.0 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -nvidia-cuda-runtime-cu12==12.8.90 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_060201-leeq2zek/files/wandb-metadata.json b/wandb/run-20260305_060201-leeq2zek/files/wandb-metadata.json deleted file mode 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/home/n5huang/dna_token/tokenizer_evaluation/baseline_bpe/tokenizer.json - - --trust_remote_code - - "True" - - --data_path - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/enhancers_types/split - - --kmer - - "-1" - - --run_name - - hg38_BPE_len2__baseline_bpe_tokenizer_3e-5_enhancers_types_seed42 - - --model_max_length - - "100" - - --per_device_train_batch_size - - "128" - - --per_device_eval_batch_size - - "128" - - --gradient_accumulation_steps - - "1" - - --learning_rate - - "3e-5" - - --num_train_epochs - - "4" - - --fp16 - - --save_steps - - "200" - - --output_dir - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/enhancers_types - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "547237388288" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T06:02:54.143598Z" - writerId: 1hix7ar1qmmpp5mmfhty1mnuiypv87zx - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_060254-j63gdhfb/files/output.log b/wandb/run-20260305_060254-j63gdhfb/files/output.log deleted file mode 100644 index 5d29d668123e87ef088191ef1bf82e1f9c6f6de4..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_060254-j63gdhfb/files/output.log +++ /dev/null @@ -1,69 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 25423.08it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_2/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -classifier.bias | MISSING | -bert.pooler.dense.bias | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 4 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 828 - Number of trainable parameters = 45,089,283 - 24%|██▍ | 199/828 [00:08<00:26, 23.43it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/enhancers_types/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/enhancers_types/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.86it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/enhancers_types/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/enhancers_types/checkpoint-200/tokenizer_config.json - 48%|████▊ | 400/828 [00:17<00:18, 23.30it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/enhancers_types/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/enhancers_types/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.60it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/enhancers_types/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/enhancers_types/checkpoint-400/tokenizer_config.json - 72%|███████▏ | 598/828 [00:26<00:09, 23.50it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/enhancers_types/checkpoint-600 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/enhancers_types/checkpoint-600/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.95it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/enhancers_types/checkpoint-600/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/enhancers_types/checkpoint-600/tokenizer_config.json - 96%|█████████▋| 799/828 [00:36<00:01, 23.49it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/enhancers_types/checkpoint-800 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/enhancers_types/checkpoint-800/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.89it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/enhancers_types/checkpoint-800/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/enhancers_types/checkpoint-800/tokenizer_config.json -100%|█████████▉| 826/828 [00:38<00:00, 21.49it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/enhancers_types/checkpoint-828 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/enhancers_types/checkpoint-828/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.52it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/enhancers_types/checkpoint-828/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/enhancers_types/checkpoint-828/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 828/828 [00:39<00:00, 21.18it/s] -{'train_runtime': '39.1', 'train_samples_per_second': '2701', 'train_steps_per_second': '21.18', 'train_loss': '0.7028', 'epoch': '4'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 81.64it/s] diff --git a/wandb/run-20260305_060254-j63gdhfb/files/requirements.txt b/wandb/run-20260305_060254-j63gdhfb/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_060254-j63gdhfb/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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/data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T06:03:47.128771Z" - writerId: 3tb2p6jwiel6z6lnxhj7lg6fvgcapvum - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_060347-2cfe79sk/files/output.log b/wandb/run-20260305_060347-2cfe79sk/files/output.log deleted file mode 100644 index 82d0286629e4386b58c5045a34223a6f8caaf578..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_060347-2cfe79sk/files/output.log +++ /dev/null @@ -1,54 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 24693.95it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_2/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -bert.pooler.dense.bias | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 25,267 - Num Epochs = 2 - Num update steps per epoch = 198 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 396 - Number of trainable parameters = 45,088,514 - 51%|█████ | 200/396 [00:08<00:06, 29.68it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/promoter_all/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/promoter_all/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.09it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/promoter_all/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/promoter_all/checkpoint-200/tokenizer_config.json -100%|█████████▉| 395/396 [00:16<00:00, 26.37it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/promoter_all/checkpoint-396 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/promoter_all/checkpoint-396/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.40it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/promoter_all/checkpoint-396/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/promoter_all/checkpoint-396/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 396/396 [00:17<00:00, 23.05it/s] -{'train_runtime': '17.18', 'train_samples_per_second': '2942', 'train_steps_per_second': '23.05', 'train_loss': '0.3855', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3159 - Batch size = 128 -100%|██████████| 25/25 [00:00<00:00, 99.01it/s] diff --git a/wandb/run-20260305_060347-2cfe79sk/files/requirements.txt b/wandb/run-20260305_060347-2cfe79sk/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_060347-2cfe79sk/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T06:04:17.486581Z" - writerId: 3klc0nkkdjlzvlzrvdzlb8zg49j1foiy - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_060417-a3dz5gk3/files/output.log b/wandb/run-20260305_060417-a3dz5gk3/files/output.log deleted file mode 100644 index 7318a76c549d079fc44cbd9633363568a6ee17d6..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_060417-a3dz5gk3/files/output.log +++ /dev/null @@ -1,54 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 22242.19it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_2/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.decoder.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -classifier.bias | MISSING | -bert.pooler.dense.weight | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 25,097 - Num Epochs = 2 - Num update steps per epoch = 197 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 394 - Number of trainable parameters = 45,088,514 - 51%|█████ | 200/394 [00:07<00:06, 28.52it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/promoter_no_tata/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/promoter_no_tata/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.88it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/promoter_no_tata/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/promoter_no_tata/checkpoint-200/tokenizer_config.json - 99%|█████████▉| 392/394 [00:15<00:00, 28.83it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/promoter_no_tata/checkpoint-394 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/promoter_no_tata/checkpoint-394/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.28it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/promoter_no_tata/checkpoint-394/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/promoter_no_tata/checkpoint-394/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 394/394 [00:15<00:00, 24.74it/s] -{'train_runtime': '15.92', 'train_samples_per_second': '3152', 'train_steps_per_second': '24.74', 'train_loss': '0.3714', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3138 - Batch size = 128 -100%|██████████| 25/25 [00:00<00:00, 89.03it/s] diff --git a/wandb/run-20260305_060417-a3dz5gk3/files/requirements.txt b/wandb/run-20260305_060417-a3dz5gk3/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_060417-a3dz5gk3/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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/data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T06:04:46.797297Z" - writerId: yckux3cje4zkm5nbg4zbqtmd64ztywyq - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_060446-d5fhoilg/files/output.log b/wandb/run-20260305_060446-d5fhoilg/files/output.log deleted file mode 100644 index f75f8830ed2ae2805653492eef23f2dd21b64354..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_060446-d5fhoilg/files/output.log +++ /dev/null @@ -1,49 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 21930.15it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_2/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -bert.pooler.dense.bias | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.weight | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 4,219 - Num Epochs = 2 - Num update steps per epoch = 33 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 66 - Number of trainable parameters = 45,088,514 - 97%|█████████▋| 64/66 [00:02<00:00, 28.70it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/promoter_tata/checkpoint-66 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/promoter_tata/checkpoint-66/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.08it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/promoter_tata/checkpoint-66/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/promoter_tata/checkpoint-66/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 66/66 [00:03<00:00, 17.71it/s] -{'train_runtime': '3.727', 'train_samples_per_second': '2264', 'train_steps_per_second': '17.71', 'train_loss': '0.5455', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 528 - Batch size = 128 -100%|██████████| 5/5 [00:00<00:00, 103.42it/s] diff --git a/wandb/run-20260305_060446-d5fhoilg/files/requirements.txt b/wandb/run-20260305_060446-d5fhoilg/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_060446-d5fhoilg/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/splice_sites_acceptors/split - - --kmer - - "-1" - - --run_name - - hg38_BPE_len2__baseline_bpe_tokenizer_3e-5_splice_sites_acceptors_seed42 - - --model_max_length - - "140" - - --per_device_train_batch_size - - "128" - - --per_device_eval_batch_size - - "128" - - --gradient_accumulation_steps - - "1" - - --learning_rate - - "3e-5" - - --num_train_epochs - - "4" - - --fp16 - - --save_steps - - "200" - - --output_dir - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/splice_sites_acceptors - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "547242110976" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T06:05:01.492378Z" - writerId: vbpwbd2tnold2cs2kgkg02eprm1w4ckm - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_060501-3hl78xdr/files/output.log b/wandb/run-20260305_060501-3hl78xdr/files/output.log deleted file mode 100644 index 4d6e13b1df818780c1cf582bc180cb6defe0fba1..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_060501-3hl78xdr/files/output.log +++ /dev/null @@ -1,69 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 22640.41it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_2/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -classifier.weight | MISSING | -classifier.bias | MISSING | -bert.pooler.dense.bias | MISSING | -bert.pooler.dense.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 4 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 828 - Number of trainable parameters = 45,088,514 - 24%|██▍ | 199/828 [00:11<00:36, 17.35it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.21it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-200/tokenizer_config.json - 48%|████▊ | 400/828 [00:24<00:24, 17.69it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.03it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-400/tokenizer_config.json - 72%|███████▏ | 599/828 [00:36<00:13, 17.54it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-600 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-600/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.79it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-600/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-600/tokenizer_config.json - 97%|█████████▋| 800/828 [00:48<00:01, 17.15it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-800 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-800/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.32it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-800/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-800/tokenizer_config.json -100%|█████████▉| 826/828 [00:51<00:00, 16.56it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-828 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-828/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.35it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-828/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-828/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 828/828 [00:52<00:00, 15.91it/s] -{'train_runtime': '52.03', 'train_samples_per_second': '2030', 'train_steps_per_second': '15.91', 'train_loss': '0.5941', 'epoch': '4'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 61.41it/s] diff --git a/wandb/run-20260305_060501-3hl78xdr/files/requirements.txt b/wandb/run-20260305_060501-3hl78xdr/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_060501-3hl78xdr/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T06:06:09.276232Z" - writerId: 24xa0sdc3s0h9tk1hvey8om8dxuwrmv0 - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_060609-561v5att/files/output.log b/wandb/run-20260305_060609-561v5att/files/output.log deleted file mode 100644 index 1dc2f7a1438970d900bcadff19216a66fc098912..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_060609-561v5att/files/output.log +++ /dev/null @@ -1,69 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 22545.22it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_2/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -bert.pooler.dense.weight | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 4 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 828 - Number of trainable parameters = 45,089,283 - 24%|██▍ | 199/828 [00:12<00:35, 17.50it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/splice_sites_all/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/splice_sites_all/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.63it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/splice_sites_all/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/splice_sites_all/checkpoint-200/tokenizer_config.json - 48%|████▊ | 399/828 [00:24<00:25, 16.88it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/splice_sites_all/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/splice_sites_all/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 2.96it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/splice_sites_all/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/splice_sites_all/checkpoint-400/tokenizer_config.json - 72%|███████▏ | 600/828 [00:37<00:13, 17.30it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/splice_sites_all/checkpoint-600 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/splice_sites_all/checkpoint-600/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.49it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/splice_sites_all/checkpoint-600/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/splice_sites_all/checkpoint-600/tokenizer_config.json - 96%|█████████▋| 799/828 [00:49<00:01, 17.45it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/splice_sites_all/checkpoint-800 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/splice_sites_all/checkpoint-800/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 2.90it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/splice_sites_all/checkpoint-800/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/splice_sites_all/checkpoint-800/tokenizer_config.json -100%|█████████▉| 827/828 [00:52<00:00, 16.70it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/splice_sites_all/checkpoint-828 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/splice_sites_all/checkpoint-828/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.14it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/splice_sites_all/checkpoint-828/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/splice_sites_all/checkpoint-828/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 828/828 [00:53<00:00, 15.56it/s] -{'train_runtime': '53.23', 'train_samples_per_second': '1984', 'train_steps_per_second': '15.56', 'train_loss': '0.9759', 'epoch': '4'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 60.76it/s] diff --git a/wandb/run-20260305_060609-561v5att/files/requirements.txt b/wandb/run-20260305_060609-561v5att/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_060609-561v5att/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 -accelerate==1.13.0 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -triton==3.6.0 -nvidia-nccl-cu12==2.27.5 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -cuda-pathfinder==1.4.0 -shellingham==1.5.4 -torchaudio==2.5.1 -nvidia-cufile-cu12==1.13.1.3 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -nvidia-nvjitlink-cu12==12.8.93 -click==8.3.1 -MarkupSafe==3.0.2 -nvidia-nvshmem-cu12==3.4.5 -urllib3==2.6.3 -cuda-bindings==12.9.4 -propcache==0.4.1 -nvidia-cusolver-cu12==11.7.3.90 -sympy==1.14.0 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -nvidia-cuda-runtime-cu12==12.8.90 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_060609-561v5att/files/wandb-metadata.json b/wandb/run-20260305_060609-561v5att/files/wandb-metadata.json deleted file mode 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- - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "547246809088" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T06:07:18.869386Z" - writerId: 47zkbtkq7bxcutodxetcu1xffa1xk0ty - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_060718-2cdrbnr7/files/output.log b/wandb/run-20260305_060718-2cdrbnr7/files/output.log deleted file mode 100644 index bde95e06414c41a2456ec6bbc9df9cf5894e877f..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_060718-2cdrbnr7/files/output.log +++ /dev/null @@ -1,69 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 22514.07it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_2/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -classifier.weight | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.bias | MISSING | -bert.pooler.dense.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 4 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 828 - Number of trainable parameters = 45,088,514 - 24%|██▍ | 199/828 [00:11<00:36, 17.45it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.86it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-200/tokenizer_config.json - 48%|████▊ | 400/828 [00:24<00:24, 17.53it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.96it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-400/tokenizer_config.json - 72%|███████▏ | 599/828 [00:36<00:13, 17.22it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-600 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-600/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.30it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-600/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-600/tokenizer_config.json - 97%|█████████▋| 800/828 [00:48<00:01, 17.34it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-800 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-800/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.15it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-800/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-800/tokenizer_config.json -100%|█████████▉| 826/828 [00:50<00:00, 17.05it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-828 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-828/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.87it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-828/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-828/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 828/828 [00:51<00:00, 16.01it/s] -{'train_runtime': '51.72', 'train_samples_per_second': '2042', 'train_steps_per_second': '16.01', 'train_loss': '0.5487', 'epoch': '4'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 61.17it/s] diff --git a/wandb/run-20260305_060718-2cdrbnr7/files/requirements.txt b/wandb/run-20260305_060718-2cdrbnr7/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_060718-2cdrbnr7/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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"2026-03-05T06:08:26.447301Z" - writerId: ddah2gty29a1ldp9kraefnaiub7xvf5f - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_060826-u3zdovdq/files/output.log b/wandb/run-20260305_060826-u3zdovdq/files/output.log deleted file mode 100644 index 8467708b6bf9fc1e33fee9f9d0181082694928cf..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_060826-u3zdovdq/files/output.log +++ /dev/null @@ -1,59 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 20394.03it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_2/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -bert.pooler.dense.weight | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 2 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 414 - Number of trainable parameters = 45,088,514 - 48%|████▊ | 199/414 [00:17<00:18, 11.46it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H2AFZ/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H2AFZ/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.22it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H2AFZ/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H2AFZ/checkpoint-200/tokenizer_config.json - 96%|█████████▋| 399/414 [00:35<00:01, 11.61it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H2AFZ/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H2AFZ/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.46it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H2AFZ/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H2AFZ/checkpoint-400/tokenizer_config.json -100%|█████████▉| 413/414 [00:37<00:00, 9.94it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H2AFZ/checkpoint-414 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H2AFZ/checkpoint-414/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.54it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H2AFZ/checkpoint-414/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H2AFZ/checkpoint-414/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 414/414 [00:38<00:00, 10.77it/s] -{'train_runtime': '38.42', 'train_samples_per_second': '1374', 'train_steps_per_second': '10.78', 'train_loss': '0.6074', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 40.23it/s] diff --git a/wandb/run-20260305_060826-u3zdovdq/files/requirements.txt b/wandb/run-20260305_060826-u3zdovdq/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_060826-u3zdovdq/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_060923-4hsgbiol/files/output.log b/wandb/run-20260305_060923-4hsgbiol/files/output.log deleted file mode 100644 index e677fcf3372a7d577208feff36aaa47be3f98f6d..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_060923-4hsgbiol/files/output.log +++ /dev/null @@ -1,54 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 23122.36it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_2/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -bert.pooler.dense.weight | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 25,292 - Num Epochs = 2 - Num update steps per epoch = 198 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 396 - Number of trainable parameters = 45,088,514 - 50%|█████ | 199/396 [00:17<00:16, 11.88it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H3K27ac/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H3K27ac/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.30it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H3K27ac/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H3K27ac/checkpoint-200/tokenizer_config.json -100%|█████████▉| 395/396 [00:35<00:00, 11.60it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H3K27ac/checkpoint-396 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H3K27ac/checkpoint-396/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.08it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H3K27ac/checkpoint-396/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H3K27ac/checkpoint-396/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 396/396 [00:36<00:00, 10.89it/s] -{'train_runtime': '36.35', 'train_samples_per_second': '1391', 'train_steps_per_second': '10.89', 'train_loss': '0.6106', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3163 - Batch size = 128 -100%|██████████| 25/25 [00:00<00:00, 39.99it/s] diff --git a/wandb/run-20260305_060923-4hsgbiol/files/requirements.txt b/wandb/run-20260305_060923-4hsgbiol/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_060923-4hsgbiol/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 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"2026-03-05T06:10:17.388776Z" - writerId: fsl6msrgep16s71yjw5wek4iq3zdcyjf - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_061017-jgi8xe3q/files/output.log b/wandb/run-20260305_061017-jgi8xe3q/files/output.log deleted file mode 100644 index 9b1b1705e6e273c7a7e95b5c2c5a5783f534ec28..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_061017-jgi8xe3q/files/output.log +++ /dev/null @@ -1,59 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 19265.30it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_2/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -classifier.weight | MISSING | -classifier.bias | MISSING | -bert.pooler.dense.bias | MISSING | -bert.pooler.dense.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 2 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 414 - Number of trainable parameters = 45,088,514 - 48%|████▊ | 199/414 [00:17<00:18, 11.63it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H3K27me3/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H3K27me3/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.44it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H3K27me3/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H3K27me3/checkpoint-200/tokenizer_config.json - 96%|█████████▋| 399/414 [00:35<00:01, 11.56it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H3K27me3/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H3K27me3/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.19it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H3K27me3/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H3K27me3/checkpoint-400/tokenizer_config.json -100%|█████████▉| 413/414 [00:37<00:00, 10.00it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H3K27me3/checkpoint-414 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H3K27me3/checkpoint-414/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.92it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H3K27me3/checkpoint-414/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H3K27me3/checkpoint-414/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 414/414 [00:38<00:00, 10.81it/s] -{'train_runtime': '38.28', 'train_samples_per_second': '1379', 'train_steps_per_second': '10.81', 'train_loss': '0.5565', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 40.00it/s] diff --git a/wandb/run-20260305_061017-jgi8xe3q/files/requirements.txt b/wandb/run-20260305_061017-jgi8xe3q/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_061017-jgi8xe3q/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 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"2026-03-05T06:11:13.554874Z" - writerId: 7apiue9zwpazjn4ngy4iy3yqdsu0mjwt - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_061113-k5iiwcae/files/output.log b/wandb/run-20260305_061113-k5iiwcae/files/output.log deleted file mode 100644 index 07958a518e00d4c57b37494edd2db68af0142f2f..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_061113-k5iiwcae/files/output.log +++ /dev/null @@ -1,59 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 24779.17it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_2/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -classifier.weight | MISSING | -classifier.bias | MISSING | -bert.pooler.dense.bias | MISSING | -bert.pooler.dense.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 2 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 414 - Number of trainable parameters = 45,088,514 - 48%|████▊ | 199/414 [00:17<00:18, 11.62it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H3K36me3/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H3K36me3/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.31it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H3K36me3/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H3K36me3/checkpoint-200/tokenizer_config.json - 96%|█████████▋| 399/414 [00:35<00:01, 11.61it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H3K36me3/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H3K36me3/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.27it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H3K36me3/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H3K36me3/checkpoint-400/tokenizer_config.json -100%|█████████▉| 413/414 [00:37<00:00, 10.02it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H3K36me3/checkpoint-414 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H3K36me3/checkpoint-414/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.42it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H3K36me3/checkpoint-414/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H3K36me3/checkpoint-414/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 414/414 [00:38<00:00, 10.82it/s] -{'train_runtime': '38.25', 'train_samples_per_second': '1380', 'train_steps_per_second': '10.82', 'train_loss': '0.556', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 39.93it/s] diff --git a/wandb/run-20260305_061113-k5iiwcae/files/requirements.txt b/wandb/run-20260305_061113-k5iiwcae/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_061113-k5iiwcae/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T06:12:10.773898Z" - writerId: ikzxev6bvqnwj03h3ywzq5duka0walsi - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_061210-pns0xb5y/files/output.log b/wandb/run-20260305_061210-pns0xb5y/files/output.log deleted file mode 100644 index 405115f116f530a6436d3ccddc09cfa2a48a5dd5..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_061210-pns0xb5y/files/output.log +++ /dev/null @@ -1,59 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 23134.98it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_2/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -classifier.bias | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 2 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 414 - Number of trainable parameters = 45,088,514 - 48%|████▊ | 199/414 [00:17<00:18, 11.56it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H3K4me1/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H3K4me1/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.33it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H3K4me1/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H3K4me1/checkpoint-200/tokenizer_config.json - 96%|█████████▋| 399/414 [00:35<00:01, 11.60it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H3K4me1/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H3K4me1/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.76it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H3K4me1/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H3K4me1/checkpoint-400/tokenizer_config.json -100%|█████████▉| 413/414 [00:37<00:00, 9.94it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H3K4me1/checkpoint-414 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H3K4me1/checkpoint-414/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.57it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H3K4me1/checkpoint-414/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H3K4me1/checkpoint-414/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 414/414 [00:38<00:00, 10.77it/s] -{'train_runtime': '38.46', 'train_samples_per_second': '1373', 'train_steps_per_second': '10.77', 'train_loss': '0.6249', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 40.07it/s] diff --git a/wandb/run-20260305_061210-pns0xb5y/files/requirements.txt b/wandb/run-20260305_061210-pns0xb5y/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_061210-pns0xb5y/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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"2026-03-05T06:13:07.954442Z" - writerId: e5pz2sciimmo8knxyafd8fmaomz1pmug - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_061307-qqpljckj/files/output.log b/wandb/run-20260305_061307-qqpljckj/files/output.log deleted file mode 100644 index 2203bfc69c3d2cd3803b14a0e1737ef213710fc8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_061307-qqpljckj/files/output.log +++ /dev/null @@ -1,59 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 20822.05it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_2/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -classifier.bias | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 25,710 - Num Epochs = 2 - Num update steps per epoch = 201 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 402 - Number of trainable parameters = 45,088,514 - 50%|████▉ | 199/402 [00:17<00:17, 11.62it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H3K4me2/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H3K4me2/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.75it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H3K4me2/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H3K4me2/checkpoint-200/tokenizer_config.json - 99%|█████████▉| 399/402 [00:35<00:00, 11.63it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H3K4me2/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H3K4me2/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.49it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H3K4me2/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H3K4me2/checkpoint-400/tokenizer_config.json -100%|█████████▉| 401/402 [00:36<00:00, 4.96it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H3K4me2/checkpoint-402 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H3K4me2/checkpoint-402/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.97it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H3K4me2/checkpoint-402/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H3K4me2/checkpoint-402/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 402/402 [00:37<00:00, 10.78it/s] -{'train_runtime': '37.28', 'train_samples_per_second': '1379', 'train_steps_per_second': '10.78', 'train_loss': '0.5729', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3215 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 40.76it/s] diff --git a/wandb/run-20260305_061307-qqpljckj/files/requirements.txt b/wandb/run-20260305_061307-qqpljckj/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_061307-qqpljckj/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 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--------------------------------------------+------------+- -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -bert.pooler.dense.bias | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.bias | MISSING | -classifier.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 14,595 - Num Epochs = 2 - Num update steps per epoch = 115 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 230 - Number of trainable parameters = 45,088,514 - 87%|████████▋ | 200/230 [00:19<00:02, 10.90it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H3K4me3/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H3K4me3/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 2.21it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H3K4me3/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H3K4me3/checkpoint-200/tokenizer_config.json -100%|██████████| 230/230 [00:22<00:00, 12.81it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H3K4me3/checkpoint-230 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H3K4me3/checkpoint-230/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.33it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H3K4me3/checkpoint-230/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H3K4me3/checkpoint-230/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 230/230 [00:23<00:00, 9.72it/s] -{'train_runtime': '23.67', 'train_samples_per_second': '1233', 'train_steps_per_second': '9.718', 'train_loss': '0.4807', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 1825 - Batch size = 128 -100%|██████████| 15/15 [00:00<00:00, 42.63it/s] diff --git a/wandb/run-20260305_061404-jrj38m8c/files/requirements.txt b/wandb/run-20260305_061404-jrj38m8c/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_061404-jrj38m8c/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T06:14:44.888127Z" - writerId: teykonlr1gvg650eilatrvp23dqkvzda - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_061444-xvvh025a/files/output.log b/wandb/run-20260305_061444-xvvh025a/files/output.log deleted file mode 100644 index d80433279546bd56da32e2b7d5cc97082273fec3..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_061444-xvvh025a/files/output.log +++ /dev/null @@ -1,54 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 25318.23it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_2/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -classifier.weight | MISSING | -bert.pooler.dense.weight | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 19,422 - Num Epochs = 2 - Num update steps per epoch = 152 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 304 - Number of trainable parameters = 45,088,514 - 65%|██████▌ | 199/304 [00:18<00:09, 10.58it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H3K9ac/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H3K9ac/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 2.49it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H3K9ac/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H3K9ac/checkpoint-200/tokenizer_config.json -100%|██████████| 304/304 [00:28<00:00, 11.93it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H3K9ac/checkpoint-304 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H3K9ac/checkpoint-304/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.71it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H3K9ac/checkpoint-304/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H3K9ac/checkpoint-304/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 304/304 [00:29<00:00, 10.23it/s] -{'train_runtime': '29.71', 'train_samples_per_second': '1308', 'train_steps_per_second': '10.23', 'train_loss': '0.5874', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 2429 - Batch size = 128 -100%|██████████| 19/19 [00:00<00:00, 40.54it/s] diff --git a/wandb/run-20260305_061444-xvvh025a/files/requirements.txt b/wandb/run-20260305_061444-xvvh025a/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_061444-xvvh025a/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 -accelerate==1.13.0 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -triton==3.6.0 -nvidia-nccl-cu12==2.27.5 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -cuda-pathfinder==1.4.0 -shellingham==1.5.4 -torchaudio==2.5.1 -nvidia-cufile-cu12==1.13.1.3 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -nvidia-nvjitlink-cu12==12.8.93 -click==8.3.1 -MarkupSafe==3.0.2 -nvidia-nvshmem-cu12==3.4.5 -urllib3==2.6.3 -cuda-bindings==12.9.4 -propcache==0.4.1 -nvidia-cusolver-cu12==11.7.3.90 -sympy==1.14.0 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -nvidia-cuda-runtime-cu12==12.8.90 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_061444-xvvh025a/files/wandb-metadata.json b/wandb/run-20260305_061444-xvvh025a/files/wandb-metadata.json deleted file mode 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disk: - /: - total: "1876350566400" - used: "547265323008" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T06:15:32.900903Z" - writerId: qv6kch00cr0pav75t31kzk3mut677ga8 - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_061532-9eqdnuks/files/output.log b/wandb/run-20260305_061532-9eqdnuks/files/output.log deleted file mode 100644 index 84135541b2d27469e8d8ecf37ea1a0b81d31b036..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_061532-9eqdnuks/files/output.log +++ /dev/null @@ -1,54 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 23287.60it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_2/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -bert.pooler.dense.bias | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 22,630 - Num Epochs = 2 - Num update steps per epoch = 177 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 354 - Number of trainable parameters = 45,088,514 - 56%|█████▌ | 199/354 [00:17<00:13, 11.55it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H3K9me3/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H3K9me3/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.68it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H3K9me3/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H3K9me3/checkpoint-200/tokenizer_config.json -100%|█████████▉| 353/354 [00:31<00:00, 11.54it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H3K9me3/checkpoint-354 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H3K9me3/checkpoint-354/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 5.37it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H3K9me3/checkpoint-354/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H3K9me3/checkpoint-354/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 354/354 [00:32<00:00, 10.98it/s] -{'train_runtime': '32.23', 'train_samples_per_second': '1404', 'train_steps_per_second': '10.98', 'train_loss': '0.6753', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 2830 - Batch size = 128 -100%|██████████| 23/23 [00:00<00:00, 40.56it/s] diff --git a/wandb/run-20260305_061532-9eqdnuks/files/requirements.txt b/wandb/run-20260305_061532-9eqdnuks/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_061532-9eqdnuks/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 -accelerate==1.13.0 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -triton==3.6.0 -nvidia-nccl-cu12==2.27.5 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -cuda-pathfinder==1.4.0 -shellingham==1.5.4 -torchaudio==2.5.1 -nvidia-cufile-cu12==1.13.1.3 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -nvidia-nvjitlink-cu12==12.8.93 -click==8.3.1 -MarkupSafe==3.0.2 -nvidia-nvshmem-cu12==3.4.5 -urllib3==2.6.3 -cuda-bindings==12.9.4 -propcache==0.4.1 -nvidia-cusolver-cu12==11.7.3.90 -sympy==1.14.0 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -nvidia-cuda-runtime-cu12==12.8.90 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_061532-9eqdnuks/files/wandb-metadata.json b/wandb/run-20260305_061532-9eqdnuks/files/wandb-metadata.json deleted file mode 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"False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "547267588096" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T06:16:21.645255Z" - writerId: b9hh72uk3d53odgzufx5fk4zaxjw0wqx - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_061621-r801a5yo/files/output.log b/wandb/run-20260305_061621-r801a5yo/files/output.log deleted file mode 100644 index b8858db38c0d94c253bb4655e7471589b6e374b0..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_061621-r801a5yo/files/output.log +++ /dev/null @@ -1,59 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 7639.90it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_2/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -bert.pooler.dense.bias | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.weight | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 25,816 - Num Epochs = 2 - Num update steps per epoch = 202 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 404 - Number of trainable parameters = 45,088,514 - 49%|████▉ | 199/404 [00:18<00:17, 11.43it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H4K20me1/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H4K20me1/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.58it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H4K20me1/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H4K20me1/checkpoint-200/tokenizer_config.json - 99%|█████████▉| 399/404 [00:36<00:00, 11.61it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H4K20me1/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H4K20me1/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 5.13it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H4K20me1/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H4K20me1/checkpoint-400/tokenizer_config.json -100%|█████████▉| 403/404 [00:37<00:00, 6.74it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H4K20me1/checkpoint-404 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H4K20me1/checkpoint-404/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.19it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H4K20me1/checkpoint-404/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__baseline_bpe_tokenizer/H4K20me1/checkpoint-404/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 404/404 [00:38<00:00, 10.59it/s] -{'train_runtime': '38.15', 'train_samples_per_second': '1353', 'train_steps_per_second': '10.59', 'train_loss': '0.5167', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3227 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 41.34it/s] diff --git a/wandb/run-20260305_061621-r801a5yo/files/requirements.txt b/wandb/run-20260305_061621-r801a5yo/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_061621-r801a5yo/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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/data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T06:17:17.121957Z" - writerId: mkfcr9wvlipa7t761p20mhyj8tmfzi8z - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_061717-shewvarc/files/output.log b/wandb/run-20260305_061717-shewvarc/files/output.log deleted file mode 100644 index ac6b66761b88662fe929037b5cdf8b9ddfb876e5..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_061717-shewvarc/files/output.log +++ /dev/null @@ -1,70 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 22878.85it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_2/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -bert.pooler.dense.bias | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 4 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 828 - Number of trainable parameters = 45,088,514 - 24%|██▍ | 199/828 [00:08<00:25, 24.60it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/enhancers/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/enhancers/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.67it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/enhancers/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/enhancers/checkpoint-200/tokenizer_config.json - 48%|████▊ | 400/828 [00:18<00:17, 23.80it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/enhancers/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/enhancers/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.60it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/enhancers/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/enhancers/checkpoint-400/tokenizer_config.json - 72%|███████▏ | 599/828 [00:27<00:10, 21.73it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/enhancers/checkpoint-600 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/enhancers/checkpoint-600/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 2.27it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/enhancers/checkpoint-600/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/enhancers/checkpoint-600/tokenizer_config.json - 97%|█████████▋| 800/828 [00:37<00:01, 23.79it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/enhancers/checkpoint-800 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/enhancers/checkpoint-800/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.85it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/enhancers/checkpoint-800/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/enhancers/checkpoint-800/tokenizer_config.json -100%|█████████▉| 827/828 [00:38<00:00, 22.05it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/enhancers/checkpoint-828 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/enhancers/checkpoint-828/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.56it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/enhancers/checkpoint-828/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/enhancers/checkpoint-828/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 828/828 [00:39<00:00, 20.78it/s] -{'train_runtime': '39.84', 'train_samples_per_second': '2651', 'train_steps_per_second': '20.78', 'train_loss': '0.5121', 'epoch': '4'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 81.00it/s] diff --git a/wandb/run-20260305_061717-shewvarc/files/requirements.txt b/wandb/run-20260305_061717-shewvarc/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_061717-shewvarc/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 -accelerate==1.13.0 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -triton==3.6.0 -nvidia-nccl-cu12==2.27.5 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -cuda-pathfinder==1.4.0 -shellingham==1.5.4 -torchaudio==2.5.1 -nvidia-cufile-cu12==1.13.1.3 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -nvidia-nvjitlink-cu12==12.8.93 -click==8.3.1 -MarkupSafe==3.0.2 -nvidia-nvshmem-cu12==3.4.5 -urllib3==2.6.3 -cuda-bindings==12.9.4 -propcache==0.4.1 -nvidia-cusolver-cu12==11.7.3.90 -sympy==1.14.0 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -nvidia-cuda-runtime-cu12==12.8.90 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_061717-shewvarc/files/wandb-metadata.json b/wandb/run-20260305_061717-shewvarc/files/wandb-metadata.json deleted file mode 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--log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "547272044544" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T06:18:11.607602Z" - writerId: aa16xymgpq12hmjstuuojagldwkxvzis - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_061811-05hni4aw/files/output.log b/wandb/run-20260305_061811-05hni4aw/files/output.log deleted file mode 100644 index 090f35e5ceba59906a41d8a09b75cedfcca22009..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_061811-05hni4aw/files/output.log +++ /dev/null @@ -1,70 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 23502.06it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_2/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -classifier.bias | MISSING | -bert.pooler.dense.bias | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 4 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 828 - Number of trainable parameters = 45,089,283 - 24%|██▍ | 199/828 [00:08<00:27, 22.83it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/enhancers_types/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/enhancers_types/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.52it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/enhancers_types/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/enhancers_types/checkpoint-200/tokenizer_config.json - 48%|████▊ | 400/828 [00:18<00:19, 21.89it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/enhancers_types/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/enhancers_types/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.37it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/enhancers_types/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/enhancers_types/checkpoint-400/tokenizer_config.json - 72%|███████▏ | 598/828 [00:27<00:09, 23.05it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/enhancers_types/checkpoint-600 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/enhancers_types/checkpoint-600/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.85it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/enhancers_types/checkpoint-600/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/enhancers_types/checkpoint-600/tokenizer_config.json - 96%|█████████▋| 799/828 [00:36<00:01, 23.88it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/enhancers_types/checkpoint-800 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/enhancers_types/checkpoint-800/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 5.02it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/enhancers_types/checkpoint-800/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/enhancers_types/checkpoint-800/tokenizer_config.json -100%|█████████▉| 826/828 [00:38<00:00, 21.79it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/enhancers_types/checkpoint-828 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/enhancers_types/checkpoint-828/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.48it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/enhancers_types/checkpoint-828/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/enhancers_types/checkpoint-828/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 828/828 [00:38<00:00, 21.31it/s] -{'train_runtime': '38.85', 'train_samples_per_second': '2718', 'train_steps_per_second': '21.31', 'train_loss': '0.639', 'epoch': '4'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 82.40it/s] diff --git a/wandb/run-20260305_061811-05hni4aw/files/requirements.txt b/wandb/run-20260305_061811-05hni4aw/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_061811-05hni4aw/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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/home/n5huang/dna_token/pretrain/models/model_len_2/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -classifier.weight | MISSING | -bert.pooler.dense.bias | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 25,267 - Num Epochs = 2 - Num update steps per epoch = 198 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 396 - Number of trainable parameters = 45,088,514 - 51%|█████ | 200/396 [00:07<00:06, 29.11it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/promoter_all/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/promoter_all/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 5.23it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/promoter_all/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/promoter_all/checkpoint-200/tokenizer_config.json -100%|█████████▉| 395/396 [00:15<00:00, 28.75it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/promoter_all/checkpoint-396 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/promoter_all/checkpoint-396/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.77it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/promoter_all/checkpoint-396/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/promoter_all/checkpoint-396/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 396/396 [00:16<00:00, 24.71it/s] -{'train_runtime': '16.03', 'train_samples_per_second': '3153', 'train_steps_per_second': '24.71', 'train_loss': '0.3356', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3159 - Batch size = 128 -100%|██████████| 25/25 [00:00<00:00, 98.45it/s] diff --git a/wandb/run-20260305_061904-s7tbqoe2/files/requirements.txt b/wandb/run-20260305_061904-s7tbqoe2/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_061904-s7tbqoe2/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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/data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T06:19:34.896802Z" - writerId: b3bt3lt51c0mtbjxi2c2thb9uwc1uuhm - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_061934-ca30wgt1/files/output.log b/wandb/run-20260305_061934-ca30wgt1/files/output.log deleted file mode 100644 index 6e379e5f2a2332a3a7f73bb98b1e7cd1ef394064..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_061934-ca30wgt1/files/output.log +++ /dev/null @@ -1,55 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 21780.19it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_2/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -classifier.bias | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 25,097 - Num Epochs = 2 - Num update steps per epoch = 197 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 394 - Number of trainable parameters = 45,088,514 - 51%|█████ | 199/394 [00:07<00:07, 26.78it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/promoter_no_tata/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/promoter_no_tata/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.29it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/promoter_no_tata/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/promoter_no_tata/checkpoint-200/tokenizer_config.json - 99%|█████████▉| 391/394 [00:15<00:00, 28.44it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/promoter_no_tata/checkpoint-394 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/promoter_no_tata/checkpoint-394/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 5.26it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/promoter_no_tata/checkpoint-394/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/promoter_no_tata/checkpoint-394/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 394/394 [00:16<00:00, 23.84it/s] -{'train_runtime': '16.52', 'train_samples_per_second': '3038', 'train_steps_per_second': '23.84', 'train_loss': '0.3184', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3138 - Batch size = 128 -100%|██████████| 25/25 [00:00<00:00, 92.04it/s] diff --git a/wandb/run-20260305_061934-ca30wgt1/files/requirements.txt b/wandb/run-20260305_061934-ca30wgt1/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_061934-ca30wgt1/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 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/data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T06:20:06.338277Z" - writerId: ayxik365sted954tirdap31vnfpsa0z4 - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_062006-q8rk4irw/files/output.log b/wandb/run-20260305_062006-q8rk4irw/files/output.log deleted file mode 100644 index 050aa4cd8b923f31a686bbf9ae094e79d851addf..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_062006-q8rk4irw/files/output.log +++ /dev/null @@ -1,50 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 26227.38it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_2/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -bert.pooler.dense.bias | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.bias | MISSING | -classifier.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 4,219 - Num Epochs = 2 - Num update steps per epoch = 33 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 66 - Number of trainable parameters = 45,088,514 - 97%|█████████▋| 64/66 [00:02<00:00, 26.90it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/promoter_tata/checkpoint-66 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/promoter_tata/checkpoint-66/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.36it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/promoter_tata/checkpoint-66/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/promoter_tata/checkpoint-66/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 66/66 [00:03<00:00, 17.78it/s] -{'train_runtime': '3.712', 'train_samples_per_second': '2273', 'train_steps_per_second': '17.78', 'train_loss': '0.4712', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 528 - Batch size = 128 -100%|██████████| 5/5 [00:00<00:00, 83.59it/s] diff --git a/wandb/run-20260305_062006-q8rk4irw/files/requirements.txt b/wandb/run-20260305_062006-q8rk4irw/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_062006-q8rk4irw/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 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genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "547276808192" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T06:20:22.464097Z" - writerId: z4hm2t0wqvfqvdyt8svjearnycbo78pi - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_062022-1bzr2oy4/files/output.log b/wandb/run-20260305_062022-1bzr2oy4/files/output.log deleted file mode 100644 index b21bf651e725eb7e0ab7dc958d0b2f4034684169..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_062022-1bzr2oy4/files/output.log +++ /dev/null @@ -1,70 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 7486.12it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_2/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -classifier.weight | MISSING | -bert.pooler.dense.bias | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 4 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 828 - Number of trainable parameters = 45,088,514 - 24%|██▍ | 199/828 [00:12<00:35, 17.76it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/splice_sites_acceptors/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/splice_sites_acceptors/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.71it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/splice_sites_acceptors/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/splice_sites_acceptors/checkpoint-200/tokenizer_config.json - 48%|████▊ | 400/828 [00:24<00:24, 17.32it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/splice_sites_acceptors/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/splice_sites_acceptors/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.98it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/splice_sites_acceptors/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/splice_sites_acceptors/checkpoint-400/tokenizer_config.json - 72%|███████▏ | 599/828 [00:37<00:13, 17.36it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/splice_sites_acceptors/checkpoint-600 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/splice_sites_acceptors/checkpoint-600/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.73it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/splice_sites_acceptors/checkpoint-600/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/splice_sites_acceptors/checkpoint-600/tokenizer_config.json - 97%|█████████▋| 800/828 [00:49<00:01, 17.47it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/splice_sites_acceptors/checkpoint-800 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/splice_sites_acceptors/checkpoint-800/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 5.00it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/splice_sites_acceptors/checkpoint-800/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/splice_sites_acceptors/checkpoint-800/tokenizer_config.json -100%|█████████▉| 826/828 [00:51<00:00, 17.01it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/splice_sites_acceptors/checkpoint-828 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/splice_sites_acceptors/checkpoint-828/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.63it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/splice_sites_acceptors/checkpoint-828/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/splice_sites_acceptors/checkpoint-828/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 828/828 [00:52<00:00, 15.85it/s] -{'train_runtime': '52.25', 'train_samples_per_second': '2021', 'train_steps_per_second': '15.85', 'train_loss': '0.4417', 'epoch': '4'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 61.28it/s] diff --git a/wandb/run-20260305_062022-1bzr2oy4/files/requirements.txt b/wandb/run-20260305_062022-1bzr2oy4/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_062022-1bzr2oy4/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T06:21:32.464052Z" - writerId: rp2n5abr0tkkx8b5rt0f3sc3ccc7j8rr - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_062132-2sxknscg/files/output.log b/wandb/run-20260305_062132-2sxknscg/files/output.log deleted file mode 100644 index 91e9e7a3b5309a56a3415e61f1762bb626a10b3a..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_062132-2sxknscg/files/output.log +++ /dev/null @@ -1,70 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 11767.35it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_2/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -bert.pooler.dense.weight | MISSING | -classifier.weight | MISSING | -classifier.bias | MISSING | -bert.pooler.dense.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 4 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 828 - Number of trainable parameters = 45,089,283 - 24%|██▍ | 199/828 [00:11<00:35, 17.61it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/splice_sites_all/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/splice_sites_all/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.84it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/splice_sites_all/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/splice_sites_all/checkpoint-200/tokenizer_config.json - 48%|████▊ | 400/828 [00:24<00:24, 17.40it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/splice_sites_all/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/splice_sites_all/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.85it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/splice_sites_all/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/splice_sites_all/checkpoint-400/tokenizer_config.json - 72%|███████▏ | 599/828 [00:36<00:13, 16.46it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/splice_sites_all/checkpoint-600 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/splice_sites_all/checkpoint-600/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 2.17it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/splice_sites_all/checkpoint-600/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/splice_sites_all/checkpoint-600/tokenizer_config.json - 97%|█████████▋| 800/828 [00:49<00:01, 17.81it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/splice_sites_all/checkpoint-800 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/splice_sites_all/checkpoint-800/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 5.31it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/splice_sites_all/checkpoint-800/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/splice_sites_all/checkpoint-800/tokenizer_config.json -100%|█████████▉| 826/828 [00:51<00:00, 17.20it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/splice_sites_all/checkpoint-828 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/splice_sites_all/checkpoint-828/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.76it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/splice_sites_all/checkpoint-828/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/splice_sites_all/checkpoint-828/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 828/828 [00:52<00:00, 15.83it/s] -{'train_runtime': '52.32', 'train_samples_per_second': '2018', 'train_steps_per_second': '15.83', 'train_loss': '0.7391', 'epoch': '4'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 60.14it/s] diff --git a/wandb/run-20260305_062132-2sxknscg/files/requirements.txt b/wandb/run-20260305_062132-2sxknscg/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_062132-2sxknscg/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 -accelerate==1.13.0 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -triton==3.6.0 -nvidia-nccl-cu12==2.27.5 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -cuda-pathfinder==1.4.0 -shellingham==1.5.4 -torchaudio==2.5.1 -nvidia-cufile-cu12==1.13.1.3 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -nvidia-nvjitlink-cu12==12.8.93 -click==8.3.1 -MarkupSafe==3.0.2 -nvidia-nvshmem-cu12==3.4.5 -urllib3==2.6.3 -cuda-bindings==12.9.4 -propcache==0.4.1 -nvidia-cusolver-cu12==11.7.3.90 -sympy==1.14.0 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -nvidia-cuda-runtime-cu12==12.8.90 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_062132-2sxknscg/files/wandb-metadata.json b/wandb/run-20260305_062132-2sxknscg/files/wandb-metadata.json deleted file mode 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- - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "547283484672" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T06:22:40.855542Z" - writerId: xc8iadqymgt86u9s58rf13cmi3w6xmy6 - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_062240-6eoc8mhf/files/output.log b/wandb/run-20260305_062240-6eoc8mhf/files/output.log deleted file mode 100644 index 0964ea083a087f34080ec36517d9ad939a3f3fc6..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_062240-6eoc8mhf/files/output.log +++ /dev/null @@ -1,70 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 23353.07it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_2/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -classifier.bias | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 4 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 828 - Number of trainable parameters = 45,088,514 - 24%|██▍ | 199/828 [00:11<00:35, 17.56it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/splice_sites_donors/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/splice_sites_donors/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.80it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/splice_sites_donors/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/splice_sites_donors/checkpoint-200/tokenizer_config.json - 48%|████▊ | 400/828 [00:23<00:24, 17.56it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/splice_sites_donors/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/splice_sites_donors/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.54it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/splice_sites_donors/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/splice_sites_donors/checkpoint-400/tokenizer_config.json - 72%|███████▏ | 599/828 [00:35<00:13, 17.44it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/splice_sites_donors/checkpoint-600 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/splice_sites_donors/checkpoint-600/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.75it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/splice_sites_donors/checkpoint-600/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/splice_sites_donors/checkpoint-600/tokenizer_config.json - 97%|█████████▋| 800/828 [00:48<00:01, 17.07it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/splice_sites_donors/checkpoint-800 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/splice_sites_donors/checkpoint-800/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.50it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/splice_sites_donors/checkpoint-800/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/splice_sites_donors/checkpoint-800/tokenizer_config.json -100%|█████████▉| 826/828 [00:50<00:00, 16.68it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/splice_sites_donors/checkpoint-828 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/splice_sites_donors/checkpoint-828/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.47it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/splice_sites_donors/checkpoint-828/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/splice_sites_donors/checkpoint-828/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 828/828 [00:51<00:00, 16.01it/s] -{'train_runtime': '51.7', 'train_samples_per_second': '2043', 'train_steps_per_second': '16.02', 'train_loss': '0.4408', 'epoch': '4'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 45.44it/s] diff --git a/wandb/run-20260305_062240-6eoc8mhf/files/requirements.txt b/wandb/run-20260305_062240-6eoc8mhf/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_062240-6eoc8mhf/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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/data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T06:23:48.726992Z" - writerId: rh4na6pl9reczltycmf5hh52z27xkv0c - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_062348-xxexafee/files/output.log b/wandb/run-20260305_062348-xxexafee/files/output.log deleted file mode 100644 index 06f8e1ffcfaed196aa9729c4762eb95d6797ec99..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_062348-xxexafee/files/output.log +++ /dev/null @@ -1,60 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 11366.68it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_2/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -classifier.weight | MISSING | -bert.pooler.dense.bias | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 2 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 414 - Number of trainable parameters = 45,088,514 - 48%|████▊ | 199/414 [00:15<00:16, 13.07it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H2AFZ/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H2AFZ/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.73it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H2AFZ/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H2AFZ/checkpoint-200/tokenizer_config.json - 96%|█████████▋| 399/414 [00:31<00:01, 12.95it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H2AFZ/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H2AFZ/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 5.01it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H2AFZ/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H2AFZ/checkpoint-400/tokenizer_config.json -100%|█████████▉| 413/414 [00:33<00:00, 11.06it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H2AFZ/checkpoint-414 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H2AFZ/checkpoint-414/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 5.35it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H2AFZ/checkpoint-414/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H2AFZ/checkpoint-414/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 414/414 [00:34<00:00, 12.09it/s] -{'train_runtime': '34.24', 'train_samples_per_second': '1542', 'train_steps_per_second': '12.09', 'train_loss': '0.5269', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 43.88it/s] diff --git a/wandb/run-20260305_062348-xxexafee/files/requirements.txt b/wandb/run-20260305_062348-xxexafee/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_062348-xxexafee/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 -accelerate==1.13.0 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -triton==3.6.0 -nvidia-nccl-cu12==2.27.5 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -cuda-pathfinder==1.4.0 -shellingham==1.5.4 -torchaudio==2.5.1 -nvidia-cufile-cu12==1.13.1.3 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -nvidia-nvjitlink-cu12==12.8.93 -click==8.3.1 -MarkupSafe==3.0.2 -nvidia-nvshmem-cu12==3.4.5 -urllib3==2.6.3 -cuda-bindings==12.9.4 -propcache==0.4.1 -nvidia-cusolver-cu12==11.7.3.90 -sympy==1.14.0 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -nvidia-cuda-runtime-cu12==12.8.90 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_062348-xxexafee/files/wandb-metadata.json b/wandb/run-20260305_062348-xxexafee/files/wandb-metadata.json deleted file mode 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- - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "547288014848" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T06:24:42.160093Z" - writerId: ura8ae2h3ou6g20bkqv49prdkthzq6th - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_062442-ji9h301g/files/output.log b/wandb/run-20260305_062442-ji9h301g/files/output.log deleted file mode 100644 index f7997a07e674a8275ebdda1c81390546008651d3..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_062442-ji9h301g/files/output.log +++ /dev/null @@ -1,55 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 18362.58it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_2/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -classifier.weight | MISSING | -bert.pooler.dense.weight | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 25,292 - Num Epochs = 2 - Num update steps per epoch = 198 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 396 - Number of trainable parameters = 45,088,514 - 50%|█████ | 199/396 [00:16<00:14, 13.74it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H3K27ac/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H3K27ac/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 5.05it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H3K27ac/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H3K27ac/checkpoint-200/tokenizer_config.json -100%|█████████▉| 395/396 [00:32<00:00, 12.65it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H3K27ac/checkpoint-396 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H3K27ac/checkpoint-396/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 2.54it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H3K27ac/checkpoint-396/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H3K27ac/checkpoint-396/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 396/396 [00:33<00:00, 11.93it/s] -{'train_runtime': '33.18', 'train_samples_per_second': '1525', 'train_steps_per_second': '11.94', 'train_loss': '0.5534', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3163 - Batch size = 128 -100%|██████████| 25/25 [00:00<00:00, 43.23it/s] diff --git a/wandb/run-20260305_062442-ji9h301g/files/requirements.txt b/wandb/run-20260305_062442-ji9h301g/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_062442-ji9h301g/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 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--seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "547290263552" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T06:25:35.863554Z" - writerId: cqtcxxf7dx3y0wscaa666gjke2tzcly7 - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_062535-zoivt4gs/files/output.log b/wandb/run-20260305_062535-zoivt4gs/files/output.log deleted file mode 100644 index b662b18351131b1b13314c0478232ac434e2d907..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_062535-zoivt4gs/files/output.log +++ /dev/null @@ -1,60 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 20233.30it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_2/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -classifier.bias | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.bias | MISSING | -bert.pooler.dense.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 2 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 414 - Number of trainable parameters = 45,088,514 - 48%|████▊ | 199/414 [00:15<00:17, 12.62it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H3K27me3/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H3K27me3/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 1.95it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H3K27me3/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H3K27me3/checkpoint-200/tokenizer_config.json - 96%|█████████▋| 399/414 [00:32<00:01, 13.07it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H3K27me3/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H3K27me3/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 5.38it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H3K27me3/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H3K27me3/checkpoint-400/tokenizer_config.json -100%|█████████▉| 413/414 [00:34<00:00, 11.38it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H3K27me3/checkpoint-414 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H3K27me3/checkpoint-414/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 5.25it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H3K27me3/checkpoint-414/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H3K27me3/checkpoint-414/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 414/414 [00:34<00:00, 11.87it/s] -{'train_runtime': '34.88', 'train_samples_per_second': '1514', 'train_steps_per_second': '11.87', 'train_loss': '0.4836', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 43.67it/s] diff --git a/wandb/run-20260305_062535-zoivt4gs/files/requirements.txt b/wandb/run-20260305_062535-zoivt4gs/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_062535-zoivt4gs/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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/data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T06:26:31.093781Z" - writerId: dw6imoenf2c0m8ppxgqxdjk882rq7z6l - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_062631-8lql24er/files/output.log b/wandb/run-20260305_062631-8lql24er/files/output.log deleted file mode 100644 index 86aa2252d607b32f122a799ed3a9e1f3fb91ab08..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_062631-8lql24er/files/output.log +++ /dev/null @@ -1,60 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 22267.91it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_2/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -bert.pooler.dense.bias | MISSING | -classifier.bias | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 2 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 414 - Number of trainable parameters = 45,088,514 - 48%|████▊ | 199/414 [00:15<00:16, 13.17it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H3K36me3/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H3K36me3/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.80it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H3K36me3/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H3K36me3/checkpoint-200/tokenizer_config.json - 96%|█████████▋| 399/414 [00:32<00:01, 12.90it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H3K36me3/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H3K36me3/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.90it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H3K36me3/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H3K36me3/checkpoint-400/tokenizer_config.json -100%|█████████▉| 413/414 [00:33<00:00, 11.31it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H3K36me3/checkpoint-414 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H3K36me3/checkpoint-414/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.98it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H3K36me3/checkpoint-414/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H3K36me3/checkpoint-414/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 414/414 [00:34<00:00, 11.90it/s] -{'train_runtime': '34.79', 'train_samples_per_second': '1518', 'train_steps_per_second': '11.9', 'train_loss': '0.4753', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 43.52it/s] diff --git a/wandb/run-20260305_062631-8lql24er/files/requirements.txt b/wandb/run-20260305_062631-8lql24er/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_062631-8lql24er/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 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- - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "547292938240" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T06:27:24.782113Z" - writerId: c2kt9blpie0d4psijoczvyisi06ks0f7 - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_062724-gr3z32a4/files/output.log b/wandb/run-20260305_062724-gr3z32a4/files/output.log deleted file mode 100644 index f2c2af339880c20734c216928ca1ac00dfbac819..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_062724-gr3z32a4/files/output.log +++ /dev/null @@ -1,60 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 24792.22it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_2/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -classifier.weight | MISSING | -bert.pooler.dense.weight | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 2 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 414 - Number of trainable parameters = 45,088,514 - 48%|████▊ | 199/414 [00:16<00:16, 12.93it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H3K4me1/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H3K4me1/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.63it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H3K4me1/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H3K4me1/checkpoint-200/tokenizer_config.json - 96%|█████████▋| 399/414 [00:32<00:01, 13.07it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H3K4me1/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H3K4me1/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.65it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H3K4me1/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H3K4me1/checkpoint-400/tokenizer_config.json -100%|█████████▉| 413/414 [00:34<00:00, 11.40it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H3K4me1/checkpoint-414 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H3K4me1/checkpoint-414/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.93it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H3K4me1/checkpoint-414/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H3K4me1/checkpoint-414/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 414/414 [00:34<00:00, 11.86it/s] -{'train_runtime': '34.91', 'train_samples_per_second': '1512', 'train_steps_per_second': '11.86', 'train_loss': '0.557', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 43.85it/s] diff --git a/wandb/run-20260305_062724-gr3z32a4/files/requirements.txt b/wandb/run-20260305_062724-gr3z32a4/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_062724-gr3z32a4/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 -accelerate==1.13.0 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -triton==3.6.0 -nvidia-nccl-cu12==2.27.5 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -cuda-pathfinder==1.4.0 -shellingham==1.5.4 -torchaudio==2.5.1 -nvidia-cufile-cu12==1.13.1.3 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -nvidia-nvjitlink-cu12==12.8.93 -click==8.3.1 -MarkupSafe==3.0.2 -nvidia-nvshmem-cu12==3.4.5 -urllib3==2.6.3 -cuda-bindings==12.9.4 -propcache==0.4.1 -nvidia-cusolver-cu12==11.7.3.90 -sympy==1.14.0 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -nvidia-cuda-runtime-cu12==12.8.90 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_062724-gr3z32a4/files/wandb-metadata.json b/wandb/run-20260305_062724-gr3z32a4/files/wandb-metadata.json deleted file mode 100644 index 1de819f9a21d06568cee6094dd19ae448cca6ac4..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_062724-gr3z32a4/files/wandb-metadata.json +++ /dev/null @@ -1,134 +0,0 @@ -{ - "os": "Linux-5.15.0-72-generic-x86_64-with-glibc2.35", - "python": "CPython 3.10.19", - "startedAt": "2026-03-05T06:27:24.782113Z", - "args": [ - "--model_name_or_path", - "/home/n5huang/dna_token/pretrain/models/model_len_2/checkpoint-100000", - "--tokenizer_path", - "/home/n5huang/dna_token/tokenizer_evaluation/merge_bpe/merge_tokenizer_unigram_len.json", - "--trust_remote_code", - "True", - "--data_path", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/H3K4me1/split", - "--kmer", - "-1", - "--run_name", - "hg38_BPE_len2__merge_bpe_merge_tokenizer_unigram_len_3e-5_H3K4me1_seed42", - "--model_max_length", - "220", - "--per_device_train_batch_size", - "128", - "--per_device_eval_batch_size", - "128", - 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- - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "547295195136" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T06:28:20.621655Z" - writerId: i3sty6nt945e834xbxevgiezsj13q8qt - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_062820-g8kkwbgl/files/output.log b/wandb/run-20260305_062820-g8kkwbgl/files/output.log deleted file mode 100644 index 2454d7ee31208d0d486c93a1482a71b71c25ab52..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_062820-g8kkwbgl/files/output.log +++ /dev/null @@ -1,60 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 25657.12it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_2/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -classifier.weight | MISSING | -bert.pooler.dense.bias | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 25,710 - Num Epochs = 2 - Num update steps per epoch = 201 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 402 - Number of trainable parameters = 45,088,514 - 50%|████▉ | 199/402 [00:16<00:15, 12.98it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H3K4me2/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H3K4me2/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.90it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H3K4me2/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H3K4me2/checkpoint-200/tokenizer_config.json - 99%|█████████▉| 399/402 [00:32<00:00, 12.91it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H3K4me2/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H3K4me2/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.67it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H3K4me2/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H3K4me2/checkpoint-400/tokenizer_config.json -100%|█████████▉| 401/402 [00:33<00:00, 5.73it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H3K4me2/checkpoint-402 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H3K4me2/checkpoint-402/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 5.09it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H3K4me2/checkpoint-402/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H3K4me2/checkpoint-402/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 402/402 [00:33<00:00, 11.88it/s] -{'train_runtime': '33.84', 'train_samples_per_second': '1519', 'train_steps_per_second': '11.88', 'train_loss': '0.4949', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3215 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 42.67it/s] diff --git a/wandb/run-20260305_062820-g8kkwbgl/files/requirements.txt b/wandb/run-20260305_062820-g8kkwbgl/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_062820-g8kkwbgl/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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- - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "547297476608" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T06:29:13.352035Z" - writerId: hk1wejobgugcv2hgi2fqn3dvwicnnfl8 - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_062913-9q16x5hu/files/output.log b/wandb/run-20260305_062913-9q16x5hu/files/output.log deleted file mode 100644 index ddacc7e1d629850b9c6b238379181a0abea09025..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_062913-9q16x5hu/files/output.log +++ /dev/null @@ -1,55 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 13544.29it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_2/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -classifier.weight | MISSING | -bert.pooler.dense.bias | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 14,595 - Num Epochs = 2 - Num update steps per epoch = 115 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 230 - Number of trainable parameters = 45,088,514 - 87%|████████▋ | 199/230 [00:15<00:02, 12.89it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H3K4me3/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H3K4me3/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.69it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H3K4me3/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H3K4me3/checkpoint-200/tokenizer_config.json -100%|█████████▉| 229/230 [00:18<00:00, 12.87it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H3K4me3/checkpoint-230 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H3K4me3/checkpoint-230/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.39it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H3K4me3/checkpoint-230/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H3K4me3/checkpoint-230/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 230/230 [00:19<00:00, 11.75it/s] -{'train_runtime': '19.57', 'train_samples_per_second': '1492', 'train_steps_per_second': '11.75', 'train_loss': '0.4217', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 1825 - Batch size = 128 -100%|██████████| 15/15 [00:00<00:00, 46.99it/s] diff --git a/wandb/run-20260305_062913-9q16x5hu/files/requirements.txt b/wandb/run-20260305_062913-9q16x5hu/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_062913-9q16x5hu/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 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/data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T06:29:49.138647Z" - writerId: st539zmpfnhgqbismj9ag15mylb3o8np - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_062949-5zmyvqax/files/output.log b/wandb/run-20260305_062949-5zmyvqax/files/output.log deleted file mode 100644 index 11a8695b1f6485c82e5c33388743b57f56d66670..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_062949-5zmyvqax/files/output.log +++ /dev/null @@ -1,55 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 7876.26it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_2/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -classifier.weight | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.bias | MISSING | -bert.pooler.dense.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 19,422 - Num Epochs = 2 - Num update steps per epoch = 152 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 304 - Number of trainable parameters = 45,088,514 - 65%|██████▌ | 199/304 [00:16<00:08, 13.10it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H3K9ac/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H3K9ac/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.33it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H3K9ac/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H3K9ac/checkpoint-200/tokenizer_config.json -100%|█████████▉| 303/304 [00:24<00:00, 12.91it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H3K9ac/checkpoint-304 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H3K9ac/checkpoint-304/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.88it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H3K9ac/checkpoint-304/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H3K9ac/checkpoint-304/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 304/304 [00:25<00:00, 11.82it/s] -{'train_runtime': '25.72', 'train_samples_per_second': '1510', 'train_steps_per_second': '11.82', 'train_loss': '0.5191', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 2429 - Batch size = 128 -100%|██████████| 19/19 [00:00<00:00, 43.69it/s] diff --git a/wandb/run-20260305_062949-5zmyvqax/files/requirements.txt b/wandb/run-20260305_062949-5zmyvqax/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_062949-5zmyvqax/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 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- - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "547299872768" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 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/data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T06:30:32.231908Z" - writerId: tfe0l2p7golzzel15sof54bvnb9zaixk - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_063032-lzize7q3/files/output.log b/wandb/run-20260305_063032-lzize7q3/files/output.log deleted file mode 100644 index f21c98ded2bea6a66659245dac0895a143214178..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_063032-lzize7q3/files/output.log +++ /dev/null @@ -1,55 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 21181.24it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_2/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -classifier.bias | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.weight | MISSING | -bert.pooler.dense.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 22,630 - Num Epochs = 2 - Num update steps per epoch = 177 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 354 - Number of trainable parameters = 45,088,514 - 56%|█████▌ | 199/354 [00:15<00:11, 12.94it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H3K9me3/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H3K9me3/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 5.20it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H3K9me3/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H3K9me3/checkpoint-200/tokenizer_config.json -100%|█████████▉| 353/354 [00:28<00:00, 12.42it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H3K9me3/checkpoint-354 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H3K9me3/checkpoint-354/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.35it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H3K9me3/checkpoint-354/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H3K9me3/checkpoint-354/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 354/354 [00:29<00:00, 11.93it/s] -{'train_runtime': '29.66', 'train_samples_per_second': '1526', 'train_steps_per_second': '11.94', 'train_loss': '0.5971', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 2830 - Batch size = 128 -100%|██████████| 23/23 [00:00<00:00, 44.81it/s] diff --git a/wandb/run-20260305_063032-lzize7q3/files/requirements.txt b/wandb/run-20260305_063032-lzize7q3/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_063032-lzize7q3/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T06:31:19.867820Z" - writerId: 8jjdzeh4nqspz6qdfi99obc5hez2ikxu - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_063119-u8eqjoh8/files/output.log b/wandb/run-20260305_063119-u8eqjoh8/files/output.log deleted file mode 100644 index 360751768e1068ce5cecfb1a24f52e812bca269a..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_063119-u8eqjoh8/files/output.log +++ /dev/null @@ -1,60 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 19823.34it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_2/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -bert.pooler.dense.weight | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.weight | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 25,816 - Num Epochs = 2 - Num update steps per epoch = 202 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 404 - Number of trainable parameters = 45,088,514 - 49%|████▉ | 199/404 [00:15<00:15, 13.13it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H4K20me1/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H4K20me1/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.94it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H4K20me1/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H4K20me1/checkpoint-200/tokenizer_config.json - 99%|█████████▉| 399/404 [00:32<00:00, 12.84it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H4K20me1/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H4K20me1/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.65it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H4K20me1/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H4K20me1/checkpoint-400/tokenizer_config.json -100%|█████████▉| 403/404 [00:33<00:00, 6.23it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H4K20me1/checkpoint-404 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H4K20me1/checkpoint-404/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 5.10it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H4K20me1/checkpoint-404/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len/H4K20me1/checkpoint-404/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 404/404 [00:33<00:00, 11.95it/s] -{'train_runtime': '33.82', 'train_samples_per_second': '1527', 'train_steps_per_second': '11.95', 'train_loss': '0.4504', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3227 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 44.22it/s] diff --git a/wandb/run-20260305_063119-u8eqjoh8/files/requirements.txt b/wandb/run-20260305_063119-u8eqjoh8/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_063119-u8eqjoh8/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 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/home/n5huang/dna_token/tokenizer_evaluation/merge_bpe/merge_tokenizer_unigram_len2.json - - --trust_remote_code - - "True" - - --data_path - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/enhancers/split - - --kmer - - "-1" - - --run_name - - hg38_BPE_len2__merge_bpe_merge_tokenizer_unigram_len2_3e-5_enhancers_seed42 - - --model_max_length - - "100" - - --per_device_train_batch_size - - "128" - - --per_device_eval_batch_size - - "128" - - --gradient_accumulation_steps - - "1" - - --learning_rate - - "3e-5" - - --num_train_epochs - - "4" - - --fp16 - - --save_steps - - "200" - - --output_dir - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/enhancers - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "547304366080" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T06:32:12.387595Z" - writerId: g31t6d3989bgx4andk1e87x3313umh3t - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_063212-yoq9gnht/files/output.log b/wandb/run-20260305_063212-yoq9gnht/files/output.log deleted file mode 100644 index 663c3bd64eeaba6778274a5b4ca8f9e7174e3d79..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_063212-yoq9gnht/files/output.log +++ /dev/null @@ -1,70 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 22768.18it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_2/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -bert.pooler.dense.weight | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.weight | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 4 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 828 - Number of trainable parameters = 45,088,514 - 24%|██▍ | 199/828 [00:09<00:27, 23.24it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/enhancers/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/enhancers/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.56it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/enhancers/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/enhancers/checkpoint-200/tokenizer_config.json - 48%|████▊ | 400/828 [00:18<00:18, 23.69it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/enhancers/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/enhancers/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.55it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/enhancers/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/enhancers/checkpoint-400/tokenizer_config.json - 72%|███████▏ | 598/828 [00:28<00:09, 23.21it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/enhancers/checkpoint-600 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/enhancers/checkpoint-600/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.58it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/enhancers/checkpoint-600/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/enhancers/checkpoint-600/tokenizer_config.json - 96%|█████████▋| 799/828 [00:37<00:01, 23.25it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/enhancers/checkpoint-800 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/enhancers/checkpoint-800/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.64it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/enhancers/checkpoint-800/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/enhancers/checkpoint-800/tokenizer_config.json -100%|█████████▉| 826/828 [00:39<00:00, 19.93it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/enhancers/checkpoint-828 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/enhancers/checkpoint-828/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.66it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/enhancers/checkpoint-828/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/enhancers/checkpoint-828/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 828/828 [00:40<00:00, 20.37it/s] -{'train_runtime': '40.65', 'train_samples_per_second': '2598', 'train_steps_per_second': '20.37', 'train_loss': '0.5072', 'epoch': '4'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 81.95it/s] diff --git a/wandb/run-20260305_063212-yoq9gnht/files/requirements.txt b/wandb/run-20260305_063212-yoq9gnht/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_063212-yoq9gnht/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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/home/n5huang/dna_token/pretrain/models/model_len_2/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -bert.pooler.dense.weight | MISSING | -classifier.bias | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 4 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 828 - Number of trainable parameters = 45,089,283 - 24%|██▍ | 199/828 [00:08<00:26, 24.06it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/enhancers_types/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/enhancers_types/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.53it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/enhancers_types/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/enhancers_types/checkpoint-200/tokenizer_config.json - 48%|████▊ | 400/828 [00:18<00:18, 23.32it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/enhancers_types/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/enhancers_types/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.89it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/enhancers_types/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/enhancers_types/checkpoint-400/tokenizer_config.json - 72%|███████▏ | 598/828 [00:27<00:10, 22.96it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/enhancers_types/checkpoint-600 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/enhancers_types/checkpoint-600/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.75it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/enhancers_types/checkpoint-600/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/enhancers_types/checkpoint-600/tokenizer_config.json - 96%|█████████▋| 799/828 [00:36<00:01, 24.42it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/enhancers_types/checkpoint-800 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/enhancers_types/checkpoint-800/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 5.07it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/enhancers_types/checkpoint-800/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/enhancers_types/checkpoint-800/tokenizer_config.json -100%|█████████▉| 826/828 [00:38<00:00, 22.23it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/enhancers_types/checkpoint-828 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/enhancers_types/checkpoint-828/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.30it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/enhancers_types/checkpoint-828/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/enhancers_types/checkpoint-828/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 828/828 [00:38<00:00, 21.37it/s] -{'train_runtime': '38.74', 'train_samples_per_second': '2726', 'train_steps_per_second': '21.37', 'train_loss': '0.6354', 'epoch': '4'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 82.70it/s] diff --git a/wandb/run-20260305_063306-j2nvhdjx/files/requirements.txt b/wandb/run-20260305_063306-j2nvhdjx/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_063306-j2nvhdjx/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 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- info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "547308871680" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T06:33:59.955784Z" - writerId: d3htdqtmtg48ibstlyc2pdcx2hqxo1iz - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_063359-qrofxf8b/files/output.log b/wandb/run-20260305_063359-qrofxf8b/files/output.log deleted file mode 100644 index 09323dd918800df2f69aa9e2dfdd14b8b3c0d184..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_063359-qrofxf8b/files/output.log +++ /dev/null @@ -1,55 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 10298.40it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_2/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -classifier.weight | MISSING | -bert.pooler.dense.weight | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 25,267 - Num Epochs = 2 - Num update steps per epoch = 198 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 396 - Number of trainable parameters = 45,088,514 - 50%|█████ | 199/396 [00:07<00:07, 27.57it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/promoter_all/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/promoter_all/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 2.70it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/promoter_all/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/promoter_all/checkpoint-200/tokenizer_config.json - 99%|█████████▉| 394/396 [00:15<00:00, 28.37it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/promoter_all/checkpoint-396 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/promoter_all/checkpoint-396/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.46it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/promoter_all/checkpoint-396/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/promoter_all/checkpoint-396/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 396/396 [00:16<00:00, 24.28it/s] -{'train_runtime': '16.31', 'train_samples_per_second': '3098', 'train_steps_per_second': '24.28', 'train_loss': '0.3347', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3159 - Batch size = 128 -100%|██████████| 25/25 [00:00<00:00, 99.77it/s] diff --git a/wandb/run-20260305_063359-qrofxf8b/files/requirements.txt b/wandb/run-20260305_063359-qrofxf8b/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_063359-qrofxf8b/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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/home/n5huang/dna_token/tokenizer_evaluation/merge_bpe/merge_tokenizer_unigram_len2.json - - --trust_remote_code - - "True" - - --data_path - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/promoter_no_tata/split - - --kmer - - "-1" - - --run_name - - hg38_BPE_len2__merge_bpe_merge_tokenizer_unigram_len2_3e-5_promoter_no_tata_seed42 - - --model_max_length - - "80" - - --per_device_train_batch_size - - "128" - - --per_device_eval_batch_size - - "128" - - --gradient_accumulation_steps - - "1" - - --learning_rate - - "3e-5" - - --num_train_epochs - - "2" - - --fp16 - - --save_steps - - "200" - - --output_dir - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/promoter_no_tata - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "547309064192" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T06:34:30.003331Z" - writerId: nrqrgzrwk7u2zo58od65rq33q1r5lhui - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_063430-wf2yo6x9/files/output.log b/wandb/run-20260305_063430-wf2yo6x9/files/output.log deleted file mode 100644 index 2f3fbe263e10671ffc897eb0f2f99d0f604095b8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_063430-wf2yo6x9/files/output.log +++ /dev/null @@ -1,55 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 24028.63it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_2/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -bert.pooler.dense.bias | MISSING | -classifier.weight | MISSING | -classifier.bias | MISSING | -bert.pooler.dense.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 25,097 - Num Epochs = 2 - Num update steps per epoch = 197 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 394 - Number of trainable parameters = 45,088,514 - 51%|█████ | 199/394 [00:07<00:08, 24.16it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/promoter_no_tata/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/promoter_no_tata/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.01it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/promoter_no_tata/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/promoter_no_tata/checkpoint-200/tokenizer_config.json -100%|██████████| 394/394 [00:15<00:00, 27.83it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/promoter_no_tata/checkpoint-394 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/promoter_no_tata/checkpoint-394/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.38it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/promoter_no_tata/checkpoint-394/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/promoter_no_tata/checkpoint-394/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 394/394 [00:16<00:00, 24.16it/s] -{'train_runtime': '16.3', 'train_samples_per_second': '3079', 'train_steps_per_second': '24.16', 'train_loss': '0.3199', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3138 - Batch size = 128 -100%|██████████| 25/25 [00:00<00:00, 92.45it/s] diff --git a/wandb/run-20260305_063430-wf2yo6x9/files/requirements.txt b/wandb/run-20260305_063430-wf2yo6x9/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_063430-wf2yo6x9/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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/home/n5huang/dna_token/pretrain/models/model_len_2/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -bert.pooler.dense.weight | MISSING | -classifier.bias | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 4,219 - Num Epochs = 2 - Num update steps per epoch = 33 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 66 - Number of trainable parameters = 45,088,514 - 97%|█████████▋| 64/66 [00:02<00:00, 27.92it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/promoter_tata/checkpoint-66 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/promoter_tata/checkpoint-66/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.72it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/promoter_tata/checkpoint-66/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/promoter_tata/checkpoint-66/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 66/66 [00:03<00:00, 18.33it/s] -{'train_runtime': '3.589', 'train_samples_per_second': '2351', 'train_steps_per_second': '18.39', 'train_loss': '0.4745', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 528 - Batch size = 128 -100%|██████████| 5/5 [00:00<00:00, 97.74it/s] diff --git a/wandb/run-20260305_063501-nsa3cbsg/files/requirements.txt b/wandb/run-20260305_063501-nsa3cbsg/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_063501-nsa3cbsg/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 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GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T06:35:17.774961Z" - writerId: sm6lazbtnkv16d7hpoydsehsdlfw5f5x - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_063517-5dosj1w9/files/output.log b/wandb/run-20260305_063517-5dosj1w9/files/output.log deleted file mode 100644 index e16059e97eea1f2f2cfaf850d27ec78b005418e3..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_063517-5dosj1w9/files/output.log +++ /dev/null @@ -1,70 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 15633.06it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_2/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -classifier.bias | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.weight | MISSING | -bert.pooler.dense.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 4 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 828 - Number of trainable parameters = 45,088,514 - 24%|██▍ | 199/828 [00:11<00:36, 17.32it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_acceptors/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_acceptors/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.88it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_acceptors/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_acceptors/checkpoint-200/tokenizer_config.json - 48%|████▊ | 400/828 [00:24<00:24, 17.30it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_acceptors/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_acceptors/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.66it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_acceptors/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_acceptors/checkpoint-400/tokenizer_config.json - 72%|███████▏ | 599/828 [00:36<00:13, 17.37it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_acceptors/checkpoint-600 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_acceptors/checkpoint-600/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.73it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_acceptors/checkpoint-600/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_acceptors/checkpoint-600/tokenizer_config.json - 97%|█████████▋| 800/828 [00:48<00:01, 17.53it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_acceptors/checkpoint-800 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_acceptors/checkpoint-800/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 5.14it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_acceptors/checkpoint-800/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_acceptors/checkpoint-800/tokenizer_config.json -100%|█████████▉| 826/828 [00:50<00:00, 17.10it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_acceptors/checkpoint-828 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_acceptors/checkpoint-828/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 5.17it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_acceptors/checkpoint-828/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_acceptors/checkpoint-828/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 828/828 [00:51<00:00, 16.13it/s] -{'train_runtime': '51.35', 'train_samples_per_second': '2057', 'train_steps_per_second': '16.12', 'train_loss': '0.4522', 'epoch': '4'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 58.75it/s] diff --git a/wandb/run-20260305_063517-5dosj1w9/files/requirements.txt b/wandb/run-20260305_063517-5dosj1w9/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_063517-5dosj1w9/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 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--log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "547313684480" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T06:36:26.164452Z" - writerId: k22jt9kem8bk3jgz3w8i30mxsmwfbt36 - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_063626-7osst31n/files/output.log b/wandb/run-20260305_063626-7osst31n/files/output.log deleted file mode 100644 index 4a0cd6109648e02aacff650f369b26cbd188dd71..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_063626-7osst31n/files/output.log +++ /dev/null @@ -1,70 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 21144.23it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_2/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -classifier.bias | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 4 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 828 - Number of trainable parameters = 45,089,283 - 24%|██▍ | 199/828 [00:12<00:36, 17.39it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_all/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_all/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.82it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_all/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_all/checkpoint-200/tokenizer_config.json - 48%|████▊ | 400/828 [00:24<00:24, 17.68it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_all/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_all/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 5.34it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_all/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_all/checkpoint-400/tokenizer_config.json - 72%|███████▏ | 599/828 [00:36<00:13, 17.41it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_all/checkpoint-600 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_all/checkpoint-600/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.14it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_all/checkpoint-600/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_all/checkpoint-600/tokenizer_config.json - 97%|█████████▋| 800/828 [00:48<00:01, 17.30it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_all/checkpoint-800 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_all/checkpoint-800/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.85it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_all/checkpoint-800/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_all/checkpoint-800/tokenizer_config.json -100%|█████████▉| 826/828 [00:51<00:00, 16.71it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_all/checkpoint-828 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_all/checkpoint-828/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.87it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_all/checkpoint-828/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_all/checkpoint-828/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 828/828 [00:51<00:00, 15.93it/s] -{'train_runtime': '51.96', 'train_samples_per_second': '2032', 'train_steps_per_second': '15.94', 'train_loss': '0.7606', 'epoch': '4'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 61.52it/s] diff --git a/wandb/run-20260305_063626-7osst31n/files/requirements.txt b/wandb/run-20260305_063626-7osst31n/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_063626-7osst31n/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T06:37:33.894456Z" - writerId: 7y1ugyk6ltx83394s5guqdtzflgcos42 - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_063733-h4f3npd6/files/output.log b/wandb/run-20260305_063733-h4f3npd6/files/output.log deleted file mode 100644 index 71489a97349c4485aed0c38e45816a9f4c0633ef..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_063733-h4f3npd6/files/output.log +++ /dev/null @@ -1,70 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 20409.75it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_2/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.dense.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -classifier.bias | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.bias | MISSING | -bert.pooler.dense.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 4 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 828 - Number of trainable parameters = 45,088,514 - 24%|██▍ | 199/828 [00:11<00:35, 17.53it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_donors/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_donors/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.52it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_donors/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_donors/checkpoint-200/tokenizer_config.json - 48%|████▊ | 400/828 [00:23<00:24, 17.59it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_donors/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_donors/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.94it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_donors/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_donors/checkpoint-400/tokenizer_config.json - 72%|███████▏ | 599/828 [00:36<00:13, 17.19it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_donors/checkpoint-600 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_donors/checkpoint-600/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.28it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_donors/checkpoint-600/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_donors/checkpoint-600/tokenizer_config.json - 97%|█████████▋| 800/828 [00:48<00:01, 16.37it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_donors/checkpoint-800 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_donors/checkpoint-800/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.27it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_donors/checkpoint-800/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_donors/checkpoint-800/tokenizer_config.json -100%|█████████▉| 826/828 [00:51<00:00, 16.52it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_donors/checkpoint-828 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_donors/checkpoint-828/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.63it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_donors/checkpoint-828/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/splice_sites_donors/checkpoint-828/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 828/828 [00:52<00:00, 15.88it/s] -{'train_runtime': '52.15', 'train_samples_per_second': '2025', 'train_steps_per_second': '15.88', 'train_loss': '0.4351', 'epoch': '4'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 61.29it/s] diff --git a/wandb/run-20260305_063733-h4f3npd6/files/requirements.txt b/wandb/run-20260305_063733-h4f3npd6/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_063733-h4f3npd6/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 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/data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T06:38:41.827325Z" - writerId: jdt47ttn2wie9851l81d1ib54pieeq4t - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_063841-yc6tb29g/files/output.log b/wandb/run-20260305_063841-yc6tb29g/files/output.log deleted file mode 100644 index 293d03d2ca9f3ddbad08281d0bbc93052f934c70..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_063841-yc6tb29g/files/output.log +++ /dev/null @@ -1,60 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 21938.10it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_2/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -classifier.weight | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.bias | MISSING | -bert.pooler.dense.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 2 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 414 - Number of trainable parameters = 45,088,514 - 48%|████▊ | 199/414 [00:16<00:17, 12.15it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H2AFZ/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H2AFZ/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.47it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H2AFZ/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H2AFZ/checkpoint-200/tokenizer_config.json - 96%|█████████▋| 399/414 [00:33<00:01, 11.79it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H2AFZ/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H2AFZ/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.71it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H2AFZ/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H2AFZ/checkpoint-400/tokenizer_config.json -100%|█████████▉| 413/414 [00:35<00:00, 10.39it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H2AFZ/checkpoint-414 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H2AFZ/checkpoint-414/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.85it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H2AFZ/checkpoint-414/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H2AFZ/checkpoint-414/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 414/414 [00:36<00:00, 11.37it/s] -{'train_runtime': '36.42', 'train_samples_per_second': '1450', 'train_steps_per_second': '11.37', 'train_loss': '0.5259', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 42.28it/s] diff --git a/wandb/run-20260305_063841-yc6tb29g/files/requirements.txt b/wandb/run-20260305_063841-yc6tb29g/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_063841-yc6tb29g/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 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/home/n5huang/dna_token/pretrain/models/model_len_2/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -bert.pooler.dense.weight | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.weight | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 25,292 - Num Epochs = 2 - Num update steps per epoch = 198 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 396 - Number of trainable parameters = 45,088,514 - 50%|█████ | 199/396 [00:16<00:15, 12.46it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H3K27ac/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H3K27ac/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.11it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H3K27ac/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H3K27ac/checkpoint-200/tokenizer_config.json -100%|██████████| 396/396 [00:33<00:00, 13.23it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H3K27ac/checkpoint-396 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H3K27ac/checkpoint-396/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 5.20it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H3K27ac/checkpoint-396/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H3K27ac/checkpoint-396/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 396/396 [00:34<00:00, 11.53it/s] -{'train_runtime': '34.35', 'train_samples_per_second': '1472', 'train_steps_per_second': '11.53', 'train_loss': '0.551', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3163 - Batch size = 128 -100%|██████████| 25/25 [00:00<00:00, 41.45it/s] diff --git a/wandb/run-20260305_063937-i2q1260h/files/requirements.txt b/wandb/run-20260305_063937-i2q1260h/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_063937-i2q1260h/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T06:40:30.313919Z" - writerId: y058zfc9iyd0qpq5bhsvfmbc5obv9e6w - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_064030-7mrxjq4i/files/output.log b/wandb/run-20260305_064030-7mrxjq4i/files/output.log deleted file mode 100644 index e37af18e124bd150a4ac1db1ecd188d7a3740db4..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_064030-7mrxjq4i/files/output.log +++ /dev/null @@ -1,60 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 24322.48it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_2/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -bert.pooler.dense.weight | MISSING | -classifier.weight | MISSING | -classifier.bias | MISSING | -bert.pooler.dense.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 2 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 414 - Number of trainable parameters = 45,088,514 - 48%|████▊ | 200/414 [00:16<00:17, 12.17it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H3K27me3/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H3K27me3/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 2.78it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H3K27me3/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H3K27me3/checkpoint-200/tokenizer_config.json - 97%|█████████▋| 400/414 [00:33<00:01, 12.31it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H3K27me3/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H3K27me3/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.82it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H3K27me3/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H3K27me3/checkpoint-400/tokenizer_config.json -100%|██████████| 414/414 [00:35<00:00, 11.75it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H3K27me3/checkpoint-414 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H3K27me3/checkpoint-414/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.12it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H3K27me3/checkpoint-414/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H3K27me3/checkpoint-414/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 414/414 [00:36<00:00, 11.34it/s] -{'train_runtime': '36.5', 'train_samples_per_second': '1446', 'train_steps_per_second': '11.34', 'train_loss': '0.474', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 42.11it/s] diff --git a/wandb/run-20260305_064030-7mrxjq4i/files/requirements.txt b/wandb/run-20260305_064030-7mrxjq4i/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_064030-7mrxjq4i/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 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cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T06:41:24.798349Z" - writerId: 1pkvrg1pdoopw9vc4sd9gb4oghchdjp6 - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_064124-gumd68k5/files/output.log b/wandb/run-20260305_064124-gumd68k5/files/output.log deleted file mode 100644 index 5a0d81a245792073de03fe5eed391fa6bdebde5e..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_064124-gumd68k5/files/output.log +++ /dev/null @@ -1,60 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 21133.68it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_2/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.decoder.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -classifier.weight | MISSING | -classifier.bias | MISSING | -bert.pooler.dense.bias | MISSING | -bert.pooler.dense.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 2 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 414 - Number of trainable parameters = 45,088,514 - 48%|████▊ | 199/414 [00:16<00:17, 12.38it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H3K36me3/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H3K36me3/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.86it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H3K36me3/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H3K36me3/checkpoint-200/tokenizer_config.json - 96%|█████████▋| 399/414 [00:33<00:01, 12.33it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H3K36me3/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H3K36me3/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.26it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H3K36me3/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H3K36me3/checkpoint-400/tokenizer_config.json -100%|█████████▉| 413/414 [00:35<00:00, 10.39it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H3K36me3/checkpoint-414 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H3K36me3/checkpoint-414/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 5.10it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H3K36me3/checkpoint-414/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H3K36me3/checkpoint-414/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 414/414 [00:35<00:00, 11.52it/s] -{'train_runtime': '35.95', 'train_samples_per_second': '1469', 'train_steps_per_second': '11.52', 'train_loss': '0.4716', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 42.33it/s] diff --git a/wandb/run-20260305_064124-gumd68k5/files/requirements.txt b/wandb/run-20260305_064124-gumd68k5/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_064124-gumd68k5/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 -accelerate==1.13.0 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -triton==3.6.0 -nvidia-nccl-cu12==2.27.5 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -cuda-pathfinder==1.4.0 -shellingham==1.5.4 -torchaudio==2.5.1 -nvidia-cufile-cu12==1.13.1.3 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -nvidia-nvjitlink-cu12==12.8.93 -click==8.3.1 -MarkupSafe==3.0.2 -nvidia-nvshmem-cu12==3.4.5 -urllib3==2.6.3 -cuda-bindings==12.9.4 -propcache==0.4.1 -nvidia-cusolver-cu12==11.7.3.90 -sympy==1.14.0 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -nvidia-cuda-runtime-cu12==12.8.90 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_064124-gumd68k5/files/wandb-metadata.json b/wandb/run-20260305_064124-gumd68k5/files/wandb-metadata.json deleted file mode 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/data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T06:42:18.933758Z" - writerId: kxnio0h21vsre7shzh76wzhenrqp4p57 - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_064218-2mvsit9p/files/output.log b/wandb/run-20260305_064218-2mvsit9p/files/output.log deleted file mode 100644 index 440dd91a0e8468fe206a159ad38066bfd4ed5aba..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_064218-2mvsit9p/files/output.log +++ /dev/null @@ -1,60 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 21283.40it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_2/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -bert.pooler.dense.bias | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.weight | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 2 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 414 - Number of trainable parameters = 45,088,514 - 48%|████▊ | 199/414 [00:16<00:17, 12.33it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H3K4me1/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H3K4me1/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.78it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H3K4me1/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H3K4me1/checkpoint-200/tokenizer_config.json - 96%|█████████▋| 399/414 [00:33<00:01, 12.61it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H3K4me1/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H3K4me1/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.61it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H3K4me1/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H3K4me1/checkpoint-400/tokenizer_config.json -100%|█████████▉| 413/414 [00:35<00:00, 10.46it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H3K4me1/checkpoint-414 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H3K4me1/checkpoint-414/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 5.05it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H3K4me1/checkpoint-414/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H3K4me1/checkpoint-414/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 414/414 [00:36<00:00, 11.45it/s] -{'train_runtime': '36.16', 'train_samples_per_second': '1460', 'train_steps_per_second': '11.45', 'train_loss': '0.5663', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 41.78it/s] diff --git a/wandb/run-20260305_064218-2mvsit9p/files/requirements.txt b/wandb/run-20260305_064218-2mvsit9p/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_064218-2mvsit9p/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T06:43:14.531466Z" - writerId: 3y52o4efd04ph0bei10wtdrod1thqa24 - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_064314-tunst6eg/files/output.log b/wandb/run-20260305_064314-tunst6eg/files/output.log deleted file mode 100644 index 8b289cf21dc676d5c8bbf3bc84dbaaf459975d94..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_064314-tunst6eg/files/output.log +++ /dev/null @@ -1,60 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 22471.07it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_2/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -classifier.weight | MISSING | -classifier.bias | MISSING | -bert.pooler.dense.bias | MISSING | -bert.pooler.dense.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 25,710 - Num Epochs = 2 - Num update steps per epoch = 201 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 402 - Number of trainable parameters = 45,088,514 - 50%|████▉ | 200/402 [00:16<00:16, 12.33it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H3K4me2/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H3K4me2/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.50it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H3K4me2/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H3K4me2/checkpoint-200/tokenizer_config.json -100%|█████████▉| 400/402 [00:33<00:00, 12.47it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H3K4me2/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H3K4me2/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 5.16it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H3K4me2/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H3K4me2/checkpoint-400/tokenizer_config.json -100%|██████████| 402/402 [00:34<00:00, 6.11it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H3K4me2/checkpoint-402 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H3K4me2/checkpoint-402/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.90it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H3K4me2/checkpoint-402/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H3K4me2/checkpoint-402/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 402/402 [00:35<00:00, 11.47it/s] -{'train_runtime': '35.03', 'train_samples_per_second': '1468', 'train_steps_per_second': '11.47', 'train_loss': '0.4967', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3215 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 43.08it/s] diff --git a/wandb/run-20260305_064314-tunst6eg/files/requirements.txt b/wandb/run-20260305_064314-tunst6eg/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_064314-tunst6eg/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 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--seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "547331981312" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - 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/data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T06:44:06.671162Z" - writerId: ogjba6ss34b2nukpwln8r3s6u8z35uql - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_064406-yoh5ra17/files/output.log b/wandb/run-20260305_064406-yoh5ra17/files/output.log deleted file mode 100644 index f4994c39324b07c070901e1f28a19064cc1f43bb..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_064406-yoh5ra17/files/output.log +++ /dev/null @@ -1,55 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 13829.93it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_2/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -classifier.weight | MISSING | -classifier.bias | MISSING | -bert.pooler.dense.bias | MISSING | -bert.pooler.dense.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 14,595 - Num Epochs = 2 - Num update steps per epoch = 115 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 230 - Number of trainable parameters = 45,088,514 - 87%|████████▋ | 200/230 [00:16<00:02, 12.54it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H3K4me3/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H3K4me3/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.80it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H3K4me3/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H3K4me3/checkpoint-200/tokenizer_config.json - 99%|█████████▉| 228/230 [00:19<00:00, 12.50it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H3K4me3/checkpoint-230 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H3K4me3/checkpoint-230/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.86it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H3K4me3/checkpoint-230/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H3K4me3/checkpoint-230/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 230/230 [00:20<00:00, 11.34it/s] -{'train_runtime': '20.27', 'train_samples_per_second': '1440', 'train_steps_per_second': '11.35', 'train_loss': '0.4194', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 1825 - Batch size = 128 -100%|██████████| 15/15 [00:00<00:00, 44.52it/s] diff --git a/wandb/run-20260305_064406-yoh5ra17/files/requirements.txt b/wandb/run-20260305_064406-yoh5ra17/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_064406-yoh5ra17/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 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/data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T06:44:41.201239Z" - writerId: 1exdo4i6yjooul03vokac2kdddzjivvk - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_064441-xr8ctikd/files/output.log b/wandb/run-20260305_064441-xr8ctikd/files/output.log deleted file mode 100644 index a97c7ea30144c659dfcb1cd9bb5aaa8902de0382..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_064441-xr8ctikd/files/output.log +++ /dev/null @@ -1,55 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 22039.68it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_2/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -bert.pooler.dense.weight | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.weight | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 19,422 - Num Epochs = 2 - Num update steps per epoch = 152 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 304 - Number of trainable parameters = 45,088,514 - 65%|██████▌ | 199/304 [00:16<00:08, 12.31it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H3K9ac/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H3K9ac/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.48it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H3K9ac/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H3K9ac/checkpoint-200/tokenizer_config.json -100%|█████████▉| 303/304 [00:25<00:00, 12.25it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H3K9ac/checkpoint-304 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H3K9ac/checkpoint-304/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.94it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H3K9ac/checkpoint-304/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H3K9ac/checkpoint-304/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 304/304 [00:26<00:00, 11.43it/s] -{'train_runtime': '26.59', 'train_samples_per_second': '1461', 'train_steps_per_second': '11.43', 'train_loss': '0.5235', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 2429 - Batch size = 128 -100%|██████████| 19/19 [00:00<00:00, 42.79it/s] diff --git a/wandb/run-20260305_064441-xr8ctikd/files/requirements.txt b/wandb/run-20260305_064441-xr8ctikd/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_064441-xr8ctikd/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T06:45:23.646760Z" - writerId: gbx5ac3id1dciphehclwdq0u3g2kxw10 - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_064523-yvy1vhnd/files/output.log b/wandb/run-20260305_064523-yvy1vhnd/files/output.log deleted file mode 100644 index 12b354761a73a21775a6ae3c3e6b2745a0137416..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_064523-yvy1vhnd/files/output.log +++ /dev/null @@ -1,55 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 23478.62it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_2/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -classifier.bias | MISSING | -bert.pooler.dense.bias | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 22,630 - Num Epochs = 2 - Num update steps per epoch = 177 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 354 - Number of trainable parameters = 45,088,514 - 56%|█████▋ | 200/354 [00:16<00:12, 12.19it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H3K9me3/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H3K9me3/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.89it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H3K9me3/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H3K9me3/checkpoint-200/tokenizer_config.json -100%|█████████▉| 353/354 [00:30<00:00, 12.43it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H3K9me3/checkpoint-354 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H3K9me3/checkpoint-354/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 5.05it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H3K9me3/checkpoint-354/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H3K9me3/checkpoint-354/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 354/354 [00:31<00:00, 11.35it/s] -{'train_runtime': '31.19', 'train_samples_per_second': '1451', 'train_steps_per_second': '11.35', 'train_loss': '0.6085', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 2830 - Batch size = 128 -100%|██████████| 23/23 [00:00<00:00, 41.86it/s] diff --git a/wandb/run-20260305_064523-yvy1vhnd/files/requirements.txt b/wandb/run-20260305_064523-yvy1vhnd/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_064523-yvy1vhnd/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 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cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T06:46:11.676535Z" - writerId: fhvap6eez0m9tf3co0i5bf9iuen9rl60 - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_064611-hqza9twn/files/output.log b/wandb/run-20260305_064611-hqza9twn/files/output.log deleted file mode 100644 index 7c15e395ff8af4160b83e79aa5634ec480e8f8a3..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_064611-hqza9twn/files/output.log +++ /dev/null @@ -1,60 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 24282.05it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_2/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -classifier.weight | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.bias | MISSING | -bert.pooler.dense.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 315}. -***** Running training ***** - Num examples = 25,816 - Num Epochs = 2 - Num update steps per epoch = 202 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 404 - Number of trainable parameters = 45,088,514 - 50%|████▉ | 200/404 [00:16<00:16, 12.74it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H4K20me1/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H4K20me1/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.18it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H4K20me1/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H4K20me1/checkpoint-200/tokenizer_config.json - 99%|█████████▉| 400/404 [00:32<00:00, 12.26it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H4K20me1/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H4K20me1/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.79it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H4K20me1/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H4K20me1/checkpoint-400/tokenizer_config.json -100%|██████████| 404/404 [00:33<00:00, 6.77it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H4K20me1/checkpoint-404 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H4K20me1/checkpoint-404/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 5.38it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H4K20me1/checkpoint-404/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_len2/H4K20me1/checkpoint-404/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 404/404 [00:34<00:00, 11.70it/s] -{'train_runtime': '34.52', 'train_samples_per_second': '1496', 'train_steps_per_second': '11.71', 'train_loss': '0.4506', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3227 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 42.43it/s] diff --git a/wandb/run-20260305_064611-hqza9twn/files/requirements.txt b/wandb/run-20260305_064611-hqza9twn/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_064611-hqza9twn/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 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/data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T06:47:03.458428Z" - writerId: 3da2d1jck8hupe5q4u3jssvarhx6ovl1 - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_064703-zmicw3v9/files/output.log b/wandb/run-20260305_064703-zmicw3v9/files/output.log deleted file mode 100644 index e70e8dd2b6118695d9c92f118635bee3dd64d37e..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_064703-zmicw3v9/files/output.log +++ /dev/null @@ -1,70 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 20425.49it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_2/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -classifier.weight | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.bias | MISSING | -bert.pooler.dense.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 755}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 4 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 828 - Number of trainable parameters = 45,088,514 - 24%|██▍ | 199/828 [00:09<00:28, 22.34it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.37it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers/checkpoint-200/tokenizer_config.json - 48%|████▊ | 400/828 [00:18<00:17, 23.79it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 5.38it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers/checkpoint-400/tokenizer_config.json - 72%|███████▏ | 598/828 [00:27<00:09, 24.08it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers/checkpoint-600 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers/checkpoint-600/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.84it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers/checkpoint-600/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers/checkpoint-600/tokenizer_config.json - 96%|█████████▋| 799/828 [00:36<00:01, 23.30it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers/checkpoint-800 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers/checkpoint-800/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.95it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers/checkpoint-800/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers/checkpoint-800/tokenizer_config.json -100%|█████████▉| 826/828 [00:38<00:00, 21.64it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers/checkpoint-828 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers/checkpoint-828/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.13it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers/checkpoint-828/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers/checkpoint-828/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 828/828 [00:39<00:00, 21.11it/s] -{'train_runtime': '39.22', 'train_samples_per_second': '2692', 'train_steps_per_second': '21.11', 'train_loss': '0.5784', 'epoch': '4'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 81.53it/s] diff --git a/wandb/run-20260305_064703-zmicw3v9/files/requirements.txt b/wandb/run-20260305_064703-zmicw3v9/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_064703-zmicw3v9/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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wandb-AsyncioManager-main:1712085 [mailbox.py:close():155] Closing mailbox, abandoning 1 handles. diff --git a/wandb/run-20260305_064703-zmicw3v9/run-zmicw3v9.wandb b/wandb/run-20260305_064703-zmicw3v9/run-zmicw3v9.wandb deleted file mode 100644 index 7c286c38ea45f87d27176192892215f8f6e04075..0000000000000000000000000000000000000000 Binary files a/wandb/run-20260305_064703-zmicw3v9/run-zmicw3v9.wandb and /dev/null differ diff --git a/wandb/run-20260305_064757-cqpvxfta/files/config.yaml b/wandb/run-20260305_064757-cqpvxfta/files/config.yaml deleted file mode 100644 index 7968cb53e126f04f890b36b1ab909bf3db7525f1..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_064757-cqpvxfta/files/config.yaml +++ /dev/null @@ -1,139 +0,0 @@ -_wandb: - value: - cli_version: 0.25.0 - e: - e5x0qzhtd40p75xt1m05llud3b8c1895: - args: - - --model_name_or_path - - /home/n5huang/dna_token/pretrain/models/model_len_2/checkpoint-100000 - - --tokenizer_path - - /home/n5huang/dna_token/tokenizer_evaluation/merge_bpe/merge_tokenizer_unigram_tf_idf.json - - --trust_remote_code - - "True" - - --data_path - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/enhancers_types/split - - --kmer - - "-1" - - --run_name - - hg38_BPE_len2__merge_bpe_merge_tokenizer_unigram_tf_idf_3e-5_enhancers_types_seed42 - - --model_max_length - - "100" - - --per_device_train_batch_size - - "128" - - --per_device_eval_batch_size - - "128" - - --gradient_accumulation_steps - - "1" - - --learning_rate - - "3e-5" - - --num_train_epochs - - "4" - - --fp16 - - --save_steps - - "200" - - --output_dir - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers_types - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "547341152256" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T06:47:57.502292Z" - writerId: e5x0qzhtd40p75xt1m05llud3b8c1895 - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_064757-cqpvxfta/files/output.log b/wandb/run-20260305_064757-cqpvxfta/files/output.log deleted file mode 100644 index 7703c871fe6c25cc51b3e1755bfbaaf78fe638ce..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_064757-cqpvxfta/files/output.log +++ /dev/null @@ -1,70 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 21892.75it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_2/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -classifier.bias | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.weight | MISSING | -bert.pooler.dense.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 755}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 4 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 828 - Number of trainable parameters = 45,089,283 - 24%|██▍ | 199/828 [00:09<00:26, 23.59it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers_types/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers_types/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.44it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers_types/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers_types/checkpoint-200/tokenizer_config.json - 48%|████▊ | 400/828 [00:18<00:18, 23.11it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers_types/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers_types/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.96it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers_types/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers_types/checkpoint-400/tokenizer_config.json - 72%|███████▏ | 598/828 [00:27<00:09, 23.17it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers_types/checkpoint-600 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers_types/checkpoint-600/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.32it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers_types/checkpoint-600/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers_types/checkpoint-600/tokenizer_config.json - 96%|█████████▋| 799/828 [00:36<00:01, 24.28it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers_types/checkpoint-800 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers_types/checkpoint-800/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.15it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers_types/checkpoint-800/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers_types/checkpoint-800/tokenizer_config.json -100%|█████████▉| 826/828 [00:38<00:00, 21.74it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers_types/checkpoint-828 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers_types/checkpoint-828/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.75it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers_types/checkpoint-828/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers_types/checkpoint-828/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 828/828 [00:39<00:00, 21.23it/s] -{'train_runtime': '39', 'train_samples_per_second': '2708', 'train_steps_per_second': '21.23', 'train_loss': '0.7106', 'epoch': '4'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 78.38it/s] diff --git a/wandb/run-20260305_064757-cqpvxfta/files/requirements.txt b/wandb/run-20260305_064757-cqpvxfta/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_064757-cqpvxfta/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 -accelerate==1.13.0 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -triton==3.6.0 -nvidia-nccl-cu12==2.27.5 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -cuda-pathfinder==1.4.0 -shellingham==1.5.4 -torchaudio==2.5.1 -nvidia-cufile-cu12==1.13.1.3 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -nvidia-nvjitlink-cu12==12.8.93 -click==8.3.1 -MarkupSafe==3.0.2 -nvidia-nvshmem-cu12==3.4.5 -urllib3==2.6.3 -cuda-bindings==12.9.4 -propcache==0.4.1 -nvidia-cusolver-cu12==11.7.3.90 -sympy==1.14.0 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -nvidia-cuda-runtime-cu12==12.8.90 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_064757-cqpvxfta/files/wandb-metadata.json b/wandb/run-20260305_064757-cqpvxfta/files/wandb-metadata.json deleted file mode 100644 index ad9693f65e042f7f2a5090c890f90a1ac1a42d74..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_064757-cqpvxfta/files/wandb-metadata.json +++ /dev/null @@ -1,134 +0,0 @@ -{ - "os": "Linux-5.15.0-72-generic-x86_64-with-glibc2.35", - "python": "CPython 3.10.19", - "startedAt": "2026-03-05T06:47:57.502292Z", - "args": [ - "--model_name_or_path", - "/home/n5huang/dna_token/pretrain/models/model_len_2/checkpoint-100000", - "--tokenizer_path", - "/home/n5huang/dna_token/tokenizer_evaluation/merge_bpe/merge_tokenizer_unigram_tf_idf.json", - "--trust_remote_code", - "True", - "--data_path", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/enhancers_types/split", - "--kmer", - "-1", - "--run_name", - "hg38_BPE_len2__merge_bpe_merge_tokenizer_unigram_tf_idf_3e-5_enhancers_types_seed42", - "--model_max_length", - "100", - "--per_device_train_batch_size", - "128", - 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/data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T06:48:51.497458Z" - writerId: 0yko07lq6xdldoaeq4q39bwjg3ermlwg - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_064851-q6nsje5s/files/output.log b/wandb/run-20260305_064851-q6nsje5s/files/output.log deleted file mode 100644 index f09514221dd62f677ab14dc6f5bc6542ffbcd05f..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_064851-q6nsje5s/files/output.log +++ /dev/null @@ -1,55 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 21964.26it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_2/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -classifier.bias | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.weight | MISSING | -bert.pooler.dense.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 755}. -***** Running training ***** - Num examples = 25,267 - Num Epochs = 2 - Num update steps per epoch = 198 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 396 - Number of trainable parameters = 45,088,514 - 51%|█████ | 200/396 [00:07<00:06, 29.27it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/promoter_all/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/promoter_all/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.70it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/promoter_all/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/promoter_all/checkpoint-200/tokenizer_config.json -100%|█████████▉| 395/396 [00:15<00:00, 28.12it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/promoter_all/checkpoint-396 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/promoter_all/checkpoint-396/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.68it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/promoter_all/checkpoint-396/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/promoter_all/checkpoint-396/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 396/396 [00:16<00:00, 24.42it/s] -{'train_runtime': '16.22', 'train_samples_per_second': '3116', 'train_steps_per_second': '24.42', 'train_loss': '0.3939', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3159 - Batch size = 128 -100%|██████████| 25/25 [00:00<00:00, 91.71it/s] diff --git a/wandb/run-20260305_064851-q6nsje5s/files/requirements.txt b/wandb/run-20260305_064851-q6nsje5s/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_064851-q6nsje5s/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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- architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T06:49:21.479933Z" - writerId: hg55tu07jl0bdbq6l2zwecd62k0f6upx - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_064921-d6bk7w8g/files/output.log b/wandb/run-20260305_064921-d6bk7w8g/files/output.log deleted file mode 100644 index 7fd8c8ffad0642af5ddf3763cb689ec0ffa792b0..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_064921-d6bk7w8g/files/output.log +++ /dev/null @@ -1,55 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 22545.22it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_2/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -classifier.weight | MISSING | -bert.pooler.dense.weight | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 755}. -***** Running training ***** - Num examples = 25,097 - Num Epochs = 2 - Num update steps per epoch = 197 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 394 - Number of trainable parameters = 45,088,514 - 51%|█████ | 199/394 [00:07<00:07, 25.61it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/promoter_no_tata/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/promoter_no_tata/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.40it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/promoter_no_tata/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/promoter_no_tata/checkpoint-200/tokenizer_config.json -100%|██████████| 394/394 [00:15<00:00, 28.08it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/promoter_no_tata/checkpoint-394 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/promoter_no_tata/checkpoint-394/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.11it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/promoter_no_tata/checkpoint-394/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/promoter_no_tata/checkpoint-394/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 394/394 [00:16<00:00, 24.32it/s] -{'train_runtime': '16.2', 'train_samples_per_second': '3099', 'train_steps_per_second': '24.32', 'train_loss': '0.3798', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3138 - Batch size = 128 -100%|██████████| 25/25 [00:00<00:00, 99.03it/s] diff --git a/wandb/run-20260305_064921-d6bk7w8g/files/requirements.txt b/wandb/run-20260305_064921-d6bk7w8g/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_064921-d6bk7w8g/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 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/data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T06:49:51.740160Z" - writerId: cwbrnglneiuee9656zoagsvfht7g95xr - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_064951-dredbz0i/files/output.log b/wandb/run-20260305_064951-dredbz0i/files/output.log deleted file mode 100644 index caea64f4950830115a0dd6af4559e6ba37a1d72b..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_064951-dredbz0i/files/output.log +++ /dev/null @@ -1,50 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 21024.60it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_2/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -classifier.bias | MISSING | -bert.pooler.dense.bias | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 755}. -***** Running training ***** - Num examples = 4,219 - Num Epochs = 2 - Num update steps per epoch = 33 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 66 - Number of trainable parameters = 45,088,514 - 97%|█████████▋| 64/66 [00:02<00:00, 25.74it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/promoter_tata/checkpoint-66 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/promoter_tata/checkpoint-66/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 2.79it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/promoter_tata/checkpoint-66/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/promoter_tata/checkpoint-66/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 66/66 [00:03<00:00, 16.97it/s] -{'train_runtime': '3.888', 'train_samples_per_second': '2170', 'train_steps_per_second': '16.97', 'train_loss': '0.5524', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 528 - Batch size = 128 -100%|██████████| 5/5 [00:00<00:00, 103.16it/s] diff --git a/wandb/run-20260305_064951-dredbz0i/files/requirements.txt b/wandb/run-20260305_064951-dredbz0i/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_064951-dredbz0i/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "547345862656" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T06:50:06.199157Z" - writerId: n871m981u1v0ec4nlbwbwrpk61lrbozs - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_065006-28ujkgbc/files/output.log b/wandb/run-20260305_065006-28ujkgbc/files/output.log deleted file mode 100644 index ffd2eaf01b005722865ad40fa8afde93b0d88fbe..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_065006-28ujkgbc/files/output.log +++ /dev/null @@ -1,70 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 24275.10it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_2/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -bert.pooler.dense.weight | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.weight | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 755}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 4 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 828 - Number of trainable parameters = 45,088,514 - 24%|██▍ | 199/828 [00:11<00:35, 17.67it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_acceptors/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_acceptors/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.31it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_acceptors/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_acceptors/checkpoint-200/tokenizer_config.json - 48%|████▊ | 400/828 [00:24<00:25, 17.03it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_acceptors/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_acceptors/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.66it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_acceptors/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_acceptors/checkpoint-400/tokenizer_config.json - 72%|███████▏ | 599/828 [00:36<00:13, 17.55it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_acceptors/checkpoint-600 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_acceptors/checkpoint-600/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 5.18it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_acceptors/checkpoint-600/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_acceptors/checkpoint-600/tokenizer_config.json - 97%|█████████▋| 800/828 [00:48<00:01, 17.54it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_acceptors/checkpoint-800 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_acceptors/checkpoint-800/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 5.08it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_acceptors/checkpoint-800/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_acceptors/checkpoint-800/tokenizer_config.json -100%|█████████▉| 826/828 [00:50<00:00, 17.04it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_acceptors/checkpoint-828 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_acceptors/checkpoint-828/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.31it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_acceptors/checkpoint-828/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_acceptors/checkpoint-828/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 828/828 [00:51<00:00, 16.01it/s] -{'train_runtime': '51.72', 'train_samples_per_second': '2042', 'train_steps_per_second': '16.01', 'train_loss': '0.6227', 'epoch': '4'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 60.05it/s] diff --git a/wandb/run-20260305_065006-28ujkgbc/files/requirements.txt b/wandb/run-20260305_065006-28ujkgbc/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_065006-28ujkgbc/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 -accelerate==1.13.0 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -triton==3.6.0 -nvidia-nccl-cu12==2.27.5 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -cuda-pathfinder==1.4.0 -shellingham==1.5.4 -torchaudio==2.5.1 -nvidia-cufile-cu12==1.13.1.3 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -nvidia-nvjitlink-cu12==12.8.93 -click==8.3.1 -MarkupSafe==3.0.2 -nvidia-nvshmem-cu12==3.4.5 -urllib3==2.6.3 -cuda-bindings==12.9.4 -propcache==0.4.1 -nvidia-cusolver-cu12==11.7.3.90 -sympy==1.14.0 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -nvidia-cuda-runtime-cu12==12.8.90 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_065006-28ujkgbc/files/wandb-metadata.json b/wandb/run-20260305_065006-28ujkgbc/files/wandb-metadata.json deleted file mode 100644 index eb189a570767a1115134228fdd96792d6cd0e936..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_065006-28ujkgbc/files/wandb-metadata.json +++ /dev/null @@ -1,134 +0,0 @@ -{ - 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memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T06:51:49.895679Z" - writerId: p7790qbogwmd1rx5ketxbqfxi3f3cfnf - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_065149-413zaicd/files/output.log b/wandb/run-20260305_065149-413zaicd/files/output.log deleted file mode 100644 index 9c1b692c874686fe6aa671871516fe2586a3e7d6..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_065149-413zaicd/files/output.log +++ /dev/null @@ -1,70 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 20520.48it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_2/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.decoder.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -bert.pooler.dense.weight | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.weight | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 755}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 4 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 828 - Number of trainable parameters = 45,089,283 - 24%|██▍ | 199/828 [00:12<00:36, 17.05it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_all/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_all/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.57it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_all/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_all/checkpoint-200/tokenizer_config.json - 48%|████▊ | 400/828 [00:24<00:26, 16.40it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_all/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_all/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.10it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_all/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_all/checkpoint-400/tokenizer_config.json - 72%|███████▏ | 599/828 [00:36<00:13, 17.35it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_all/checkpoint-600 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_all/checkpoint-600/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.56it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_all/checkpoint-600/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_all/checkpoint-600/tokenizer_config.json - 97%|█████████▋| 800/828 [00:49<00:01, 17.61it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_all/checkpoint-800 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_all/checkpoint-800/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 5.11it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_all/checkpoint-800/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_all/checkpoint-800/tokenizer_config.json -100%|█████████▉| 826/828 [00:51<00:00, 17.24it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_all/checkpoint-828 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_all/checkpoint-828/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.80it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_all/checkpoint-828/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_all/checkpoint-828/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 828/828 [00:52<00:00, 15.91it/s] -{'train_runtime': '52.05', 'train_samples_per_second': '2029', 'train_steps_per_second': '15.91', 'train_loss': '1.005', 'epoch': '4'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 60.03it/s] diff --git a/wandb/run-20260305_065149-413zaicd/files/requirements.txt b/wandb/run-20260305_065149-413zaicd/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_065149-413zaicd/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 -accelerate==1.13.0 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -triton==3.6.0 -nvidia-nccl-cu12==2.27.5 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -cuda-pathfinder==1.4.0 -shellingham==1.5.4 -torchaudio==2.5.1 -nvidia-cufile-cu12==1.13.1.3 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -nvidia-nvjitlink-cu12==12.8.93 -click==8.3.1 -MarkupSafe==3.0.2 -nvidia-nvshmem-cu12==3.4.5 -urllib3==2.6.3 -cuda-bindings==12.9.4 -propcache==0.4.1 -nvidia-cusolver-cu12==11.7.3.90 -sympy==1.14.0 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -nvidia-cuda-runtime-cu12==12.8.90 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_065149-413zaicd/files/wandb-metadata.json b/wandb/run-20260305_065149-413zaicd/files/wandb-metadata.json deleted file mode 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/home/n5huang/dna_token/tokenizer_evaluation/merge_bpe/merge_tokenizer_unigram_tf_idf.json - - --trust_remote_code - - "True" - - --data_path - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/splice_sites_donors/split - - --kmer - - "-1" - - --run_name - - hg38_BPE_len2__merge_bpe_merge_tokenizer_unigram_tf_idf_3e-5_splice_sites_donors_seed42 - - --model_max_length - - "140" - - --per_device_train_batch_size - - "128" - - --per_device_eval_batch_size - - "128" - - --gradient_accumulation_steps - - "1" - - --learning_rate - - "3e-5" - - --num_train_epochs - - "4" - - --fp16 - - --save_steps - - "200" - - --output_dir - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_donors - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "547352760320" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T06:52:57.408837Z" - writerId: y5199afpfngfjnqakk6w43omm2v0htgr - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_065257-90the7y8/files/output.log b/wandb/run-20260305_065257-90the7y8/files/output.log deleted file mode 100644 index e3916fffd29d5abc3edf6331d065edef2dadeb72..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_065257-90the7y8/files/output.log +++ /dev/null @@ -1,70 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 13358.92it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_2/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -bert.pooler.dense.bias | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.weight | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 755}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 4 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 828 - Number of trainable parameters = 45,088,514 - 24%|██▍ | 199/828 [00:12<00:35, 17.56it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_donors/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_donors/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.91it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_donors/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_donors/checkpoint-200/tokenizer_config.json - 48%|████▊ | 400/828 [00:24<00:24, 17.25it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_donors/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_donors/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.48it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_donors/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_donors/checkpoint-400/tokenizer_config.json - 72%|███████▏ | 599/828 [00:36<00:13, 16.85it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_donors/checkpoint-600 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_donors/checkpoint-600/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.76it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_donors/checkpoint-600/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_donors/checkpoint-600/tokenizer_config.json - 97%|█████████▋| 800/828 [00:48<00:01, 17.47it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_donors/checkpoint-800 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_donors/checkpoint-800/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.87it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_donors/checkpoint-800/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_donors/checkpoint-800/tokenizer_config.json -100%|█████████▉| 826/828 [00:50<00:00, 16.99it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_donors/checkpoint-828 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_donors/checkpoint-828/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.21it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_donors/checkpoint-828/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_donors/checkpoint-828/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 828/828 [00:51<00:00, 16.01it/s] -{'train_runtime': '51.72', 'train_samples_per_second': '2042', 'train_steps_per_second': '16.01', 'train_loss': '0.5864', 'epoch': '4'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 58.51it/s] diff --git a/wandb/run-20260305_065257-90the7y8/files/requirements.txt b/wandb/run-20260305_065257-90the7y8/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_065257-90the7y8/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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/data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T06:54:05.496189Z" - writerId: bvayda331qovzj83dcl0mgjrkwtww4w2 - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_065405-2qbwwxn8/files/output.log b/wandb/run-20260305_065405-2qbwwxn8/files/output.log deleted file mode 100644 index 857ca595c5b281d8717c6946bd55df8b28747c1f..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_065405-2qbwwxn8/files/output.log +++ /dev/null @@ -1,60 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 21320.89it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_2/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -classifier.weight | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.bias | MISSING | -bert.pooler.dense.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 755}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 2 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 414 - Number of trainable parameters = 45,088,514 - 48%|████▊ | 199/414 [00:15<00:16, 12.88it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H2AFZ/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H2AFZ/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 5.05it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H2AFZ/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H2AFZ/checkpoint-200/tokenizer_config.json - 96%|█████████▋| 399/414 [00:32<00:01, 12.89it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H2AFZ/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H2AFZ/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.85it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H2AFZ/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H2AFZ/checkpoint-400/tokenizer_config.json -100%|█████████▉| 413/414 [00:33<00:00, 10.94it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H2AFZ/checkpoint-414 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H2AFZ/checkpoint-414/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.51it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H2AFZ/checkpoint-414/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H2AFZ/checkpoint-414/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 414/414 [00:34<00:00, 11.96it/s] -{'train_runtime': '34.61', 'train_samples_per_second': '1525', 'train_steps_per_second': '11.96', 'train_loss': '0.6023', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 43.76it/s] diff --git a/wandb/run-20260305_065405-2qbwwxn8/files/requirements.txt b/wandb/run-20260305_065405-2qbwwxn8/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_065405-2qbwwxn8/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 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- --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "547357347840" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T06:54:58.730148Z" - writerId: qiufbxlpfvv7d0ut0q7q6sbdrn5kqszl - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_065458-wo5qbnh0/files/output.log b/wandb/run-20260305_065458-wo5qbnh0/files/output.log deleted file mode 100644 index 0fb31f22cf806c40eb5766574e0d28fad9380857..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_065458-wo5qbnh0/files/output.log +++ /dev/null @@ -1,55 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 21296.23it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_2/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -bert.pooler.dense.weight | MISSING | -classifier.bias | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 755}. -***** Running training ***** - Num examples = 25,292 - Num Epochs = 2 - Num update steps per epoch = 198 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 396 - Number of trainable parameters = 45,088,514 - 50%|█████ | 199/396 [00:15<00:14, 13.27it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K27ac/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K27ac/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.02it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K27ac/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K27ac/checkpoint-200/tokenizer_config.json -100%|█████████▉| 395/396 [00:31<00:00, 12.85it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K27ac/checkpoint-396 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K27ac/checkpoint-396/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.52it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K27ac/checkpoint-396/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K27ac/checkpoint-396/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 396/396 [00:32<00:00, 12.09it/s] -{'train_runtime': '32.76', 'train_samples_per_second': '1544', 'train_steps_per_second': '12.09', 'train_loss': '0.6132', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3163 - Batch size = 128 -100%|██████████| 25/25 [00:00<00:00, 43.52it/s] diff --git a/wandb/run-20260305_065458-wo5qbnh0/files/requirements.txt b/wandb/run-20260305_065458-wo5qbnh0/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_065458-wo5qbnh0/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 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info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "547359621120" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T06:55:49.767394Z" - writerId: g5cxd65m0l1lipqu9qk48u1crv2a7mo5 - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_065549-v4on0oud/files/output.log b/wandb/run-20260305_065549-v4on0oud/files/output.log deleted file mode 100644 index bb090fbbf6451d16b3b76530a90b8d3ce97045df..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_065549-v4on0oud/files/output.log +++ /dev/null @@ -1,60 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 5629.56it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_2/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -bert.pooler.dense.weight | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.bias | MISSING | -classifier.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 755}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 2 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 414 - Number of trainable parameters = 45,088,514 - 48%|████▊ | 199/414 [00:16<00:16, 13.08it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K27me3/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K27me3/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.73it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K27me3/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K27me3/checkpoint-200/tokenizer_config.json - 96%|█████████▋| 399/414 [00:32<00:01, 12.98it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K27me3/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K27me3/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.27it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K27me3/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K27me3/checkpoint-400/tokenizer_config.json -100%|█████████▉| 413/414 [00:34<00:00, 10.86it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K27me3/checkpoint-414 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K27me3/checkpoint-414/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.56it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K27me3/checkpoint-414/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K27me3/checkpoint-414/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 414/414 [00:35<00:00, 11.80it/s] -{'train_runtime': '35.09', 'train_samples_per_second': '1505', 'train_steps_per_second': '11.8', 'train_loss': '0.5562', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 42.12it/s] diff --git a/wandb/run-20260305_065549-v4on0oud/files/requirements.txt b/wandb/run-20260305_065549-v4on0oud/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_065549-v4on0oud/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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/data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T06:56:44.061926Z" - writerId: yofy6p9ftdjyaze5wqfrks1lkow8u1hc - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_065644-1twl65wu/files/output.log b/wandb/run-20260305_065644-1twl65wu/files/output.log deleted file mode 100644 index f448d2ecc10306a28c688593b55fad73c59cf43b..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_065644-1twl65wu/files/output.log +++ /dev/null @@ -1,60 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 12094.23it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_2/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -bert.pooler.dense.bias | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.weight | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 755}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 2 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 414 - Number of trainable parameters = 45,088,514 - 48%|████▊ | 199/414 [00:15<00:16, 12.96it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K36me3/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K36me3/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.18it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K36me3/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K36me3/checkpoint-200/tokenizer_config.json - 96%|█████████▋| 399/414 [00:32<00:01, 13.08it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K36me3/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K36me3/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.40it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K36me3/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K36me3/checkpoint-400/tokenizer_config.json -100%|█████████▉| 413/414 [00:34<00:00, 10.68it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K36me3/checkpoint-414 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K36me3/checkpoint-414/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.68it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K36me3/checkpoint-414/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K36me3/checkpoint-414/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 414/414 [00:35<00:00, 11.74it/s] -{'train_runtime': '35.28', 'train_samples_per_second': '1497', 'train_steps_per_second': '11.73', 'train_loss': '0.5518', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 42.76it/s] diff --git a/wandb/run-20260305_065644-1twl65wu/files/requirements.txt b/wandb/run-20260305_065644-1twl65wu/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_065644-1twl65wu/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 -accelerate==1.13.0 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -triton==3.6.0 -nvidia-nccl-cu12==2.27.5 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -cuda-pathfinder==1.4.0 -shellingham==1.5.4 -torchaudio==2.5.1 -nvidia-cufile-cu12==1.13.1.3 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -nvidia-nvjitlink-cu12==12.8.93 -click==8.3.1 -MarkupSafe==3.0.2 -nvidia-nvshmem-cu12==3.4.5 -urllib3==2.6.3 -cuda-bindings==12.9.4 -propcache==0.4.1 -nvidia-cusolver-cu12==11.7.3.90 -sympy==1.14.0 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -nvidia-cuda-runtime-cu12==12.8.90 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_065644-1twl65wu/files/wandb-metadata.json b/wandb/run-20260305_065644-1twl65wu/files/wandb-metadata.json deleted file mode 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cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T06:57:37.265252Z" - writerId: 1hv71dyk29xoiu6z3svnkcwoesmp12fg - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_065737-vbmvu7d4/files/output.log b/wandb/run-20260305_065737-vbmvu7d4/files/output.log deleted file mode 100644 index 8f8054b4011632d31167e2fe633d47c5967e9955..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_065737-vbmvu7d4/files/output.log +++ /dev/null @@ -1,60 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 24134.03it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_2/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -classifier.weight | MISSING | -bert.pooler.dense.bias | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 755}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 2 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 414 - Number of trainable parameters = 45,088,514 - 48%|████▊ | 199/414 [00:15<00:16, 13.08it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me1/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me1/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.57it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me1/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me1/checkpoint-200/tokenizer_config.json - 96%|█████████▋| 399/414 [00:32<00:01, 12.94it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me1/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me1/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.27it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me1/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me1/checkpoint-400/tokenizer_config.json -100%|█████████▉| 413/414 [00:34<00:00, 10.92it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me1/checkpoint-414 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me1/checkpoint-414/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.28it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me1/checkpoint-414/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me1/checkpoint-414/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 414/414 [00:35<00:00, 11.81it/s] -{'train_runtime': '35.05', 'train_samples_per_second': '1506', 'train_steps_per_second': '11.81', 'train_loss': '0.6261', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 43.40it/s] diff --git a/wandb/run-20260305_065737-vbmvu7d4/files/requirements.txt b/wandb/run-20260305_065737-vbmvu7d4/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_065737-vbmvu7d4/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 -accelerate==1.13.0 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -triton==3.6.0 -nvidia-nccl-cu12==2.27.5 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -cuda-pathfinder==1.4.0 -shellingham==1.5.4 -torchaudio==2.5.1 -nvidia-cufile-cu12==1.13.1.3 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -nvidia-nvjitlink-cu12==12.8.93 -click==8.3.1 -MarkupSafe==3.0.2 -nvidia-nvshmem-cu12==3.4.5 -urllib3==2.6.3 -cuda-bindings==12.9.4 -propcache==0.4.1 -nvidia-cusolver-cu12==11.7.3.90 -sympy==1.14.0 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -nvidia-cuda-runtime-cu12==12.8.90 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_065737-vbmvu7d4/files/wandb-metadata.json b/wandb/run-20260305_065737-vbmvu7d4/files/wandb-metadata.json deleted file mode 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/data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T06:58:31.443636Z" - writerId: cymgcyp50jnawzsrkoy0ja4ln04nwj8m - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_065831-bdw2xw77/files/output.log b/wandb/run-20260305_065831-bdw2xw77/files/output.log deleted file mode 100644 index a5a2246f6b3e8fb8ddf6769f6fb8148d4d3ba799..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_065831-bdw2xw77/files/output.log +++ /dev/null @@ -1,60 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 20973.60it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_2/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -bert.pooler.dense.weight | MISSING | -classifier.weight | MISSING | -classifier.bias | MISSING | -bert.pooler.dense.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 755}. -***** Running training ***** - Num examples = 25,710 - Num Epochs = 2 - Num update steps per epoch = 201 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 402 - Number of trainable parameters = 45,088,514 - 50%|████▉ | 199/402 [00:15<00:15, 12.85it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me2/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me2/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 5.10it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me2/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me2/checkpoint-200/tokenizer_config.json - 99%|█████████▉| 399/402 [00:32<00:00, 13.06it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me2/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me2/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 5.17it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me2/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me2/checkpoint-400/tokenizer_config.json -100%|█████████▉| 401/402 [00:32<00:00, 5.56it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me2/checkpoint-402 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me2/checkpoint-402/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.11it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me2/checkpoint-402/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me2/checkpoint-402/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 402/402 [00:33<00:00, 11.92it/s] -{'train_runtime': '33.74', 'train_samples_per_second': '1524', 'train_steps_per_second': '11.92', 'train_loss': '0.5719', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3215 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 44.52it/s] diff --git a/wandb/run-20260305_065831-bdw2xw77/files/requirements.txt b/wandb/run-20260305_065831-bdw2xw77/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_065831-bdw2xw77/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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/home/n5huang/dna_token/pretrain/models/model_len_2/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.decoder.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -bert.pooler.dense.weight | MISSING | -classifier.bias | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 755}. -***** Running training ***** - Num examples = 14,595 - Num Epochs = 2 - Num update steps per epoch = 115 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 230 - Number of trainable parameters = 45,088,514 - 87%|████████▋ | 199/230 [00:15<00:02, 13.04it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me3/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me3/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.57it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me3/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me3/checkpoint-200/tokenizer_config.json -100%|█████████▉| 229/230 [00:19<00:00, 12.75it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me3/checkpoint-230 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me3/checkpoint-230/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 2.91it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me3/checkpoint-230/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K4me3/checkpoint-230/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 230/230 [00:19<00:00, 11.53it/s] -{'train_runtime': '19.94', 'train_samples_per_second': '1464', 'train_steps_per_second': '11.54', 'train_loss': '0.486', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 1825 - Batch size = 128 -100%|██████████| 15/15 [00:00<00:00, 47.06it/s] diff --git a/wandb/run-20260305_065923-1cqtt03p/files/requirements.txt b/wandb/run-20260305_065923-1cqtt03p/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_065923-1cqtt03p/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T06:59:59.182326Z" - writerId: f7yp4oumgkb7yfhothz6big9jftuu6dz - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_065959-66dc1ke7/files/output.log b/wandb/run-20260305_065959-66dc1ke7/files/output.log deleted file mode 100644 index b5af00dbd455dd385d7cb8d93898505fa24019f5..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_065959-66dc1ke7/files/output.log +++ /dev/null @@ -1,55 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 24201.59it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_2/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -bert.pooler.dense.bias | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 755}. -***** Running training ***** - Num examples = 19,422 - Num Epochs = 2 - Num update steps per epoch = 152 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 304 - Number of trainable parameters = 45,088,514 - 65%|██████▌ | 199/304 [00:15<00:08, 12.75it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K9ac/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K9ac/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.55it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K9ac/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K9ac/checkpoint-200/tokenizer_config.json -100%|█████████▉| 303/304 [00:24<00:00, 12.63it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K9ac/checkpoint-304 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K9ac/checkpoint-304/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.63it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K9ac/checkpoint-304/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K9ac/checkpoint-304/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 304/304 [00:25<00:00, 11.95it/s] -{'train_runtime': '25.43', 'train_samples_per_second': '1528', 'train_steps_per_second': '11.96', 'train_loss': '0.5877', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 2429 - Batch size = 128 -100%|██████████| 19/19 [00:00<00:00, 44.21it/s] diff --git a/wandb/run-20260305_065959-66dc1ke7/files/requirements.txt b/wandb/run-20260305_065959-66dc1ke7/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_065959-66dc1ke7/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 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- --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "547371151360" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T07:00:41.616277Z" - writerId: 5omqbnr6y9zp2w6nbo6eei6b47sd8w08 - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_070041-comuuqvx/files/output.log b/wandb/run-20260305_070041-comuuqvx/files/output.log deleted file mode 100644 index 9b626ccf07d8b1c0a30e8a2c098087c6ef1fa7c1..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_070041-comuuqvx/files/output.log +++ /dev/null @@ -1,55 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 25187.27it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_2/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -bert.pooler.dense.weight | MISSING | -classifier.bias | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 755}. -***** Running training ***** - Num examples = 22,630 - Num Epochs = 2 - Num update steps per epoch = 177 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 354 - Number of trainable parameters = 45,088,514 - 56%|█████▋ | 200/354 [00:15<00:11, 13.00it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K9me3/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K9me3/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.96it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K9me3/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K9me3/checkpoint-200/tokenizer_config.json -100%|██████████| 354/354 [00:28<00:00, 13.24it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K9me3/checkpoint-354 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K9me3/checkpoint-354/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 5.23it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K9me3/checkpoint-354/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H3K9me3/checkpoint-354/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 354/354 [00:29<00:00, 12.13it/s] -{'train_runtime': '29.19', 'train_samples_per_second': '1551', 'train_steps_per_second': '12.13', 'train_loss': '0.6756', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 2830 - Batch size = 128 -100%|██████████| 23/23 [00:00<00:00, 44.05it/s] diff --git a/wandb/run-20260305_070041-comuuqvx/files/requirements.txt b/wandb/run-20260305_070041-comuuqvx/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_070041-comuuqvx/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T07:01:28.660814Z" - writerId: 2x0h5n4fmbopneej6xdknueq4v0epn5p - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_070128-wlx2ul24/files/output.log b/wandb/run-20260305_070128-wlx2ul24/files/output.log deleted file mode 100644 index 495a4ee9a21791dc6f9d0610406b779e64d74b99..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_070128-wlx2ul24/files/output.log +++ /dev/null @@ -1,60 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 20333.34it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_len_2/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -classifier.weight | MISSING | -classifier.bias | MISSING | -bert.pooler.dense.weight | MISSING | -bert.pooler.dense.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 755}. -***** Running training ***** - Num examples = 25,816 - Num Epochs = 2 - Num update steps per epoch = 202 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 404 - Number of trainable parameters = 45,088,514 - 49%|████▉ | 199/404 [00:15<00:15, 13.13it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H4K20me1/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H4K20me1/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.52it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H4K20me1/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H4K20me1/checkpoint-200/tokenizer_config.json - 99%|█████████▉| 399/404 [00:31<00:00, 12.79it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H4K20me1/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H4K20me1/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.13it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H4K20me1/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H4K20me1/checkpoint-400/tokenizer_config.json -100%|█████████▉| 403/404 [00:33<00:00, 6.55it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H4K20me1/checkpoint-404 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H4K20me1/checkpoint-404/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.03it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H4K20me1/checkpoint-404/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/len2__merge_bpe_merge_tokenizer_unigram_tf_idf/H4K20me1/checkpoint-404/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 404/404 [00:33<00:00, 11.93it/s] -{'train_runtime': '33.86', 'train_samples_per_second': '1525', 'train_steps_per_second': '11.93', 'train_loss': '0.5198', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3227 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 44.71it/s] diff --git a/wandb/run-20260305_070128-wlx2ul24/files/requirements.txt b/wandb/run-20260305_070128-wlx2ul24/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_070128-wlx2ul24/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 -accelerate==1.13.0 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -triton==3.6.0 -nvidia-nccl-cu12==2.27.5 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -cuda-pathfinder==1.4.0 -shellingham==1.5.4 -torchaudio==2.5.1 -nvidia-cufile-cu12==1.13.1.3 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -nvidia-nvjitlink-cu12==12.8.93 -click==8.3.1 -MarkupSafe==3.0.2 -nvidia-nvshmem-cu12==3.4.5 -urllib3==2.6.3 -cuda-bindings==12.9.4 -propcache==0.4.1 -nvidia-cusolver-cu12==11.7.3.90 -sympy==1.14.0 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -nvidia-cuda-runtime-cu12==12.8.90 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_070128-wlx2ul24/files/wandb-metadata.json b/wandb/run-20260305_070128-wlx2ul24/files/wandb-metadata.json deleted file mode 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/home/n5huang/dna_token/tokenizer_evaluation/baseline_bpe/tokenizer.json - - --trust_remote_code - - "True" - - --data_path - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/enhancers/split - - --kmer - - "-1" - - --run_name - - hg38_BPE_tfidf__baseline_bpe_tokenizer_3e-5_enhancers_seed42 - - --model_max_length - - "100" - - --per_device_train_batch_size - - "128" - - --per_device_eval_batch_size - - "128" - - --gradient_accumulation_steps - - "1" - - --learning_rate - - "3e-5" - - --num_train_epochs - - "4" - - --fp16 - - --save_steps - - "200" - - --output_dir - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/enhancers - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "547373666304" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T07:02:20.734800Z" - writerId: a7ew8xz6636k5pz52gvz25k306nb0vup - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_070220-lyujxhdx/files/output.log b/wandb/run-20260305_070220-lyujxhdx/files/output.log deleted file mode 100644 index d33c3f0718d7010e3ca471f8d944c22f6f427d63..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_070220-lyujxhdx/files/output.log +++ /dev/null @@ -1,69 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 22983.11it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_tfidf/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -bert.pooler.dense.weight | MISSING | -classifier.bias | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 4 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 828 - Number of trainable parameters = 44,302,082 - 24%|██▍ | 199/828 [00:08<00:26, 23.41it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/enhancers/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/enhancers/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.39it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/enhancers/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/enhancers/checkpoint-200/tokenizer_config.json - 48%|████▊ | 400/828 [00:17<00:17, 24.21it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/enhancers/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/enhancers/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.95it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/enhancers/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/enhancers/checkpoint-400/tokenizer_config.json - 72%|███████▏ | 598/828 [00:26<00:09, 23.83it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/enhancers/checkpoint-600 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/enhancers/checkpoint-600/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.68it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/enhancers/checkpoint-600/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/enhancers/checkpoint-600/tokenizer_config.json - 96%|█████████▋| 799/828 [00:35<00:01, 23.70it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/enhancers/checkpoint-800 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/enhancers/checkpoint-800/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.46it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/enhancers/checkpoint-800/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/enhancers/checkpoint-800/tokenizer_config.json -100%|█████████▉| 826/828 [00:37<00:00, 22.17it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/enhancers/checkpoint-828 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/enhancers/checkpoint-828/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.48it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/enhancers/checkpoint-828/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/enhancers/checkpoint-828/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 828/828 [00:38<00:00, 21.40it/s] -{'train_runtime': '38.69', 'train_samples_per_second': '2730', 'train_steps_per_second': '21.4', 'train_loss': '0.5631', 'epoch': '4'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 82.17it/s] diff --git a/wandb/run-20260305_070220-lyujxhdx/files/requirements.txt b/wandb/run-20260305_070220-lyujxhdx/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_070220-lyujxhdx/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 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/home/n5huang/dna_token/pretrain/models/model_tfidf/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -bert.pooler.dense.weight | MISSING | -classifier.bias | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 4 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 828 - Number of trainable parameters = 44,302,851 - 24%|██▍ | 199/828 [00:09<00:28, 22.45it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/enhancers_types/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/enhancers_types/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.15it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/enhancers_types/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/enhancers_types/checkpoint-200/tokenizer_config.json - 48%|████▊ | 400/828 [00:18<00:17, 23.91it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/enhancers_types/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/enhancers_types/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.58it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/enhancers_types/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/enhancers_types/checkpoint-400/tokenizer_config.json - 72%|███████▏ | 598/828 [00:28<00:09, 24.33it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/enhancers_types/checkpoint-600 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/enhancers_types/checkpoint-600/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.61it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/enhancers_types/checkpoint-600/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/enhancers_types/checkpoint-600/tokenizer_config.json - 96%|█████████▋| 799/828 [00:37<00:01, 23.50it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/enhancers_types/checkpoint-800 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/enhancers_types/checkpoint-800/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 2.89it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/enhancers_types/checkpoint-800/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/enhancers_types/checkpoint-800/tokenizer_config.json -100%|█████████▉| 826/828 [00:39<00:00, 21.44it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/enhancers_types/checkpoint-828 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/enhancers_types/checkpoint-828/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.54it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/enhancers_types/checkpoint-828/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/enhancers_types/checkpoint-828/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 828/828 [00:40<00:00, 20.34it/s] -{'train_runtime': '40.7', 'train_samples_per_second': '2595', 'train_steps_per_second': '20.35', 'train_loss': '0.6974', 'epoch': '4'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 78.89it/s] diff --git a/wandb/run-20260305_070313-21qn1ssm/files/requirements.txt b/wandb/run-20260305_070313-21qn1ssm/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_070313-21qn1ssm/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 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--find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "547378257920" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T07:04:09.524440Z" - writerId: do5ajwm3fs4nj7oowil3uzkdghakpfdl - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_070409-5itujevo/files/output.log b/wandb/run-20260305_070409-5itujevo/files/output.log deleted file mode 100644 index 992bf111fe549c62a0879bd94645146039cba0cc..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_070409-5itujevo/files/output.log +++ /dev/null @@ -1,54 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 24556.53it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_tfidf/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -classifier.weight | MISSING | -classifier.bias | MISSING | -bert.pooler.dense.weight | MISSING | -bert.pooler.dense.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 25,267 - Num Epochs = 2 - Num update steps per epoch = 198 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 396 - Number of trainable parameters = 44,302,082 - 51%|█████ | 200/396 [00:08<00:06, 29.28it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/promoter_all/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/promoter_all/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 2.60it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/promoter_all/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/promoter_all/checkpoint-200/tokenizer_config.json -100%|█████████▉| 395/396 [00:16<00:00, 26.75it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/promoter_all/checkpoint-396 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/promoter_all/checkpoint-396/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.97it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/promoter_all/checkpoint-396/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/promoter_all/checkpoint-396/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 396/396 [00:16<00:00, 23.54it/s] -{'train_runtime': '16.82', 'train_samples_per_second': '3004', 'train_steps_per_second': '23.54', 'train_loss': '0.3815', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3159 - Batch size = 128 -100%|██████████| 25/25 [00:00<00:00, 99.17it/s] diff --git a/wandb/run-20260305_070409-5itujevo/files/requirements.txt b/wandb/run-20260305_070409-5itujevo/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_070409-5itujevo/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 -accelerate==1.13.0 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -triton==3.6.0 -nvidia-nccl-cu12==2.27.5 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -cuda-pathfinder==1.4.0 -shellingham==1.5.4 -torchaudio==2.5.1 -nvidia-cufile-cu12==1.13.1.3 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -nvidia-nvjitlink-cu12==12.8.93 -click==8.3.1 -MarkupSafe==3.0.2 -nvidia-nvshmem-cu12==3.4.5 -urllib3==2.6.3 -cuda-bindings==12.9.4 -propcache==0.4.1 -nvidia-cusolver-cu12==11.7.3.90 -sympy==1.14.0 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -nvidia-cuda-runtime-cu12==12.8.90 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_070409-5itujevo/files/wandb-metadata.json b/wandb/run-20260305_070409-5itujevo/files/wandb-metadata.json deleted file mode 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/data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T07:04:39.970010Z" - writerId: kzz26xbu19gdyh2ncvgx02ekn0naj56o - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_070439-at1tp4wl/files/output.log b/wandb/run-20260305_070439-at1tp4wl/files/output.log deleted file mode 100644 index acb6d7ed41398a2605a4f1d6a045db900125a46f..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_070439-at1tp4wl/files/output.log +++ /dev/null @@ -1,54 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 14294.26it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_tfidf/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -classifier.weight | MISSING | -classifier.bias | MISSING | -bert.pooler.dense.weight | MISSING | -bert.pooler.dense.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 25,097 - Num Epochs = 2 - Num update steps per epoch = 197 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 394 - Number of trainable parameters = 44,302,082 - 51%|█████ | 199/394 [00:08<00:07, 27.65it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/promoter_no_tata/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/promoter_no_tata/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.02it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/promoter_no_tata/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/promoter_no_tata/checkpoint-200/tokenizer_config.json - 99%|█████████▉| 391/394 [00:15<00:00, 26.96it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/promoter_no_tata/checkpoint-394 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/promoter_no_tata/checkpoint-394/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.13it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/promoter_no_tata/checkpoint-394/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/promoter_no_tata/checkpoint-394/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 394/394 [00:16<00:00, 23.83it/s] -{'train_runtime': '16.53', 'train_samples_per_second': '3036', 'train_steps_per_second': '23.83', 'train_loss': '0.3611', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3138 - Batch size = 128 -100%|██████████| 25/25 [00:00<00:00, 99.87it/s] diff --git a/wandb/run-20260305_070439-at1tp4wl/files/requirements.txt b/wandb/run-20260305_070439-at1tp4wl/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_070439-at1tp4wl/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 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memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T07:05:09.708461Z" - writerId: j9fdqbg32p5i07jdnu9rpwmhz4iy00tb - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_070509-vh5gy2qq/files/output.log b/wandb/run-20260305_070509-vh5gy2qq/files/output.log deleted file mode 100644 index 28c1ce44dbdd682ddb959e2e1d63da2ec1341520..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_070509-vh5gy2qq/files/output.log +++ /dev/null @@ -1,49 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 13360.18it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_tfidf/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -classifier.weight | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.bias | MISSING | -bert.pooler.dense.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 4,219 - Num Epochs = 2 - Num update steps per epoch = 33 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 66 - Number of trainable parameters = 44,302,082 - 97%|█████████▋| 64/66 [00:02<00:00, 28.30it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/promoter_tata/checkpoint-66 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/promoter_tata/checkpoint-66/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.39it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/promoter_tata/checkpoint-66/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/promoter_tata/checkpoint-66/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 66/66 [00:03<00:00, 18.70it/s] -{'train_runtime': '3.529', 'train_samples_per_second': '2391', 'train_steps_per_second': '18.7', 'train_loss': '0.5576', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 528 - Batch size = 128 -100%|██████████| 5/5 [00:00<00:00, 84.89it/s] diff --git a/wandb/run-20260305_070509-vh5gy2qq/files/requirements.txt b/wandb/run-20260305_070509-vh5gy2qq/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_070509-vh5gy2qq/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 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python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_070523-118ubzfp/files/output.log b/wandb/run-20260305_070523-118ubzfp/files/output.log deleted file mode 100644 index 7e47432026bc7fe4d2915b808711c38e4a0803ac..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_070523-118ubzfp/files/output.log +++ /dev/null @@ -1,69 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 23890.41it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_tfidf/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.dense.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -classifier.bias | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 4 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 828 - Number of trainable parameters = 44,302,082 - 24%|██▍ | 199/828 [00:11<00:35, 17.67it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.42it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-200/tokenizer_config.json - 48%|████▊ | 400/828 [00:24<00:24, 17.56it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.10it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-400/tokenizer_config.json - 72%|███████▏ | 599/828 [00:36<00:12, 17.69it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-600 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-600/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.28it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-600/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-600/tokenizer_config.json - 97%|█████████▋| 800/828 [00:48<00:01, 17.16it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-800 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-800/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.07it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-800/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-800/tokenizer_config.json -100%|█████████▉| 826/828 [00:51<00:00, 16.29it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-828 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-828/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.06it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-828/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-828/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 828/828 [00:52<00:00, 15.92it/s] -{'train_runtime': '52.01', 'train_samples_per_second': '2030', 'train_steps_per_second': '15.92', 'train_loss': '0.5823', 'epoch': '4'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 61.35it/s] diff --git a/wandb/run-20260305_070523-118ubzfp/files/requirements.txt b/wandb/run-20260305_070523-118ubzfp/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_070523-118ubzfp/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 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--find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "547383078912" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T07:06:30.807582Z" - writerId: dba68ozdrxhi46jnf7m6xv8a3ys3fssj - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_070630-wzer5vvj/files/output.log b/wandb/run-20260305_070630-wzer5vvj/files/output.log deleted file mode 100644 index dbac555b1f4a9098aa8edf9e0144c193143bbf40..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_070630-wzer5vvj/files/output.log +++ /dev/null @@ -1,69 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 22020.21it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_tfidf/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.decoder.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -bert.pooler.dense.bias | MISSING | -classifier.bias | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 4 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 828 - Number of trainable parameters = 44,302,851 - 24%|██▍ | 199/828 [00:12<00:36, 17.22it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/splice_sites_all/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/splice_sites_all/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.52it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/splice_sites_all/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/splice_sites_all/checkpoint-200/tokenizer_config.json - 48%|████▊ | 400/828 [00:24<00:24, 17.30it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/splice_sites_all/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/splice_sites_all/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.58it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/splice_sites_all/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/splice_sites_all/checkpoint-400/tokenizer_config.json - 72%|███████▏ | 599/828 [00:36<00:12, 17.62it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/splice_sites_all/checkpoint-600 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/splice_sites_all/checkpoint-600/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.56it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/splice_sites_all/checkpoint-600/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/splice_sites_all/checkpoint-600/tokenizer_config.json - 97%|█████████▋| 800/828 [00:48<00:01, 16.85it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/splice_sites_all/checkpoint-800 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/splice_sites_all/checkpoint-800/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.05it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/splice_sites_all/checkpoint-800/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/splice_sites_all/checkpoint-800/tokenizer_config.json -100%|█████████▉| 826/828 [00:51<00:00, 16.98it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/splice_sites_all/checkpoint-828 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/splice_sites_all/checkpoint-828/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.33it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/splice_sites_all/checkpoint-828/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/splice_sites_all/checkpoint-828/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 828/828 [00:52<00:00, 15.90it/s] -{'train_runtime': '52.07', 'train_samples_per_second': '2028', 'train_steps_per_second': '15.9', 'train_loss': '0.9707', 'epoch': '4'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 61.59it/s] diff --git a/wandb/run-20260305_070630-wzer5vvj/files/requirements.txt b/wandb/run-20260305_070630-wzer5vvj/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_070630-wzer5vvj/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 -accelerate==1.13.0 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -triton==3.6.0 -nvidia-nccl-cu12==2.27.5 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -cuda-pathfinder==1.4.0 -shellingham==1.5.4 -torchaudio==2.5.1 -nvidia-cufile-cu12==1.13.1.3 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -nvidia-nvjitlink-cu12==12.8.93 -click==8.3.1 -MarkupSafe==3.0.2 -nvidia-nvshmem-cu12==3.4.5 -urllib3==2.6.3 -cuda-bindings==12.9.4 -propcache==0.4.1 -nvidia-cusolver-cu12==11.7.3.90 -sympy==1.14.0 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -nvidia-cuda-runtime-cu12==12.8.90 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_070630-wzer5vvj/files/wandb-metadata.json b/wandb/run-20260305_070630-wzer5vvj/files/wandb-metadata.json deleted file mode 100644 index b54cb5e94e440b267026d8be6ae2b25bdd8edc80..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_070630-wzer5vvj/files/wandb-metadata.json +++ /dev/null @@ -1,134 +0,0 @@ -{ - "os": "Linux-5.15.0-72-generic-x86_64-with-glibc2.35", - "python": "CPython 3.10.19", - "startedAt": "2026-03-05T07:06:30.807582Z", - "args": [ - "--model_name_or_path", - "/home/n5huang/dna_token/pretrain/models/model_tfidf/checkpoint-100000", - "--tokenizer_path", - "/home/n5huang/dna_token/tokenizer_evaluation/baseline_bpe/tokenizer.json", - "--trust_remote_code", - "True", - "--data_path", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/splice_sites_all/split", - "--kmer", - "-1", - "--run_name", - "hg38_BPE_tfidf__baseline_bpe_tokenizer_3e-5_splice_sites_all_seed42", - "--model_max_length", - "140", - "--per_device_train_batch_size", - "128", - "--per_device_eval_batch_size", - "128", - 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/home/n5huang/dna_token/pretrain/models/model_tfidf/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -bert.pooler.dense.bias | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 4 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 828 - Number of trainable parameters = 44,302,082 - 24%|██▍ | 199/828 [00:12<00:36, 17.39it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.20it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-200/tokenizer_config.json - 48%|████▊ | 400/828 [00:24<00:25, 16.69it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.52it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-400/tokenizer_config.json - 72%|███████▏ | 599/828 [00:36<00:13, 16.82it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-600 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-600/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.65it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-600/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-600/tokenizer_config.json - 97%|█████████▋| 800/828 [00:49<00:01, 17.25it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-800 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-800/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.36it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-800/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-800/tokenizer_config.json -100%|█████████▉| 826/828 [00:51<00:00, 16.54it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-828 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-828/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.46it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-828/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-828/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 828/828 [00:52<00:00, 15.77it/s] -{'train_runtime': '52.51', 'train_samples_per_second': '2011', 'train_steps_per_second': '15.77', 'train_loss': '0.535', 'epoch': '4'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 59.33it/s] diff --git a/wandb/run-20260305_070737-0lfm1rva/files/requirements.txt b/wandb/run-20260305_070737-0lfm1rva/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_070737-0lfm1rva/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 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"False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "547827990528" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T07:08:45.557742Z" - writerId: b1l9slwjo6ziscrj65yen4r6u3iglzdr - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_070845-v7b0z0mz/files/output.log b/wandb/run-20260305_070845-v7b0z0mz/files/output.log deleted file mode 100644 index e24b3f9344f3179478e33023a0f692b55a11b340..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_070845-v7b0z0mz/files/output.log +++ /dev/null @@ -1,59 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 20469.91it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_tfidf/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -classifier.weight | MISSING | -classifier.bias | MISSING | -bert.pooler.dense.weight | MISSING | -bert.pooler.dense.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 2 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 414 - Number of trainable parameters = 44,302,082 - 48%|████▊ | 199/414 [00:17<00:18, 11.38it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/H2AFZ/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/H2AFZ/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.23it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/H2AFZ/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/H2AFZ/checkpoint-200/tokenizer_config.json - 96%|█████████▋| 399/414 [00:35<00:01, 11.54it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/H2AFZ/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/H2AFZ/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.10it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/H2AFZ/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/H2AFZ/checkpoint-400/tokenizer_config.json -100%|█████████▉| 413/414 [00:37<00:00, 10.24it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/H2AFZ/checkpoint-414 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/H2AFZ/checkpoint-414/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.33it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/H2AFZ/checkpoint-414/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/H2AFZ/checkpoint-414/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 414/414 [00:38<00:00, 10.85it/s] -{'train_runtime': '38.17', 'train_samples_per_second': '1383', 'train_steps_per_second': '10.85', 'train_loss': '0.5876', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 39.77it/s] diff --git a/wandb/run-20260305_070845-v7b0z0mz/files/requirements.txt b/wandb/run-20260305_070845-v7b0z0mz/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_070845-v7b0z0mz/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 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"False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "547830247424" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T07:09:41.328745Z" - writerId: mkjg0kxqdvde4yg2zu43o9qqovxn9s2z - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_070941-gek32c2x/files/output.log b/wandb/run-20260305_070941-gek32c2x/files/output.log deleted file mode 100644 index b83b51dd673061a687b436b91dbaee831e672670..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_070941-gek32c2x/files/output.log +++ /dev/null @@ -1,54 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 26942.99it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_tfidf/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -classifier.weight | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.bias | MISSING | -bert.pooler.dense.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 25,292 - Num Epochs = 2 - Num update steps per epoch = 198 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 396 - Number of trainable parameters = 44,302,082 - 50%|█████ | 199/396 [00:17<00:16, 12.18it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/H3K27ac/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/H3K27ac/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.19it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/H3K27ac/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/H3K27ac/checkpoint-200/tokenizer_config.json -100%|█████████▉| 395/396 [00:35<00:00, 11.56it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/H3K27ac/checkpoint-396 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/H3K27ac/checkpoint-396/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.30it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/H3K27ac/checkpoint-396/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/H3K27ac/checkpoint-396/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 396/396 [00:36<00:00, 10.95it/s] -{'train_runtime': '36.16', 'train_samples_per_second': '1399', 'train_steps_per_second': '10.95', 'train_loss': '0.5994', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3163 - Batch size = 128 -100%|██████████| 25/25 [00:00<00:00, 40.31it/s] diff --git a/wandb/run-20260305_070941-gek32c2x/files/requirements.txt b/wandb/run-20260305_070941-gek32c2x/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_070941-gek32c2x/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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"2026-03-05T07:10:35.300315Z" - writerId: utm08e990yz7f3moew2nbnzjtrhklqf1 - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_071035-c0veku9v/files/output.log b/wandb/run-20260305_071035-c0veku9v/files/output.log deleted file mode 100644 index a6449915f7f6732256e47efd2d0663b1f55771ed..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_071035-c0veku9v/files/output.log +++ /dev/null @@ -1,59 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 19389.63it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_tfidf/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -bert.pooler.dense.weight | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.bias | MISSING | -classifier.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 2 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 414 - Number of trainable parameters = 44,302,082 - 48%|████▊ | 199/414 [00:17<00:18, 11.53it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/H3K27me3/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/H3K27me3/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.09it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/H3K27me3/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/H3K27me3/checkpoint-200/tokenizer_config.json - 96%|█████████▋| 399/414 [00:36<00:01, 11.55it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/H3K27me3/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/H3K27me3/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.60it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/H3K27me3/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/H3K27me3/checkpoint-400/tokenizer_config.json -100%|█████████▉| 413/414 [00:37<00:00, 10.11it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/H3K27me3/checkpoint-414 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/H3K27me3/checkpoint-414/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.48it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/H3K27me3/checkpoint-414/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/H3K27me3/checkpoint-414/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 414/414 [00:38<00:00, 10.73it/s] -{'train_runtime': '38.58', 'train_samples_per_second': '1368', 'train_steps_per_second': '10.73', 'train_loss': '0.5475', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 40.34it/s] diff --git a/wandb/run-20260305_071035-c0veku9v/files/requirements.txt b/wandb/run-20260305_071035-c0veku9v/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_071035-c0veku9v/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T07:11:33.198591Z" - writerId: wfgq6ksxhhm0rt7a9g5jcftyrhpgph4m - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_071133-6461su3x/files/output.log b/wandb/run-20260305_071133-6461su3x/files/output.log deleted file mode 100644 index 1c20105eab5e5f9f3db8af76d923b005ab6f4d79..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_071133-6461su3x/files/output.log +++ /dev/null @@ -1,59 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 22763.28it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_tfidf/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -classifier.bias | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 2 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 414 - Number of trainable parameters = 44,302,082 - 48%|████▊ | 199/414 [00:17<00:18, 11.60it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/H3K36me3/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/H3K36me3/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.18it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/H3K36me3/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/H3K36me3/checkpoint-200/tokenizer_config.json - 96%|█████████▋| 399/414 [00:35<00:01, 11.47it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/H3K36me3/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/H3K36me3/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.14it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/H3K36me3/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/H3K36me3/checkpoint-400/tokenizer_config.json -100%|█████████▉| 413/414 [00:37<00:00, 10.06it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/H3K36me3/checkpoint-414 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/H3K36me3/checkpoint-414/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.81it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/H3K36me3/checkpoint-414/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/H3K36me3/checkpoint-414/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 414/414 [00:38<00:00, 10.80it/s] -{'train_runtime': '38.34', 'train_samples_per_second': '1377', 'train_steps_per_second': '10.8', 'train_loss': '0.5479', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 40.02it/s] diff --git a/wandb/run-20260305_071133-6461su3x/files/requirements.txt b/wandb/run-20260305_071133-6461su3x/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_071133-6461su3x/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 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NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T07:12:29.632298Z" - writerId: p90txma2zx94uy16svt1qss0i93g7sb4 - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_071229-rm84sicz/files/output.log b/wandb/run-20260305_071229-rm84sicz/files/output.log deleted file mode 100644 index d3550b7bed8843a793d7a78897f2477a86701f48..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_071229-rm84sicz/files/output.log +++ /dev/null @@ -1,59 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 20189.91it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_tfidf/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -classifier.weight | MISSING | -bert.pooler.dense.weight | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 2 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 414 - Number of trainable parameters = 44,302,082 - 48%|████▊ | 199/414 [00:17<00:18, 11.58it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/H3K4me1/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/H3K4me1/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.22it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/H3K4me1/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/H3K4me1/checkpoint-200/tokenizer_config.json - 96%|█████████▋| 399/414 [00:35<00:01, 11.62it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/H3K4me1/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/H3K4me1/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.38it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/H3K4me1/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/H3K4me1/checkpoint-400/tokenizer_config.json -100%|█████████▉| 413/414 [00:37<00:00, 10.07it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/H3K4me1/checkpoint-414 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/H3K4me1/checkpoint-414/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.58it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/H3K4me1/checkpoint-414/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/H3K4me1/checkpoint-414/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 414/414 [00:38<00:00, 10.75it/s] -{'train_runtime': '38.5', 'train_samples_per_second': '1371', 'train_steps_per_second': '10.75', 'train_loss': '0.6134', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 39.26it/s] diff --git a/wandb/run-20260305_071229-rm84sicz/files/requirements.txt b/wandb/run-20260305_071229-rm84sicz/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_071229-rm84sicz/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 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--------------------------------------------+------------+- -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -classifier.weight | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.bias | MISSING | -bert.pooler.dense.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 25,710 - Num Epochs = 2 - Num update steps per epoch = 201 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 402 - Number of trainable parameters = 44,302,082 - 50%|████▉ | 199/402 [00:17<00:17, 11.61it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/H3K4me2/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/H3K4me2/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.56it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/H3K4me2/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/H3K4me2/checkpoint-200/tokenizer_config.json - 99%|█████████▉| 399/402 [00:35<00:00, 11.54it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/H3K4me2/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/H3K4me2/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.84it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/H3K4me2/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/H3K4me2/checkpoint-400/tokenizer_config.json -100%|█████████▉| 401/402 [00:36<00:00, 5.00it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/H3K4me2/checkpoint-402 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/H3K4me2/checkpoint-402/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.70it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/H3K4me2/checkpoint-402/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/H3K4me2/checkpoint-402/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 402/402 [00:37<00:00, 10.76it/s] -{'train_runtime': '37.37', 'train_samples_per_second': '1376', 'train_steps_per_second': '10.76', 'train_loss': '0.5573', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3215 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 39.33it/s] diff --git a/wandb/run-20260305_071325-7thxpliv/files/requirements.txt b/wandb/run-20260305_071325-7thxpliv/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_071325-7thxpliv/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T07:14:23.108955Z" - writerId: uklqljf9bwlwku508edjttxi1i5t5zvm - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_071423-bf5ri9af/files/output.log b/wandb/run-20260305_071423-bf5ri9af/files/output.log deleted file mode 100644 index 6efe81e425afcba6dd55ab0d7538c20a98b6f395..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_071423-bf5ri9af/files/output.log +++ /dev/null @@ -1,54 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 12001.38it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_tfidf/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -bert.pooler.dense.bias | MISSING | -classifier.weight | MISSING | -classifier.bias | MISSING | -bert.pooler.dense.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 14,595 - Num Epochs = 2 - Num update steps per epoch = 115 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 230 - Number of trainable parameters = 44,302,082 - 87%|████████▋ | 199/230 [00:17<00:02, 11.45it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/H3K4me3/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/H3K4me3/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 2.63it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/H3K4me3/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/H3K4me3/checkpoint-200/tokenizer_config.json -100%|█████████▉| 229/230 [00:21<00:00, 11.49it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/H3K4me3/checkpoint-230 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/H3K4me3/checkpoint-230/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 2.17it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/H3K4me3/checkpoint-230/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/H3K4me3/checkpoint-230/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 230/230 [00:22<00:00, 10.17it/s] -{'train_runtime': '22.61', 'train_samples_per_second': '1291', 'train_steps_per_second': '10.17', 'train_loss': '0.4737', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 1825 - Batch size = 128 -100%|██████████| 15/15 [00:00<00:00, 43.10it/s] diff --git a/wandb/run-20260305_071423-bf5ri9af/files/requirements.txt b/wandb/run-20260305_071423-bf5ri9af/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_071423-bf5ri9af/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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-WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 20627.39it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_tfidf/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -bert.pooler.dense.weight | MISSING | -classifier.bias | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 19,422 - Num Epochs = 2 - Num update steps per epoch = 152 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 304 - Number of trainable parameters = 44,302,082 - 65%|██████▌ | 199/304 [00:17<00:09, 11.61it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/H3K9ac/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/H3K9ac/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 2.70it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/H3K9ac/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/tfidf__baseline_bpe_tokenizer/H3K9ac/checkpoint-200/tokenizer_config.json -Traceback (most recent call last): - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/serialization.py", line 977, in save - _save( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/torch/serialization.py", line 1286, in _save - zip_file.write_record(name, storage, num_bytes) -RuntimeError: basic_ios::clear: iostream error - -During handling of the above exception, another exception occurred: - -Traceback (most recent call last): - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 464, in - train() - File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 445, in train - trainer.train() - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1424, in train - return inner_training_loop( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1506, in _inner_training_loop - self._run_epoch( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 1775, in _run_epoch - self._maybe_log_save_evaluate( - File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/trainer.py", line 2088, in _maybe_log_save_evaluate diff --git a/wandb/run-20260305_071500-s9lajvj7/files/requirements.txt b/wandb/run-20260305_071500-s9lajvj7/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- 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55u3bqndmmg3f68g1xvqkke5x4xj05ic: - args: - - --model_name_or_path - - /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 - - --tokenizer_path - - /home/n5huang/dna_token/tokenizer_evaluation/baseline_bpe/tokenizer.json - - --trust_remote_code - - "True" - - --data_path - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/enhancers/split - - --kmer - - "-1" - - --run_name - - hg38_BPE_base__baseline_bpe_tokenizer_3e-5_enhancers_seed42 - - --model_max_length - - "100" - - --per_device_train_batch_size - - "128" - - --per_device_eval_batch_size - - "128" - - --gradient_accumulation_steps - - "1" - - --learning_rate - - "3e-5" - - --num_train_epochs - - "4" - - --fp16 - - --save_steps - - "200" - - --output_dir - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "556394528768" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T07:41:50.189936Z" - writerId: 55u3bqndmmg3f68g1xvqkke5x4xj05ic - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_074150-gnih9gzg/files/output.log b/wandb/run-20260305_074150-gnih9gzg/files/output.log deleted file mode 100644 index 1bc3151a3090ed20b655bb42daeda1e5b3d3f6f5..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_074150-gnih9gzg/files/output.log +++ /dev/null @@ -1,69 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 24407.97it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -classifier.bias | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 4 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 828 - Number of trainable parameters = 44,302,082 - 24%|██▍ | 198/828 [00:11<00:25, 24.39it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.41it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers/checkpoint-200/tokenizer_config.json - 48%|████▊ | 399/828 [00:20<00:17, 24.19it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.82it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers/checkpoint-400/tokenizer_config.json - 72%|███████▏ | 600/828 [00:29<00:09, 24.62it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers/checkpoint-600 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers/checkpoint-600/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.30it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers/checkpoint-600/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers/checkpoint-600/tokenizer_config.json - 96%|█████████▋| 798/828 [00:39<00:01, 24.56it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers/checkpoint-800 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers/checkpoint-800/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.75it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers/checkpoint-800/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers/checkpoint-800/tokenizer_config.json -100%|██████████| 828/828 [00:41<00:00, 23.31it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers/checkpoint-828 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers/checkpoint-828/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.64it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers/checkpoint-828/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers/checkpoint-828/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 828/828 [00:42<00:00, 19.69it/s] -{'train_runtime': '42.05', 'train_samples_per_second': '2512', 'train_steps_per_second': '19.69', 'train_loss': '0.5009', 'epoch': '4'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 80.55it/s] diff --git a/wandb/run-20260305_074150-gnih9gzg/files/requirements.txt b/wandb/run-20260305_074150-gnih9gzg/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_074150-gnih9gzg/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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/data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T07:42:47.143999Z" - writerId: kb5yh4mfejkn698yznlvo4nkqj2wzk19 - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_074247-a6j1rlmz/files/output.log b/wandb/run-20260305_074247-a6j1rlmz/files/output.log deleted file mode 100644 index 021c9dd5bf4e6af3a0c4e532c3094d4079adb4b6..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_074247-a6j1rlmz/files/output.log +++ /dev/null @@ -1,69 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 11807.37it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -bert.pooler.dense.bias | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.bias | MISSING | -classifier.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 4 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 828 - Number of trainable parameters = 44,302,851 - 24%|██▍ | 199/828 [00:09<00:27, 23.23it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers_types/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers_types/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.22it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers_types/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers_types/checkpoint-200/tokenizer_config.json - 48%|████▊ | 400/828 [00:18<00:18, 23.39it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers_types/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers_types/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.29it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers_types/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers_types/checkpoint-400/tokenizer_config.json - 72%|███████▏ | 598/828 [00:28<00:10, 22.63it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers_types/checkpoint-600 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers_types/checkpoint-600/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.11it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers_types/checkpoint-600/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers_types/checkpoint-600/tokenizer_config.json - 96%|█████████▋| 799/828 [00:37<00:01, 22.14it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers_types/checkpoint-800 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers_types/checkpoint-800/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.12it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers_types/checkpoint-800/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers_types/checkpoint-800/tokenizer_config.json -100%|█████████▉| 826/828 [00:39<00:00, 20.59it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers_types/checkpoint-828 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers_types/checkpoint-828/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.57it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers_types/checkpoint-828/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers_types/checkpoint-828/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 828/828 [00:40<00:00, 20.37it/s] -{'train_runtime': '40.64', 'train_samples_per_second': '2599', 'train_steps_per_second': '20.38', 'train_loss': '0.6291', 'epoch': '4'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 82.23it/s] diff --git a/wandb/run-20260305_074247-a6j1rlmz/files/requirements.txt b/wandb/run-20260305_074247-a6j1rlmz/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_074247-a6j1rlmz/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 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memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T07:43:43.589619Z" - writerId: nsdy4bae289woyxkh5gzv1wit2ab17rv - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_074343-1wx3t9s3/files/output.log b/wandb/run-20260305_074343-1wx3t9s3/files/output.log deleted file mode 100644 index 80e2e96ae6512860d177a00ec14bbb9965d16ce7..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_074343-1wx3t9s3/files/output.log +++ /dev/null @@ -1,54 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 17302.10it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -classifier.bias | MISSING | -bert.pooler.dense.bias | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 25,267 - Num Epochs = 2 - Num update steps per epoch = 198 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 396 - Number of trainable parameters = 44,302,082 - 50%|█████ | 199/396 [00:07<00:07, 25.46it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/promoter_all/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/promoter_all/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.13it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/promoter_all/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/promoter_all/checkpoint-200/tokenizer_config.json - 99%|█████████▉| 394/396 [00:15<00:00, 26.93it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/promoter_all/checkpoint-396 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/promoter_all/checkpoint-396/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.03it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/promoter_all/checkpoint-396/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/promoter_all/checkpoint-396/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 396/396 [00:16<00:00, 23.90it/s] -{'train_runtime': '16.57', 'train_samples_per_second': '3050', 'train_steps_per_second': '23.9', 'train_loss': '0.3266', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3159 - Batch size = 128 -100%|██████████| 25/25 [00:00<00:00, 98.75it/s] diff --git a/wandb/run-20260305_074343-1wx3t9s3/files/requirements.txt b/wandb/run-20260305_074343-1wx3t9s3/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_074343-1wx3t9s3/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 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--find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "556401913856" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T07:44:16.725752Z" - writerId: o69qmvhbewbkus8k1vds4o6005u9cbtv - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_074416-8u6z1pnl/files/output.log b/wandb/run-20260305_074416-8u6z1pnl/files/output.log deleted file mode 100644 index 596738e063aa1ac9ea9796a4858195d91706ffbb..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_074416-8u6z1pnl/files/output.log +++ /dev/null @@ -1,54 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 16380.20it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -classifier.bias | MISSING | -bert.pooler.dense.weight | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 25,097 - Num Epochs = 2 - Num update steps per epoch = 197 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 394 - Number of trainable parameters = 44,302,082 - 51%|█████ | 199/394 [00:07<00:06, 28.55it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/promoter_no_tata/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/promoter_no_tata/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.53it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/promoter_no_tata/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/promoter_no_tata/checkpoint-200/tokenizer_config.json -100%|██████████| 394/394 [00:15<00:00, 26.18it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/promoter_no_tata/checkpoint-394 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/promoter_no_tata/checkpoint-394/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.35it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/promoter_no_tata/checkpoint-394/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/promoter_no_tata/checkpoint-394/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 394/394 [00:16<00:00, 23.91it/s] -{'train_runtime': '16.48', 'train_samples_per_second': '3046', 'train_steps_per_second': '23.91', 'train_loss': '0.3115', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3138 - Batch size = 128 -100%|██████████| 25/25 [00:00<00:00, 95.94it/s] diff --git a/wandb/run-20260305_074416-8u6z1pnl/files/requirements.txt b/wandb/run-20260305_074416-8u6z1pnl/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_074416-8u6z1pnl/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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/home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -classifier.bias | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.weight | MISSING | -bert.pooler.dense.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 4,219 - Num Epochs = 2 - Num update steps per epoch = 33 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 66 - Number of trainable parameters = 44,302,082 - 97%|█████████▋| 64/66 [00:02<00:00, 28.97it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/promoter_tata/checkpoint-66 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/promoter_tata/checkpoint-66/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.57it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/promoter_tata/checkpoint-66/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/promoter_tata/checkpoint-66/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 66/66 [00:03<00:00, 17.41it/s] -{'train_runtime': '3.79', 'train_samples_per_second': '2226', 'train_steps_per_second': '17.41', 'train_loss': '0.4538', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 528 - Batch size = 128 -100%|██████████| 5/5 [00:00<00:00, 101.37it/s] diff --git a/wandb/run-20260305_074447-43ew0igm/files/requirements.txt b/wandb/run-20260305_074447-43ew0igm/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_074447-43ew0igm/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 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architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T07:45:02.471680Z" - writerId: xhu1f44jgnxklcf8p0npwjhlaonydhar - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_074502-j973slif/files/output.log b/wandb/run-20260305_074502-j973slif/files/output.log deleted file mode 100644 index 3670c7d464c81831e79aa352b24611adaa390952..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_074502-j973slif/files/output.log +++ /dev/null @@ -1,69 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 21335.92it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -bert.pooler.dense.weight | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 4 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 828 - Number of trainable parameters = 44,302,082 - 24%|██▍ | 199/828 [00:12<00:36, 17.32it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.04it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-200/tokenizer_config.json - 48%|████▊ | 400/828 [00:24<00:24, 17.56it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.70it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-400/tokenizer_config.json - 72%|███████▏ | 599/828 [00:36<00:12, 17.66it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-600 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-600/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 2.78it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-600/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-600/tokenizer_config.json - 97%|█████████▋| 800/828 [00:49<00:01, 17.34it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-800 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-800/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.47it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-800/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-800/tokenizer_config.json -100%|█████████▉| 826/828 [00:51<00:00, 16.48it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-828 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-828/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.36it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-828/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_acceptors/checkpoint-828/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 828/828 [00:52<00:00, 15.73it/s] -{'train_runtime': '52.65', 'train_samples_per_second': '2006', 'train_steps_per_second': '15.73', 'train_loss': '0.4043', 'epoch': '4'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 58.83it/s] diff --git a/wandb/run-20260305_074502-j973slif/files/requirements.txt b/wandb/run-20260305_074502-j973slif/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_074502-j973slif/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 -accelerate==1.13.0 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -triton==3.6.0 -nvidia-nccl-cu12==2.27.5 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -cuda-pathfinder==1.4.0 -shellingham==1.5.4 -torchaudio==2.5.1 -nvidia-cufile-cu12==1.13.1.3 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -nvidia-nvjitlink-cu12==12.8.93 -click==8.3.1 -MarkupSafe==3.0.2 -nvidia-nvshmem-cu12==3.4.5 -urllib3==2.6.3 -cuda-bindings==12.9.4 -propcache==0.4.1 -nvidia-cusolver-cu12==11.7.3.90 -sympy==1.14.0 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -nvidia-cuda-runtime-cu12==12.8.90 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_074502-j973slif/files/wandb-metadata.json b/wandb/run-20260305_074502-j973slif/files/wandb-metadata.json deleted file mode 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/home/n5huang/dna_token/tokenizer_evaluation/baseline_bpe/tokenizer.json - - --trust_remote_code - - "True" - - --data_path - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/splice_sites_all/split - - --kmer - - "-1" - - --run_name - - hg38_BPE_base__baseline_bpe_tokenizer_3e-5_splice_sites_all_seed42 - - --model_max_length - - "140" - - --per_device_train_batch_size - - "128" - - --per_device_eval_batch_size - - "128" - - --gradient_accumulation_steps - - "1" - - --learning_rate - - "3e-5" - - --num_train_epochs - - "4" - - --fp16 - - --save_steps - - "200" - - --output_dir - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_all - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "556406530048" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T07:46:16.136901Z" - writerId: zexauhzsmwa7i7471vnuczgdbe3b0jn7 - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_074616-njcxc9vz/files/output.log b/wandb/run-20260305_074616-njcxc9vz/files/output.log deleted file mode 100644 index 8fae73216eccd122d09312eb2178e98067644e6d..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_074616-njcxc9vz/files/output.log +++ /dev/null @@ -1,69 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 24916.17it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -classifier.bias | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 4 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 828 - Number of trainable parameters = 44,302,851 - 24%|██▍ | 199/828 [00:11<00:35, 17.57it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_all/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_all/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.07it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_all/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_all/checkpoint-200/tokenizer_config.json - 48%|████▊ | 400/828 [00:24<00:24, 17.28it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_all/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_all/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.72it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_all/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_all/checkpoint-400/tokenizer_config.json - 72%|███████▏ | 599/828 [00:36<00:13, 17.21it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_all/checkpoint-600 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_all/checkpoint-600/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.57it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_all/checkpoint-600/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_all/checkpoint-600/tokenizer_config.json - 97%|█████████▋| 800/828 [00:48<00:01, 17.57it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_all/checkpoint-800 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_all/checkpoint-800/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.88it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_all/checkpoint-800/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_all/checkpoint-800/tokenizer_config.json -100%|█████████▉| 826/828 [00:51<00:00, 17.08it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_all/checkpoint-828 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_all/checkpoint-828/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.18it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_all/checkpoint-828/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_all/checkpoint-828/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 828/828 [00:51<00:00, 15.94it/s] -{'train_runtime': '51.93', 'train_samples_per_second': '2033', 'train_steps_per_second': '15.94', 'train_loss': '0.6731', 'epoch': '4'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 59.61it/s] diff --git a/wandb/run-20260305_074616-njcxc9vz/files/requirements.txt b/wandb/run-20260305_074616-njcxc9vz/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_074616-njcxc9vz/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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/data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T07:47:24.716462Z" - writerId: rb7s674a8ghja8dculna0d1p5pd26rnt - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_074724-bxc4p54t/files/output.log b/wandb/run-20260305_074724-bxc4p54t/files/output.log deleted file mode 100644 index 52fc52fc70b71f1b610cf91aabd8398ac837607b..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_074724-bxc4p54t/files/output.log +++ /dev/null @@ -1,69 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 23118.57it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -classifier.bias | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.bias | MISSING | -bert.pooler.dense.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 4 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 828 - Number of trainable parameters = 44,302,082 - 24%|██▍ | 199/828 [00:12<00:35, 17.56it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.64it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-200/tokenizer_config.json - 48%|████▊ | 400/828 [00:24<00:24, 17.52it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.39it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-400/tokenizer_config.json - 72%|███████▏ | 599/828 [00:36<00:13, 17.06it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-600 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-600/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.31it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-600/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-600/tokenizer_config.json - 97%|█████████▋| 800/828 [00:49<00:01, 17.42it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-800 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-800/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.70it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-800/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-800/tokenizer_config.json -100%|█████████▉| 826/828 [00:51<00:00, 16.93it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-828 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-828/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.94it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-828/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_donors/checkpoint-828/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 828/828 [00:52<00:00, 15.73it/s] -{'train_runtime': '52.64', 'train_samples_per_second': '2006', 'train_steps_per_second': '15.73', 'train_loss': '0.3772', 'epoch': '4'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 59.18it/s] diff --git a/wandb/run-20260305_074724-bxc4p54t/files/requirements.txt b/wandb/run-20260305_074724-bxc4p54t/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_074724-bxc4p54t/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 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- - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "556413190144" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T07:48:33.022633Z" - writerId: ihxoh3kgm9fov5ewhbuw1t113g7wvvt2 - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_074833-m3lcx37i/files/output.log b/wandb/run-20260305_074833-m3lcx37i/files/output.log deleted file mode 100644 index d23f40df2af87fad1814be8fac10857ea1332ab5..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_074833-m3lcx37i/files/output.log +++ /dev/null @@ -1,59 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 23319.65it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.decoder.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -classifier.bias | MISSING | -bert.pooler.dense.bias | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 2 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 414 - Number of trainable parameters = 44,302,082 - 48%|████▊ | 199/414 [00:17<00:18, 11.52it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H2AFZ/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H2AFZ/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.07it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H2AFZ/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H2AFZ/checkpoint-200/tokenizer_config.json - 96%|█████████▋| 399/414 [00:36<00:01, 11.43it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H2AFZ/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H2AFZ/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.15it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H2AFZ/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H2AFZ/checkpoint-400/tokenizer_config.json -100%|█████████▉| 413/414 [00:38<00:00, 10.06it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H2AFZ/checkpoint-414 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H2AFZ/checkpoint-414/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.14it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H2AFZ/checkpoint-414/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H2AFZ/checkpoint-414/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 414/414 [00:38<00:00, 10.65it/s] -{'train_runtime': '38.88', 'train_samples_per_second': '1358', 'train_steps_per_second': '10.65', 'train_loss': '0.5188', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 39.42it/s] diff --git a/wandb/run-20260305_074833-m3lcx37i/files/requirements.txt b/wandb/run-20260305_074833-m3lcx37i/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_074833-m3lcx37i/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 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NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T07:49:31.709294Z" - writerId: bn3fkx57blpqunjujnr4tom0txnqnn9l - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_074931-o4njfui1/files/output.log b/wandb/run-20260305_074931-o4njfui1/files/output.log deleted file mode 100644 index 898b2b3f4fa07f27c98d6ed08ee30287b3a457c0..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_074931-o4njfui1/files/output.log +++ /dev/null @@ -1,54 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 21429.82it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -classifier.weight | MISSING | -bert.pooler.dense.weight | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 25,292 - Num Epochs = 2 - Num update steps per epoch = 198 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 396 - Number of trainable parameters = 44,302,082 - 50%|█████ | 199/396 [00:17<00:16, 12.22it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K27ac/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K27ac/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.62it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K27ac/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K27ac/checkpoint-200/tokenizer_config.json -100%|█████████▉| 395/396 [00:35<00:00, 11.37it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K27ac/checkpoint-396 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K27ac/checkpoint-396/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.65it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K27ac/checkpoint-396/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K27ac/checkpoint-396/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 396/396 [00:36<00:00, 10.83it/s] -{'train_runtime': '36.55', 'train_samples_per_second': '1384', 'train_steps_per_second': '10.83', 'train_loss': '0.5384', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3163 - Batch size = 128 -100%|██████████| 25/25 [00:00<00:00, 40.21it/s] diff --git a/wandb/run-20260305_074931-o4njfui1/files/requirements.txt b/wandb/run-20260305_074931-o4njfui1/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_074931-o4njfui1/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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--------------------------------------------+------------+- -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -classifier.weight | MISSING | -classifier.bias | MISSING | -bert.pooler.dense.weight | MISSING | -bert.pooler.dense.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 2 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 414 - Number of trainable parameters = 44,302,082 - 48%|████▊ | 199/414 [00:17<00:18, 11.49it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K27me3/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K27me3/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.21it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K27me3/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K27me3/checkpoint-200/tokenizer_config.json - 96%|█████████▋| 399/414 [00:35<00:01, 11.57it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K27me3/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K27me3/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.28it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K27me3/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K27me3/checkpoint-400/tokenizer_config.json -100%|█████████▉| 413/414 [00:37<00:00, 9.93it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K27me3/checkpoint-414 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K27me3/checkpoint-414/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.73it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K27me3/checkpoint-414/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K27me3/checkpoint-414/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 414/414 [00:38<00:00, 10.66it/s] -{'train_runtime': '38.84', 'train_samples_per_second': '1359', 'train_steps_per_second': '10.66', 'train_loss': '0.4656', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 39.87it/s] diff --git a/wandb/run-20260305_075026-g7afju5a/files/requirements.txt b/wandb/run-20260305_075026-g7afju5a/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_075026-g7afju5a/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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"False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "556418195456" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T07:51:23.943615Z" - writerId: zicc7vwstdyqz38zrwvvid0dul4bnlyl - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_075123-qfnqvqrh/files/output.log b/wandb/run-20260305_075123-qfnqvqrh/files/output.log deleted file mode 100644 index 27ffb3980cd21891f0b0dcd320b8b2df92f78ed0..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_075123-qfnqvqrh/files/output.log +++ /dev/null @@ -1,59 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 20065.59it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -classifier.bias | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 2 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 414 - Number of trainable parameters = 44,302,082 - 48%|████▊ | 199/414 [00:17<00:18, 11.62it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K36me3/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K36me3/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.69it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K36me3/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K36me3/checkpoint-200/tokenizer_config.json - 96%|█████████▋| 399/414 [00:36<00:01, 11.45it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K36me3/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K36me3/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.62it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K36me3/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K36me3/checkpoint-400/tokenizer_config.json -100%|█████████▉| 413/414 [00:38<00:00, 9.94it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K36me3/checkpoint-414 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K36me3/checkpoint-414/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.64it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K36me3/checkpoint-414/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K36me3/checkpoint-414/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 414/414 [00:38<00:00, 10.65it/s] -{'train_runtime': '38.87', 'train_samples_per_second': '1358', 'train_steps_per_second': '10.65', 'train_loss': '0.4653', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 39.46it/s] diff --git a/wandb/run-20260305_075123-qfnqvqrh/files/requirements.txt b/wandb/run-20260305_075123-qfnqvqrh/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_075123-qfnqvqrh/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 -accelerate==1.13.0 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -triton==3.6.0 -nvidia-nccl-cu12==2.27.5 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -cuda-pathfinder==1.4.0 -shellingham==1.5.4 -torchaudio==2.5.1 -nvidia-cufile-cu12==1.13.1.3 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -nvidia-nvjitlink-cu12==12.8.93 -click==8.3.1 -MarkupSafe==3.0.2 -nvidia-nvshmem-cu12==3.4.5 -urllib3==2.6.3 -cuda-bindings==12.9.4 -propcache==0.4.1 -nvidia-cusolver-cu12==11.7.3.90 -sympy==1.14.0 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -nvidia-cuda-runtime-cu12==12.8.90 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_075123-qfnqvqrh/files/wandb-metadata.json b/wandb/run-20260305_075123-qfnqvqrh/files/wandb-metadata.json deleted file mode 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"False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "556420591616" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T07:52:21.031108Z" - writerId: 93ne7jj6lqdrqol51441g4vr343y3fmo - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_075221-jdcg5v99/files/output.log b/wandb/run-20260305_075221-jdcg5v99/files/output.log deleted file mode 100644 index 2e7de4d5a7064319defbf9bdaa2aa5044e2736da..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_075221-jdcg5v99/files/output.log +++ /dev/null @@ -1,59 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 22178.14it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -bert.pooler.dense.weight | MISSING | -classifier.bias | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 2 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 414 - Number of trainable parameters = 44,302,082 - 48%|████▊ | 199/414 [00:17<00:19, 10.98it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K4me1/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K4me1/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.35it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K4me1/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K4me1/checkpoint-200/tokenizer_config.json - 96%|█████████▋| 399/414 [00:36<00:01, 10.72it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K4me1/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K4me1/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.67it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K4me1/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K4me1/checkpoint-400/tokenizer_config.json -100%|█████████▉| 413/414 [00:38<00:00, 9.60it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K4me1/checkpoint-414 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K4me1/checkpoint-414/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.30it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K4me1/checkpoint-414/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K4me1/checkpoint-414/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 414/414 [00:39<00:00, 10.43it/s] -{'train_runtime': '39.68', 'train_samples_per_second': '1331', 'train_steps_per_second': '10.43', 'train_loss': '0.5469', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 39.46it/s] diff --git a/wandb/run-20260305_075221-jdcg5v99/files/requirements.txt b/wandb/run-20260305_075221-jdcg5v99/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_075221-jdcg5v99/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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--------------------------------------------+------------+- -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -bert.pooler.dense.weight | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 25,710 - Num Epochs = 2 - Num update steps per epoch = 201 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 402 - Number of trainable parameters = 44,302,082 - 50%|████▉ | 199/402 [00:17<00:17, 11.66it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K4me2/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K4me2/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.79it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K4me2/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K4me2/checkpoint-200/tokenizer_config.json - 99%|█████████▉| 399/402 [00:35<00:00, 11.62it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K4me2/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K4me2/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.69it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K4me2/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K4me2/checkpoint-400/tokenizer_config.json -100%|█████████▉| 401/402 [00:36<00:00, 5.11it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K4me2/checkpoint-402 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K4me2/checkpoint-402/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 2.86it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K4me2/checkpoint-402/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K4me2/checkpoint-402/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 402/402 [00:37<00:00, 10.63it/s] -{'train_runtime': '37.83', 'train_samples_per_second': '1359', 'train_steps_per_second': '10.63', 'train_loss': '0.4855', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3215 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 40.87it/s] diff --git a/wandb/run-20260305_075319-gslylpll/files/requirements.txt b/wandb/run-20260305_075319-gslylpll/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_075319-gslylpll/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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"2026-03-05T07:54:15.681034Z" - writerId: kufwntnd8rudh9c10gl5j9vmyn8r0qis - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_075415-rrjp7w49/files/output.log b/wandb/run-20260305_075415-rrjp7w49/files/output.log deleted file mode 100644 index 667af7cf06590cec7886e5b94b450b9d0eb8a72c..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_075415-rrjp7w49/files/output.log +++ /dev/null @@ -1,54 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 22892.45it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -bert.pooler.dense.weight | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 14,595 - Num Epochs = 2 - Num update steps per epoch = 115 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 230 - Number of trainable parameters = 44,302,082 - 87%|████████▋ | 199/230 [00:17<00:02, 11.61it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K4me3/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K4me3/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.20it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K4me3/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K4me3/checkpoint-200/tokenizer_config.json -100%|█████████▉| 229/230 [00:21<00:00, 11.37it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K4me3/checkpoint-230 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K4me3/checkpoint-230/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.12it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K4me3/checkpoint-230/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K4me3/checkpoint-230/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 230/230 [00:21<00:00, 10.46it/s] -{'train_runtime': '21.98', 'train_samples_per_second': '1328', 'train_steps_per_second': '10.46', 'train_loss': '0.4142', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 1825 - Batch size = 128 -100%|██████████| 15/15 [00:00<00:00, 41.83it/s] diff --git a/wandb/run-20260305_075415-rrjp7w49/files/requirements.txt b/wandb/run-20260305_075415-rrjp7w49/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_075415-rrjp7w49/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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"2026-03-05T07:54:53.136369Z" - writerId: ps9uyenvh3udi5sqbwuyvps50qklt9ae - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_075453-ctoj1z7k/files/output.log b/wandb/run-20260305_075453-ctoj1z7k/files/output.log deleted file mode 100644 index d277ae0df8efff55a9583c4889c7733780d2b819..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_075453-ctoj1z7k/files/output.log +++ /dev/null @@ -1,54 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 25386.51it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -bert.pooler.dense.bias | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 19,422 - Num Epochs = 2 - Num update steps per epoch = 152 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 304 - Number of trainable parameters = 44,302,082 - 65%|██████▌ | 199/304 [00:17<00:09, 11.42it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K9ac/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K9ac/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.00it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K9ac/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K9ac/checkpoint-200/tokenizer_config.json -100%|█████████▉| 303/304 [00:27<00:00, 11.63it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K9ac/checkpoint-304 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K9ac/checkpoint-304/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.40it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K9ac/checkpoint-304/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K9ac/checkpoint-304/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 304/304 [00:28<00:00, 10.68it/s] -{'train_runtime': '28.45', 'train_samples_per_second': '1365', 'train_steps_per_second': '10.69', 'train_loss': '0.5085', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 2429 - Batch size = 128 -100%|██████████| 19/19 [00:00<00:00, 40.53it/s] diff --git a/wandb/run-20260305_075453-ctoj1z7k/files/requirements.txt b/wandb/run-20260305_075453-ctoj1z7k/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_075453-ctoj1z7k/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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"2026-03-05T07:55:40.356947Z" - writerId: sw2yrcxvcyq9j74rgb1knzawlvkpnnv0 - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_075540-jtbwppqw/files/output.log b/wandb/run-20260305_075540-jtbwppqw/files/output.log deleted file mode 100644 index 094954967cf3f3307c4dc92ca0963a32d55e0a56..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_075540-jtbwppqw/files/output.log +++ /dev/null @@ -1,54 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 23142.57it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -bert.pooler.dense.bias | MISSING | -classifier.bias | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 22,630 - Num Epochs = 2 - Num update steps per epoch = 177 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 354 - Number of trainable parameters = 44,302,082 - 56%|█████▌ | 199/354 [00:17<00:13, 11.65it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K9me3/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K9me3/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.68it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K9me3/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K9me3/checkpoint-200/tokenizer_config.json -100%|█████████▉| 353/354 [00:31<00:00, 11.61it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K9me3/checkpoint-354 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K9me3/checkpoint-354/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.48it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K9me3/checkpoint-354/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H3K9me3/checkpoint-354/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 354/354 [00:32<00:00, 10.78it/s] -{'train_runtime': '32.84', 'train_samples_per_second': '1378', 'train_steps_per_second': '10.78', 'train_loss': '0.5906', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 2830 - Batch size = 128 -100%|██████████| 23/23 [00:00<00:00, 41.29it/s] diff --git a/wandb/run-20260305_075540-jtbwppqw/files/requirements.txt b/wandb/run-20260305_075540-jtbwppqw/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_075540-jtbwppqw/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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--------------------------------------------+------------+- -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -bert.pooler.dense.bias | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -***** Running training ***** - Num examples = 25,816 - Num Epochs = 2 - Num update steps per epoch = 202 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 404 - Number of trainable parameters = 44,302,082 - 49%|████▉ | 199/404 [00:17<00:17, 11.56it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H4K20me1/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H4K20me1/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.86it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H4K20me1/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H4K20me1/checkpoint-200/tokenizer_config.json - 99%|█████████▉| 399/404 [00:35<00:00, 11.48it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H4K20me1/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H4K20me1/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.84it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H4K20me1/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H4K20me1/checkpoint-400/tokenizer_config.json -100%|█████████▉| 403/404 [00:36<00:00, 6.12it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H4K20me1/checkpoint-404 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H4K20me1/checkpoint-404/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.32it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H4K20me1/checkpoint-404/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/H4K20me1/checkpoint-404/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 404/404 [00:37<00:00, 10.73it/s] -{'train_runtime': '37.66', 'train_samples_per_second': '1371', 'train_steps_per_second': '10.73', 'train_loss': '0.4409', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3227 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 41.12it/s] diff --git a/wandb/run-20260305_075632-t2kr3hv5/files/requirements.txt b/wandb/run-20260305_075632-t2kr3hv5/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_075632-t2kr3hv5/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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wandb-AsyncioManager-main:3798850 [mailbox.py:close():155] Closing mailbox, abandoning 1 handles. diff --git a/wandb/run-20260305_075632-t2kr3hv5/run-t2kr3hv5.wandb b/wandb/run-20260305_075632-t2kr3hv5/run-t2kr3hv5.wandb deleted file mode 100644 index 62ee7b4fb58b06d2ad6295c8633b68758f2d388a..0000000000000000000000000000000000000000 Binary files a/wandb/run-20260305_075632-t2kr3hv5/run-t2kr3hv5.wandb and /dev/null differ diff --git a/wandb/run-20260305_075729-ejfchnle/files/config.yaml b/wandb/run-20260305_075729-ejfchnle/files/config.yaml deleted file mode 100644 index 91ab45d2eccc6f67651968b6bc8da9339d683425..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_075729-ejfchnle/files/config.yaml +++ /dev/null @@ -1,139 +0,0 @@ -_wandb: - value: - cli_version: 0.25.0 - e: - ey9mtitpncoczkdrirfea3coqss9d2mn: - args: - - --model_name_or_path - - /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 - - --tokenizer_path - - /home/n5huang/dna_token/tokenizer_evaluation/merge_bpe/merge_tokenizer_unigram_tf_idf.json - - --trust_remote_code - - "True" - - --data_path - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/enhancers/split - - --kmer - - "-1" - - --run_name - - hg38_BPE_base__merge_bpe_merge_tokenizer_unigram_tf_idf_3e-5_enhancers_seed42 - - --model_max_length - - "100" - - --per_device_train_batch_size - - "128" - - --per_device_eval_batch_size - - "128" - - --gradient_accumulation_steps - - "1" - - --learning_rate - - "3e-5" - - --num_train_epochs - - "4" - - --fp16 - - --save_steps - - "200" - - --output_dir - - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers - - --evaluation_strategy - - steps - - --eval_steps - - "200" - - --warmup_steps - - "30" - - --logging_steps - - "100000" - - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "556432707584" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T07:57:29.795889Z" - writerId: ey9mtitpncoczkdrirfea3coqss9d2mn - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_075729-ejfchnle/files/output.log b/wandb/run-20260305_075729-ejfchnle/files/output.log deleted file mode 100644 index 3d8e45d17459f2512cc0da8574885a2e5be17552..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_075729-ejfchnle/files/output.log +++ /dev/null @@ -1,70 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 9373.89it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -classifier.bias | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 755}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 4 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 828 - Number of trainable parameters = 44,302,082 - 24%|██▍ | 199/828 [00:09<00:27, 22.93it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.57it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers/checkpoint-200/tokenizer_config.json - 48%|████▊ | 400/828 [00:18<00:18, 23.38it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.85it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers/checkpoint-400/tokenizer_config.json - 72%|███████▏ | 598/828 [00:27<00:09, 23.98it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers/checkpoint-600 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers/checkpoint-600/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.66it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers/checkpoint-600/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers/checkpoint-600/tokenizer_config.json - 96%|█████████▋| 799/828 [00:37<00:01, 23.98it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers/checkpoint-800 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers/checkpoint-800/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.94it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers/checkpoint-800/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers/checkpoint-800/tokenizer_config.json -100%|█████████▉| 826/828 [00:39<00:00, 21.02it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers/checkpoint-828 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers/checkpoint-828/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.87it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers/checkpoint-828/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers/checkpoint-828/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 828/828 [00:40<00:00, 20.45it/s] -{'train_runtime': '40.49', 'train_samples_per_second': '2608', 'train_steps_per_second': '20.45', 'train_loss': '0.5734', 'epoch': '4'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 81.20it/s] diff --git a/wandb/run-20260305_075729-ejfchnle/files/requirements.txt b/wandb/run-20260305_075729-ejfchnle/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_075729-ejfchnle/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 -accelerate==1.13.0 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -triton==3.6.0 -nvidia-nccl-cu12==2.27.5 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -cuda-pathfinder==1.4.0 -shellingham==1.5.4 -torchaudio==2.5.1 -nvidia-cufile-cu12==1.13.1.3 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -nvidia-nvjitlink-cu12==12.8.93 -click==8.3.1 -MarkupSafe==3.0.2 -nvidia-nvshmem-cu12==3.4.5 -urllib3==2.6.3 -cuda-bindings==12.9.4 -propcache==0.4.1 -nvidia-cusolver-cu12==11.7.3.90 -sympy==1.14.0 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -nvidia-cuda-runtime-cu12==12.8.90 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_075729-ejfchnle/files/wandb-metadata.json b/wandb/run-20260305_075729-ejfchnle/files/wandb-metadata.json deleted file mode 100644 index 24f220a1bb92e7dd2743966d5c9aaf74ce817096..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_075729-ejfchnle/files/wandb-metadata.json +++ /dev/null @@ -1,134 +0,0 @@ -{ - "os": "Linux-5.15.0-72-generic-x86_64-with-glibc2.35", - "python": "CPython 3.10.19", - "startedAt": "2026-03-05T07:57:29.795889Z", - "args": [ - "--model_name_or_path", - "/home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000", - "--tokenizer_path", - "/home/n5huang/dna_token/tokenizer_evaluation/merge_bpe/merge_tokenizer_unigram_tf_idf.json", - "--trust_remote_code", - "True", - "--data_path", - "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/enhancers/split", - "--kmer", - "-1", - "--run_name", - "hg38_BPE_base__merge_bpe_merge_tokenizer_unigram_tf_idf_3e-5_enhancers_seed42", - "--model_max_length", - "100", - "--per_device_train_batch_size", - "128", - 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/data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T07:58:26.014870Z" - writerId: cga6axjhbuymss5d075geln9p9afm1rx - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_075826-vqza403x/files/output.log b/wandb/run-20260305_075826-vqza403x/files/output.log deleted file mode 100644 index 2c01ffd21c15a088e4e73a6693456100478add6a..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_075826-vqza403x/files/output.log +++ /dev/null @@ -1,70 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 21358.51it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -bert.pooler.dense.weight | MISSING | -classifier.bias | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 755}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 4 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 828 - Number of trainable parameters = 44,302,851 - 24%|██▍ | 199/828 [00:09<00:25, 24.37it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers_types/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers_types/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.65it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers_types/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers_types/checkpoint-200/tokenizer_config.json - 48%|████▊ | 400/828 [00:18<00:17, 23.84it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers_types/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers_types/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 2.91it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers_types/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers_types/checkpoint-400/tokenizer_config.json - 72%|███████▏ | 598/828 [00:27<00:09, 23.16it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers_types/checkpoint-600 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers_types/checkpoint-600/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.29it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers_types/checkpoint-600/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers_types/checkpoint-600/tokenizer_config.json - 96%|█████████▋| 799/828 [00:36<00:01, 23.18it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers_types/checkpoint-800 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers_types/checkpoint-800/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 2.66it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers_types/checkpoint-800/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers_types/checkpoint-800/tokenizer_config.json -100%|█████████▉| 826/828 [00:38<00:00, 21.19it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers_types/checkpoint-828 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers_types/checkpoint-828/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.36it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers_types/checkpoint-828/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/enhancers_types/checkpoint-828/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 828/828 [00:39<00:00, 20.94it/s] -{'train_runtime': '39.54', 'train_samples_per_second': '2671', 'train_steps_per_second': '20.94', 'train_loss': '0.7038', 'epoch': '4'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 81.99it/s] diff --git a/wandb/run-20260305_075826-vqza403x/files/requirements.txt b/wandb/run-20260305_075826-vqza403x/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_075826-vqza403x/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 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--log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "556437446656" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T07:59:20.204334Z" - writerId: uf6ph076sim5emztlxfy2a7d707ns62j - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_075920-s28klq7x/files/output.log b/wandb/run-20260305_075920-s28klq7x/files/output.log deleted file mode 100644 index 77d7de079c270ae55889c6c0a5f95d2c609da3b0..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_075920-s28klq7x/files/output.log +++ /dev/null @@ -1,55 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 23001.83it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -classifier.bias | MISSING | -bert.pooler.dense.bias | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 755}. -***** Running training ***** - Num examples = 25,267 - Num Epochs = 2 - Num update steps per epoch = 198 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 396 - Number of trainable parameters = 44,302,082 - 51%|█████ | 200/396 [00:08<00:06, 29.59it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/promoter_all/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/promoter_all/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.03it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/promoter_all/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/promoter_all/checkpoint-200/tokenizer_config.json -100%|█████████▉| 395/396 [00:15<00:00, 27.32it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/promoter_all/checkpoint-396 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/promoter_all/checkpoint-396/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.06it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/promoter_all/checkpoint-396/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/promoter_all/checkpoint-396/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 396/396 [00:16<00:00, 23.76it/s] -{'train_runtime': '16.67', 'train_samples_per_second': '3032', 'train_steps_per_second': '23.76', 'train_loss': '0.3937', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3159 - Batch size = 128 -100%|██████████| 25/25 [00:00<00:00, 98.58it/s] diff --git a/wandb/run-20260305_075920-s28klq7x/files/requirements.txt b/wandb/run-20260305_075920-s28klq7x/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_075920-s28klq7x/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 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- - --log_level - - info - - --seed - - "42" - - --find_unused_parameters - - "False" - - --project_name - - genomic_bench_tune_hg38_1024 - cpu_count: 128 - cpu_count_logical: 255 - cudaVersion: "12.2" - disk: - /: - total: "1876350566400" - used: "556439666688" - email: mtapiapacheco@ucsd.edu - executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python - git: - commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6 - remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks - gpu: NVIDIA A100 80GB PCIe - gpu_count: 8 - gpu_nvidia: - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0 - - architecture: Ampere - cudaCores: 6912 - memoryTotal: "85899345920" - name: NVIDIA A100 80GB PCIe - uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044 - host: sn4622116170 - memory: - total: "4316310355968" - os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35 - program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py - python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T07:59:51.323392Z" - writerId: iuukv1blxjc7ycoa1aive9g1hyu8uysc - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_075951-zk0x5rw1/files/output.log b/wandb/run-20260305_075951-zk0x5rw1/files/output.log deleted file mode 100644 index 13851de458e717515a5d037152bbb307cc1c49e8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_075951-zk0x5rw1/files/output.log +++ /dev/null @@ -1,55 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 20668.65it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -classifier.weight | MISSING | -bert.pooler.dense.weight | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 755}. -***** Running training ***** - Num examples = 25,097 - Num Epochs = 2 - Num update steps per epoch = 197 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 394 - Number of trainable parameters = 44,302,082 - 51%|█████ | 199/394 [00:07<00:06, 28.21it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/promoter_no_tata/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/promoter_no_tata/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.59it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/promoter_no_tata/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/promoter_no_tata/checkpoint-200/tokenizer_config.json - 99%|█████████▉| 391/394 [00:15<00:00, 27.28it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/promoter_no_tata/checkpoint-394 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/promoter_no_tata/checkpoint-394/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.92it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/promoter_no_tata/checkpoint-394/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/promoter_no_tata/checkpoint-394/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 394/394 [00:16<00:00, 23.57it/s] -{'train_runtime': '16.72', 'train_samples_per_second': '3003', 'train_steps_per_second': '23.57', 'train_loss': '0.3698', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 3138 - Batch size = 128 -100%|██████████| 25/25 [00:00<00:00, 98.38it/s] diff --git a/wandb/run-20260305_075951-zk0x5rw1/files/requirements.txt b/wandb/run-20260305_075951-zk0x5rw1/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_075951-zk0x5rw1/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 -accelerate==1.13.0 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -triton==3.6.0 -nvidia-nccl-cu12==2.27.5 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -cuda-pathfinder==1.4.0 -shellingham==1.5.4 -torchaudio==2.5.1 -nvidia-cufile-cu12==1.13.1.3 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -nvidia-nvjitlink-cu12==12.8.93 -click==8.3.1 -MarkupSafe==3.0.2 -nvidia-nvshmem-cu12==3.4.5 -urllib3==2.6.3 -cuda-bindings==12.9.4 -propcache==0.4.1 -nvidia-cusolver-cu12==11.7.3.90 -sympy==1.14.0 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -nvidia-cuda-runtime-cu12==12.8.90 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_075951-zk0x5rw1/files/wandb-metadata.json b/wandb/run-20260305_075951-zk0x5rw1/files/wandb-metadata.json deleted file mode 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/home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -classifier.bias | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.weight | MISSING | -bert.pooler.dense.weight | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 755}. -***** Running training ***** - Num examples = 4,219 - Num Epochs = 2 - Num update steps per epoch = 33 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 66 - Number of trainable parameters = 44,302,082 - 97%|█████████▋| 64/66 [00:02<00:00, 27.60it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/promoter_tata/checkpoint-66 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/promoter_tata/checkpoint-66/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.49it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/promoter_tata/checkpoint-66/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/promoter_tata/checkpoint-66/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 66/66 [00:03<00:00, 16.90it/s] -{'train_runtime': '3.905', 'train_samples_per_second': '2161', 'train_steps_per_second': '16.9', 'train_loss': '0.5586', 'epoch': '2'} - -***** Running Evaluation ***** - Num examples = 528 - Batch size = 128 -100%|██████████| 5/5 [00:00<00:00, 77.28it/s] diff --git a/wandb/run-20260305_080028-br91uwgy/files/requirements.txt b/wandb/run-20260305_080028-br91uwgy/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_080028-br91uwgy/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 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python: CPython 3.10.19 - root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data - startedAt: "2026-03-05T08:00:43.618828Z" - writerId: 75buqol92bg5gwl1m9qcpqvxafeth7f4 - m: [] - python_version: 3.10.19 - t: - "1": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "2": - - 1 - - 5 - - 11 - - 49 - - 51 - - 53 - - 71 - "4": 3.10.19 - "5": 0.25.0 - "6": 5.3.0 - "12": 0.25.0 - "13": linux-x86_64 diff --git a/wandb/run-20260305_080043-n0lrkruq/files/output.log b/wandb/run-20260305_080043-n0lrkruq/files/output.log deleted file mode 100644 index 1f083cfa05c740ade966e8fe6be271137163d91a..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_080043-n0lrkruq/files/output.log +++ /dev/null @@ -1,70 +0,0 @@ -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -WARNING:root:Perform single sequence classification... -Loading weights: 100%|██████████| 101/101 [00:00<00:00, 22225.85it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.decoder.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.dense.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -classifier.weight | MISSING | -bert.pooler.dense.weight | MISSING | -bert.pooler.dense.bias | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 755}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 4 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 828 - Number of trainable parameters = 44,302,082 - 24%|██▍ | 199/828 [00:11<00:36, 17.31it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_acceptors/checkpoint-200 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_acceptors/checkpoint-200/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.15it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_acceptors/checkpoint-200/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_acceptors/checkpoint-200/tokenizer_config.json - 48%|████▊ | 400/828 [00:24<00:24, 17.54it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_acceptors/checkpoint-400 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_acceptors/checkpoint-400/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.30it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_acceptors/checkpoint-400/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_acceptors/checkpoint-400/tokenizer_config.json - 72%|███████▏ | 599/828 [00:36<00:12, 17.64it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_acceptors/checkpoint-600 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_acceptors/checkpoint-600/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.42it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_acceptors/checkpoint-600/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_acceptors/checkpoint-600/tokenizer_config.json - 97%|█████████▋| 800/828 [00:48<00:01, 17.58it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_acceptors/checkpoint-800 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_acceptors/checkpoint-800/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 3.88it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_acceptors/checkpoint-800/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_acceptors/checkpoint-800/tokenizer_config.json -100%|█████████▉| 826/828 [00:51<00:00, 16.78it/s]Saving model checkpoint to /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_acceptors/checkpoint-828 -Configuration saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_acceptors/checkpoint-828/config.json -Writing model shards: 100%|██████████| 1/1 [00:00<00:00, 4.42it/s] -Model weights saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_acceptors/checkpoint-828/model.safetensors -tokenizer config file saved in /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__merge_bpe_merge_tokenizer_unigram_tf_idf/splice_sites_acceptors/checkpoint-828/tokenizer_config.json - - -Training completed. Do not forget to share your model on huggingface.co/models =) - - -100%|██████████| 828/828 [00:51<00:00, 15.99it/s] -{'train_runtime': '51.8', 'train_samples_per_second': '2039', 'train_steps_per_second': '15.98', 'train_loss': '0.6013', 'epoch': '4'} - -***** Running Evaluation ***** - Num examples = 3300 - Batch size = 128 -100%|██████████| 26/26 [00:00<00:00, 61.36it/s] diff --git a/wandb/run-20260305_080043-n0lrkruq/files/requirements.txt b/wandb/run-20260305_080043-n0lrkruq/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_080043-n0lrkruq/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 -GitPython==3.1.46 -nvidia-cusparselt-cu12==0.7.1 -idna==3.11 -pycparser==2.23 -numpy==2.0.1 -numpy==2.2.6 -python-dateutil==2.9.0.post0 -gitdb==4.0.12 -rich==14.3.3 -PyYAML==6.0.3 -pytz==2026.1.post1 -packaging==25.0 -transformers==5.3.0 -networkx==3.4.2 -platformdirs==4.9.2 -ittapi==1.2.1 -yarl==1.23.0 -aiohttp==3.13.3 -typer==0.24.1 -mkl_fft==1.3.11 -psutil==7.2.2 -scipy==1.15.3 -httpcore==1.0.9 -Jinja2==3.1.6 -pip==26.0.1 -torch==2.10.0 -nvidia-cuda-nvrtc-cu12==12.8.93 -nvidia-curand-cu12==10.3.9.90 -six==1.17.0 -frozenlist==1.8.0 -filelock==3.20.3 -annotated-doc==0.0.4 -multiprocess==0.70.18 -threadpoolctl==3.6.0 -typing_extensions==4.15.0 -pydantic==2.12.5 -async-timeout==5.0.1 -Pygments==2.19.2 -mkl_random==1.2.8 -certifi==2026.2.25 -exceptiongroup==1.3.1 -nvidia-cuda-cupti-cu12==12.8.90 -charset-normalizer==3.4.4 -wandb==0.25.0 -nvidia-cublas-cu12==12.8.4.1 -PySocks==1.7.1 -pandas==2.3.3 -smmap==5.0.2 -pyarrow==23.0.1 -nvidia-cufft-cu12==11.3.3.83 -safetensors==0.7.0 -tokenizers==0.22.2 -requests==2.32.5 -fsspec==2026.2.0 -aiosignal==1.4.0 -multidict==6.7.1 -typing-inspection==0.4.2 -nvidia-cudnn-cu12==9.10.2.21 -accelerate==1.13.0 -brotlicffi==1.2.0.0 -gmpy2==2.2.2 -datasets==4.6.1 -triton==3.6.0 -nvidia-nccl-cu12==2.27.5 -anyio==4.12.1 -annotated-types==0.7.0 -tqdm==4.67.3 -mkl-service==2.4.0 -sentry-sdk==2.54.0 -cuda-pathfinder==1.4.0 -shellingham==1.5.4 -torchaudio==2.5.1 -nvidia-cufile-cu12==1.13.1.3 -h11==0.16.0 -pillow==12.1.1 -protobuf==6.33.5 -nvidia-nvjitlink-cu12==12.8.93 -click==8.3.1 -MarkupSafe==3.0.2 -nvidia-nvshmem-cu12==3.4.5 -urllib3==2.6.3 -cuda-bindings==12.9.4 -propcache==0.4.1 -nvidia-cusolver-cu12==11.7.3.90 -sympy==1.14.0 -regex==2026.2.28 -xxhash==3.6.0 -setuptools==80.10.2 -nvidia-cuda-runtime-cu12==12.8.90 -scikit-learn==1.7.2 -huggingface_hub==1.5.0 -joblib==1.5.3 -aiohappyeyeballs==2.6.1 diff --git a/wandb/run-20260305_080043-n0lrkruq/files/wandb-metadata.json b/wandb/run-20260305_080043-n0lrkruq/files/wandb-metadata.json deleted file mode 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12982.68it/s] -BertForSequenceClassification LOAD REPORT from: /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000 -Key | Status | --------------------------------------------+------------+- -cls.predictions.transform.dense.bias | UNEXPECTED | -bert.embeddings.position_ids | UNEXPECTED | -cls.predictions.transform.LayerNorm.bias | UNEXPECTED | -cls.predictions.transform.LayerNorm.weight | UNEXPECTED | -cls.predictions.decoder.weight | UNEXPECTED | -cls.predictions.transform.dense.weight | UNEXPECTED | -cls.predictions.bias | UNEXPECTED | -cls.predictions.decoder.bias | UNEXPECTED | -bert.pooler.dense.bias | MISSING | -bert.pooler.dense.weight | MISSING | -classifier.weight | MISSING | -classifier.bias | MISSING | - -Notes: -- UNEXPECTED :can be ignored when loading from different task/architecture; not ok if you expect identical arch. -- MISSING :those params were newly initialized because missing from the checkpoint. Consider training on your downstream task. -The tokenizer has new PAD/BOS/EOS tokens that differ from the model config and generation config. The model config and generation config were aligned accordingly, being updated with the tokenizer's values. Updated tokens: {'pad_token_id': 755}. -***** Running training ***** - Num examples = 26,400 - Num Epochs = 4 - Num update steps per epoch = 207 - Instantaneous batch size per device = 128 - Total train batch size (w. parallel, distributed & accumulation) = 128 - Gradient Accumulation steps = 1 - Total optimization steps = 828 - Number of trainable parameters = 44,302,851 - 18%|█▊ | 151/828 [00:09<00:38, 17.55it/s] diff --git a/wandb/run-20260305_080152-rg61703v/files/requirements.txt b/wandb/run-20260305_080152-rg61703v/files/requirements.txt deleted file mode 100644 index 8e59654cac57ed8ef38b32b00d31413da5e3bff8..0000000000000000000000000000000000000000 --- a/wandb/run-20260305_080152-rg61703v/files/requirements.txt +++ /dev/null @@ -1,106 +0,0 @@ -hf-xet==1.3.2 -mpmath==1.3.0 -httpx==0.28.1 -markdown-it-py==4.0.0 -attrs==25.4.0 -nvidia-cusparse-cu12==12.5.8.93 -nvidia-nvtx-cu12==12.8.90 -pydantic_core==2.41.5 -cffi==2.0.0 -wheel==0.46.3 -tzdata==2025.3 -mdurl==0.1.2 -dill==0.4.0 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run started, returning control to user process diff --git a/wandb/run-20260305_080152-rg61703v/run-rg61703v.wandb b/wandb/run-20260305_080152-rg61703v/run-rg61703v.wandb deleted file mode 100644 index 30977402b08eb894463b83d7de7a007255879a32..0000000000000000000000000000000000000000 Binary files a/wandb/run-20260305_080152-rg61703v/run-rg61703v.wandb and /dev/null differ