mtapiapacheco commited on
Commit
e1d6bcb
·
verified ·
1 Parent(s): a1beb5f

Delete pretrain_tokens/wandb

Browse files
Files changed (20) hide show
  1. pretrain_tokens/wandb/debug-internal.log +0 -15
  2. pretrain_tokens/wandb/debug.log +0 -27
  3. pretrain_tokens/wandb/run-20260409_024256-4yonu3x2/files/config.yaml +0 -613
  4. pretrain_tokens/wandb/run-20260409_024256-4yonu3x2/files/output.log +0 -268
  5. pretrain_tokens/wandb/run-20260409_024256-4yonu3x2/files/requirements.txt +0 -148
  6. pretrain_tokens/wandb/run-20260409_024256-4yonu3x2/files/wandb-metadata.json +0 -149
  7. pretrain_tokens/wandb/run-20260409_024256-4yonu3x2/files/wandb-summary.json +0 -1
  8. pretrain_tokens/wandb/run-20260409_024256-4yonu3x2/logs/debug-core.log +0 -14
  9. pretrain_tokens/wandb/run-20260409_024256-4yonu3x2/logs/debug-internal.log +0 -11
  10. pretrain_tokens/wandb/run-20260409_024256-4yonu3x2/logs/debug.log +0 -27
  11. pretrain_tokens/wandb/run-20260409_024256-4yonu3x2/run-4yonu3x2.wandb +0 -3
  12. pretrain_tokens/wandb/run-20260409_031927-9ph1pkcx/files/config.yaml +0 -613
  13. pretrain_tokens/wandb/run-20260409_031927-9ph1pkcx/files/output.log +0 -0
  14. pretrain_tokens/wandb/run-20260409_031927-9ph1pkcx/files/requirements.txt +0 -148
  15. pretrain_tokens/wandb/run-20260409_031927-9ph1pkcx/files/wandb-metadata.json +0 -149
  16. pretrain_tokens/wandb/run-20260409_031927-9ph1pkcx/files/wandb-summary.json +0 -1
  17. pretrain_tokens/wandb/run-20260409_031927-9ph1pkcx/logs/debug-core.log +0 -14
  18. pretrain_tokens/wandb/run-20260409_031927-9ph1pkcx/logs/debug-internal.log +0 -15
  19. pretrain_tokens/wandb/run-20260409_031927-9ph1pkcx/logs/debug.log +0 -27
  20. pretrain_tokens/wandb/run-20260409_031927-9ph1pkcx/run-9ph1pkcx.wandb +0 -3
pretrain_tokens/wandb/debug-internal.log DELETED
@@ -1,15 +0,0 @@
1
- {"time":"2026-04-09T03:19:28.253252886Z","level":"INFO","msg":"stream: starting","core version":"0.23.1"}
2
- {"time":"2026-04-09T03:19:28.588342136Z","level":"INFO","msg":"stream: created new stream","id":"9ph1pkcx"}
3
- {"time":"2026-04-09T03:19:28.588502646Z","level":"INFO","msg":"handler: started","stream_id":"9ph1pkcx"}
4
- {"time":"2026-04-09T03:19:28.588564816Z","level":"INFO","msg":"stream: started","id":"9ph1pkcx"}
5
- {"time":"2026-04-09T03:19:28.588589346Z","level":"INFO","msg":"writer: started","stream_id":"9ph1pkcx"}
6
- {"time":"2026-04-09T03:19:28.588586606Z","level":"INFO","msg":"sender: started","stream_id":"9ph1pkcx"}
7
- {"time":"2026-04-09T07:38:54.243251922Z","level":"INFO","msg":"api: retrying error","error":"Post \"https://api.wandb.ai/files/mtapiapacheco-university-of-california-san-diego/uncategorized/9ph1pkcx/file_stream\": dial tcp: lookup api.wandb.ai on 127.0.0.53:53: read udp 127.0.0.1:46273->127.0.0.53:53: i/o timeout"}
8
- {"time":"2026-04-10T15:10:52.177204385Z","level":"INFO","msg":"api: retrying error","error":"Post \"https://api.wandb.ai/files/mtapiapacheco-university-of-california-san-diego/uncategorized/9ph1pkcx/file_stream\": context deadline exceeded (Client.Timeout exceeded while awaiting headers)"}
9
- {"time":"2026-04-10T17:40:21.310822834Z","level":"INFO","msg":"api: retrying error","error":"Post \"https://api.wandb.ai/files/mtapiapacheco-university-of-california-san-diego/uncategorized/9ph1pkcx/file_stream\": context deadline exceeded (Client.Timeout exceeded while awaiting headers)"}
10
- {"time":"2026-04-10T18:17:02.326710103Z","level":"INFO","msg":"api: retrying error","error":"Post \"https://api.wandb.ai/files/mtapiapacheco-university-of-california-san-diego/uncategorized/9ph1pkcx/file_stream\": context deadline exceeded (Client.Timeout exceeded while awaiting headers)"}
11
- {"time":"2026-04-12T03:29:56.516755613Z","level":"INFO","msg":"stream: closing","id":"9ph1pkcx"}
12
- {"time":"2026-04-12T03:29:56.970094158Z","level":"INFO","msg":"fileTransfer: Close: file transfer manager closed"}
13
- {"time":"2026-04-12T03:29:57.220807579Z","level":"INFO","msg":"handler: closed","stream_id":"9ph1pkcx"}
14
- {"time":"2026-04-12T03:29:57.220969499Z","level":"INFO","msg":"sender: closed","stream_id":"9ph1pkcx"}
15
- {"time":"2026-04-12T03:29:57.220985529Z","level":"INFO","msg":"stream: closed","id":"9ph1pkcx"}
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
pretrain_tokens/wandb/debug.log DELETED
@@ -1,27 +0,0 @@
1
- 2026-04-09 03:19:27,927 INFO MainThread:3566905 [wandb_setup.py:_flush():80] Current SDK version is 0.23.1
2
- 2026-04-09 03:19:27,927 INFO MainThread:3566905 [wandb_setup.py:_flush():80] Configure stats pid to 3566905
3
- 2026-04-09 03:19:27,927 INFO MainThread:3566905 [wandb_setup.py:_flush():80] Loading settings from /home/n5huang/.config/wandb/settings
4
- 2026-04-09 03:19:27,927 INFO MainThread:3566905 [wandb_setup.py:_flush():80] Loading settings from /data/n5huang/dna_token/output_tokens/wandb/settings
5
- 2026-04-09 03:19:27,927 INFO MainThread:3566905 [wandb_setup.py:_flush():80] Loading settings from environment variables
6
- 2026-04-09 03:19:27,927 INFO MainThread:3566905 [wandb_init.py:setup_run_log_directory():714] Logging user logs to /data/n5huang/dna_token/output_tokens/wandb/run-20260409_031927-9ph1pkcx/logs/debug.log
7
- 2026-04-09 03:19:27,927 INFO MainThread:3566905 [wandb_init.py:setup_run_log_directory():715] Logging internal logs to /data/n5huang/dna_token/output_tokens/wandb/run-20260409_031927-9ph1pkcx/logs/debug-internal.log
8
- 2026-04-09 03:19:27,927 INFO MainThread:3566905 [wandb_init.py:init():841] calling init triggers
9
- 2026-04-09 03:19:27,927 INFO MainThread:3566905 [wandb_init.py:init():846] wandb.init called with sweep_config: {}
10
- config: {'_wandb': {}}
11
- 2026-04-09 03:19:27,927 INFO MainThread:3566905 [wandb_init.py:init():889] starting backend
12
- 2026-04-09 03:19:28,217 INFO MainThread:3566905 [wandb_init.py:init():892] sending inform_init request
13
- 2026-04-09 03:19:28,251 INFO MainThread:3566905 [wandb_init.py:init():900] backend started and connected
14
- 2026-04-09 03:19:28,254 INFO MainThread:3566905 [wandb_init.py:init():970] updated telemetry
15
- 2026-04-09 03:19:28,256 INFO MainThread:3566905 [wandb_init.py:init():994] communicating run to backend with 90.0 second timeout
16
- 2026-04-09 03:19:28,885 INFO MainThread:3566905 [wandb_init.py:init():1041] starting run threads in backend
17
- 2026-04-09 03:19:28,994 INFO MainThread:3566905 [wandb_run.py:_console_start():2521] atexit reg
18
- 2026-04-09 03:19:28,994 INFO MainThread:3566905 [wandb_run.py:_redirect():2369] redirect: wrap_raw
19
- 2026-04-09 03:19:28,994 INFO MainThread:3566905 [wandb_run.py:_redirect():2438] Wrapping output streams.
20
- 2026-04-09 03:19:28,995 INFO MainThread:3566905 [wandb_run.py:_redirect():2461] Redirects installed.
21
- 2026-04-09 03:19:29,000 INFO MainThread:3566905 [wandb_init.py:init():1081] run started, returning control to user process
22
- 2026-04-09 03:19:29,346 INFO MainThread:3566905 [wandb_run.py:_config_callback():1396] config_cb None None {'output_dir': '/home/n5huang/dna_token/pretrain/models/len2_5120', 'overwrite_output_dir': False, 'do_train': True, 'do_eval': True, 'do_predict': False, 'evaluation_strategy': 'NO', 'prediction_loss_only': False, 'per_device_train_batch_size': 96, 'per_device_eval_batch_size': 96, 'per_gpu_train_batch_size': None, 'per_gpu_eval_batch_size': None, 'gradient_accumulation_steps': 1, 'eval_accumulation_steps': None, 'eval_delay': 0, 'learning_rate': 4e-05, 'weight_decay': 0.01, 'adam_beta1': 0.9, 'adam_beta2': 0.98, 'adam_epsilon': 1e-06, 'max_grad_norm': 1.0, 'num_train_epochs': 3.0, 'max_steps': 200000, 'lr_scheduler_type': 'LINEAR', 'warmup_ratio': 0.0, 'warmup_steps': 10000, 'log_level': 'passive', 'log_level_replica': 'warning', 'log_on_each_node': True, 'logging_dir': '/home/n5huang/dna_token/pretrain/models/len2_5120/runs/Apr09_03-19-29_sn4622116170', 'logging_strategy': 'STEPS', 'logging_first_step': False, 'logging_steps': 1000, 'logging_nan_inf_filter': True, 'save_strategy': 'STEPS', 'save_steps': 1000, 'save_total_limit': 10, 'save_safetensors': True, 'save_on_each_node': False, 'no_cuda': False, 'use_cpu': False, 'use_mps_device': False, 'seed': 42, 'data_seed': None, 'jit_mode_eval': False, 'use_ipex': False, 'bf16': False, 'fp16': False, 'fp16_opt_level': 'O1', 'half_precision_backend': 'auto', 'bf16_full_eval': False, 'fp16_full_eval': False, 'tf32': None, 'local_rank': 0, 'ddp_backend': None, 'tpu_num_cores': None, 'tpu_metrics_debug': False, 'debug': [], 'dataloader_drop_last': False, 'eval_steps': None, 'dataloader_num_workers': 0, 'past_index': -1, 'run_name': '/home/n5huang/dna_token/pretrain/models/len2_5120', 'disable_tqdm': False, 'remove_unused_columns': True, 'label_names': None, 'load_best_model_at_end': False, 'metric_for_best_model': None, 'greater_is_better': None, 'ignore_data_skip': False, 'fsdp': [], 'fsdp_min_num_params': 0, 'fsdp_config': {'min_num_params': 0, 'xla': False, 'xla_fsdp_grad_ckpt': False}, 'fsdp_transformer_layer_cls_to_wrap': None, 'deepspeed': None, 'label_smoothing_factor': 0.0, 'optim': 'ADAMW_TORCH', 'optim_args': None, 'adafactor': False, 'group_by_length': False, 'length_column_name': 'length', 'report_to': ['wandb'], 'ddp_find_unused_parameters': None, 'ddp_bucket_cap_mb': None, 'ddp_broadcast_buffers': None, 'dataloader_pin_memory': True, 'skip_memory_metrics': True, 'use_legacy_prediction_loop': False, 'push_to_hub': False, 'resume_from_checkpoint': '/home/n5huang/dna_token/pretrain/models/len2_5120/checkpoint-100000', 'hub_model_id': None, 'hub_strategy': 'EVERY_SAVE', 'hub_token': None, 'hub_private_repo': False, 'hub_always_push': False, 'gradient_checkpointing': False, 'gradient_checkpointing_kwargs': None, 'include_inputs_for_metrics': False, 'fp16_backend': 'auto', 'push_to_hub_model_id': None, 'push_to_hub_organization': None, 'push_to_hub_token': None, 'mp_parameters': '', 'auto_find_batch_size': False, 'full_determinism': False, 'torchdynamo': None, 'ray_scope': 'last', 'ddp_timeout': 1800, 'torch_compile': False, 'torch_compile_backend': None, 'torch_compile_mode': None, 'dispatch_batches': None, 'split_batches': False, 'include_tokens_per_second': False, 'neftune_noise_alpha': None, 'distributed_state': 'Distributed environment: NO\nNum processes: 1\nProcess index: 0\nLocal process index: 0\nDevice: cuda\n', '_n_gpu': 1, '__cached__setup_devices': 'cuda:0', 'deepspeed_plugin': None}
23
- 2026-04-09 03:19:29,348 INFO MainThread:3566905 [wandb_run.py:_config_callback():1396] config_cb None None {'model_name_or_path': None, 'model_type': 'bert', 'config_overrides': None, 'config_name': '/home/n5huang/dna_token/pretrain/models/len2_5120/config.json', 'tokenizer_name': '/home/n5huang/dna_token/tokenizer_evaluation/merge_bpe/vocab_5120/merge_tokenizer_unigram_len2.json', 'cache_dir': '/home/n5huang/dna_token/output_tokens/cache', 'use_fast_tokenizer': True, 'model_revision': 'main', 'token': None, 'trust_remote_code': False, 'torch_dtype': None, 'low_cpu_mem_usage': False, 'model_max_length': 512}
24
- 2026-04-09 03:19:29,349 INFO MainThread:3566905 [wandb_run.py:_config_callback():1396] config_cb None None {'dataset_name': None, 'dataset_config_name': None, 'train_file': '/home/n5huang/dna_token/output_tokens/merge_bpe_5120_allchr_all_tokenized_train_chrOnly.tsv', 'validation_file': '/home/n5huang/dna_token/output_tokens/merge_bpe_5120_allchr_all_tokenized_val_chrOnly.tsv', 'overwrite_cache': False, 'validation_split_percentage': 5, 'max_seq_length': 512, 'preprocessing_num_workers': 8, 'mlm_probability': 0.15, 'line_by_line': True, 'pad_to_max_length': True, 'max_train_samples': None, 'max_eval_samples': None, 'project_name': 'token_eval_len2_5120', 'streaming': False}
25
- 2026-04-09 03:19:50,773 INFO MainThread:3566905 [wandb_run.py:_config_callback():1396] config_cb None None {'return_dict': True, 'output_hidden_states': False, 'output_attentions': False, 'torchscript': False, 'torch_dtype': 'float32', 'use_bfloat16': False, 'tf_legacy_loss': False, 'pruned_heads': {}, 'tie_word_embeddings': True, 'is_encoder_decoder': False, 'is_decoder': False, 'cross_attention_hidden_size': None, 'add_cross_attention': False, 'tie_encoder_decoder': False, 'max_length': 512, 'min_length': 0, 'do_sample': False, 'early_stopping': False, 'num_beams': 1, 'num_beam_groups': 1, 'diversity_penalty': 0.0, 'temperature': 1.0, 'top_k': 50, 'top_p': 1.0, 'typical_p': 1.0, 'repetition_penalty': 1.0, 'length_penalty': 1.0, 'no_repeat_ngram_size': 0, 'encoder_no_repeat_ngram_size': 0, 'bad_words_ids': None, 'num_return_sequences': 1, 'chunk_size_feed_forward': 0, 'output_scores': False, 'return_dict_in_generate': False, 'forced_bos_token_id': None, 'forced_eos_token_id': None, 'remove_invalid_values': False, 'exponential_decay_length_penalty': None, 'suppress_tokens': None, 'begin_suppress_tokens': None, 'architectures': ['BertForMaskedLM'], 'finetuning_task': None, 'id2label': {0: 'LABEL_0', 1: 'LABEL_1'}, 'label2id': {'LABEL_0': 0, 'LABEL_1': 1}, 'tokenizer_class': None, 'prefix': None, 'bos_token_id': None, 'pad_token_id': 0, 'eos_token_id': None, 'sep_token_id': None, 'decoder_start_token_id': None, 'task_specific_params': None, 'problem_type': None, '_name_or_path': '', 'transformers_version': '4.35.2', 'model_type': 'bert', 'vocab_size': 5120, 'hidden_size': 768, 'num_hidden_layers': 12, 'num_attention_heads': 12, 'hidden_act': 'gelu', 'intermediate_size': 3072, 'hidden_dropout_prob': 0.1, 'attention_probs_dropout_prob': 0.1, 'max_position_embeddings': 512, 'type_vocab_size': 2, 'initializer_range': 0.02, 'layer_norm_eps': 1e-12, 'position_embedding_type': 'absolute', 'use_cache': True, 'classifier_dropout': None, 'output_dir': '/home/n5huang/dna_token/pretrain/models/len2_5120', 'overwrite_output_dir': False, 'do_train': True, 'do_eval': True, 'do_predict': False, 'evaluation_strategy': 'no', 'prediction_loss_only': False, 'per_device_train_batch_size': 96, 'per_device_eval_batch_size': 96, 'per_gpu_train_batch_size': None, 'per_gpu_eval_batch_size': None, 'gradient_accumulation_steps': 1, 'eval_accumulation_steps': None, 'eval_delay': 0, 'learning_rate': 4e-05, 'weight_decay': 0.01, 'adam_beta1': 0.9, 'adam_beta2': 0.98, 'adam_epsilon': 1e-06, 'max_grad_norm': 1.0, 'num_train_epochs': 3.0, 'max_steps': 200000, 'lr_scheduler_type': 'linear', 'warmup_ratio': 0.0, 'warmup_steps': 10000, 'log_level': 'passive', 'log_level_replica': 'warning', 'log_on_each_node': True, 'logging_dir': '/home/n5huang/dna_token/pretrain/models/len2_5120/runs/Apr09_03-19-29_sn4622116170', 'logging_strategy': 'steps', 'logging_first_step': False, 'logging_steps': 1000, 'logging_nan_inf_filter': True, 'save_strategy': 'steps', 'save_steps': 1000, 'save_total_limit': 10, 'save_safetensors': True, 'save_on_each_node': False, 'no_cuda': False, 'use_cpu': False, 'use_mps_device': False, 'seed': 42, 'data_seed': None, 'jit_mode_eval': False, 'use_ipex': False, 'bf16': False, 'fp16': False, 'fp16_opt_level': 'O1', 'half_precision_backend': 'auto', 'bf16_full_eval': False, 'fp16_full_eval': False, 'tf32': None, 'local_rank': 0, 'ddp_backend': None, 'tpu_num_cores': None, 'tpu_metrics_debug': False, 'debug': [], 'dataloader_drop_last': False, 'eval_steps': None, 'dataloader_num_workers': 0, 'past_index': -1, 'run_name': '/home/n5huang/dna_token/pretrain/models/len2_5120', 'disable_tqdm': False, 'remove_unused_columns': True, 'label_names': None, 'load_best_model_at_end': False, 'metric_for_best_model': None, 'greater_is_better': None, 'ignore_data_skip': False, 'fsdp': [], 'fsdp_min_num_params': 0, 'fsdp_config': {'min_num_params': 0, 'xla': False, 'xla_fsdp_grad_ckpt': False}, 'fsdp_transformer_layer_cls_to_wrap': None, 'deepspeed': None, 'label_smoothing_factor': 0.0, 'optim': 'adamw_torch', 'optim_args': None, 'adafactor': False, 'group_by_length': False, 'length_column_name': 'length', 'report_to': ['wandb'], 'ddp_find_unused_parameters': None, 'ddp_bucket_cap_mb': None, 'ddp_broadcast_buffers': None, 'dataloader_pin_memory': True, 'skip_memory_metrics': True, 'use_legacy_prediction_loop': False, 'push_to_hub': False, 'resume_from_checkpoint': '/home/n5huang/dna_token/pretrain/models/len2_5120/checkpoint-100000', 'hub_model_id': None, 'hub_strategy': 'every_save', 'hub_token': '<HUB_TOKEN>', 'hub_private_repo': False, 'hub_always_push': False, 'gradient_checkpointing': False, 'gradient_checkpointing_kwargs': None, 'include_inputs_for_metrics': False, 'fp16_backend': 'auto', 'push_to_hub_model_id': None, 'push_to_hub_organization': None, 'push_to_hub_token': '<PUSH_TO_HUB_TOKEN>', 'mp_parameters': '', 'auto_find_batch_size': False, 'full_determinism': False, 'torchdynamo': None, 'ray_scope': 'last', 'ddp_timeout': 1800, 'torch_compile': False, 'torch_compile_backend': None, 'torch_compile_mode': None, 'dispatch_batches': None, 'split_batches': False, 'include_tokens_per_second': False, 'neftune_noise_alpha': None}
26
- 2026-04-12 03:29:56,516 INFO wandb-AsyncioManager-main:3566905 [service_client.py:_forward_responses():80] Reached EOF.
27
- 2026-04-12 03:29:56,516 INFO wandb-AsyncioManager-main:3566905 [mailbox.py:close():137] Closing mailbox, abandoning 1 handles.
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
pretrain_tokens/wandb/run-20260409_024256-4yonu3x2/files/config.yaml DELETED
@@ -1,613 +0,0 @@
1
- __cached__setup_devices:
2
- value: cuda:0
3
- _n_gpu:
4
- value: 1
5
- _name_or_path:
6
- value: ""
7
- _wandb:
8
- value:
9
- cli_version: 0.23.1
10
- e:
11
- 8xva522u4d798tgf5m4gfomp910saafd:
12
- args:
13
- - --output_dir
14
- - /home/n5huang/dna_token/pretrain/models/len2_5120
15
- - --model_type
16
- - bert
17
- - --tokenizer_name
18
- - /home/n5huang/dna_token/tokenizer_evaluation/merge_bpe/vocab_5120/merge_tokenizer_unigram_len2.json
19
- - --config_name
20
- - /home/n5huang/dna_token/pretrain/models/len2_5120/config.json
21
- - --project_name
22
- - token_eval_len2_5120
23
- - --do_train
24
- - "True"
25
- - --model_max_length
26
- - "512"
27
- - --max_seq_length
28
- - "512"
29
- - --line_by_line
30
- - "True"
31
- - --pad_to_max_length
32
- - "True"
33
- - --train_file
34
- - /home/n5huang/dna_token/output_tokens/merge_bpe_5120_allchr_all_tokenized_train_chrOnly.tsv
35
- - --validation_file
36
- - /home/n5huang/dna_token/output_tokens/merge_bpe_5120_allchr_all_tokenized_val_chrOnly.tsv
37
- - --cache_dir
38
- - /home/n5huang/dna_token/output_tokens/cache
39
- - --use_fast_tokenizer
40
- - "True"
41
- - --do_eval
42
- - "True"
43
- - --gradient_accumulation_steps
44
- - "1"
45
- - --per_device_train_batch_size
46
- - "96"
47
- - --per_device_eval_batch_size
48
- - "96"
49
- - --save_steps
50
- - "1000"
51
- - --save_total_limit
52
- - "10"
53
- - --max_steps
54
- - "100000"
55
- - --logging_steps
56
- - "1000"
57
- - --learning_rate
58
- - "4e-5"
59
- - --adam_epsilon
60
- - "1e-6"
61
- - --weight_decay
62
- - "0.01"
63
- - --adam_beta1
64
- - "0.9"
65
- - --adam_beta2
66
- - "0.98"
67
- - --mlm_probability
68
- - "0.15"
69
- - --warmup_steps
70
- - "10000"
71
- - --seed
72
- - "42"
73
- - --preprocessing_num_workers
74
- - "8"
75
- - --resume_from_checkpoint
76
- - /home/n5huang/dna_token/pretrain/models/len2_5120/checkpoint-100000
77
- cpu_count: 128
78
- cpu_count_logical: 255
79
- cudaVersion: "12.2"
80
- disk:
81
- /:
82
- total: "1876350566400"
83
- used: "405230526464"
84
- email: mtapiapacheco@ucsd.edu
85
- executable: /home/n5huang/miniconda3/envs/bpe/bin/python
86
- gpu: NVIDIA A100 80GB PCIe
87
- gpu_count: 8
88
- gpu_nvidia:
89
- - architecture: Ampere
90
- cudaCores: 6912
91
- memoryTotal: "85899345920"
92
- name: NVIDIA A100 80GB PCIe
93
- uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3
94
- - architecture: Ampere
95
- cudaCores: 6912
96
- memoryTotal: "85899345920"
97
- name: NVIDIA A100 80GB PCIe
98
- uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809
99
- - architecture: Ampere
100
- cudaCores: 6912
101
- memoryTotal: "85899345920"
102
- name: NVIDIA A100 80GB PCIe
103
- uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab
104
- - architecture: Ampere
105
- cudaCores: 6912
106
- memoryTotal: "85899345920"
107
- name: NVIDIA A100 80GB PCIe
108
- uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af
109
- - architecture: Ampere
110
- cudaCores: 6912
111
- memoryTotal: "85899345920"
112
- name: NVIDIA A100 80GB PCIe
113
- uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10
114
- - architecture: Ampere
115
- cudaCores: 6912
116
- memoryTotal: "85899345920"
117
- name: NVIDIA A100 80GB PCIe
118
- uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e
119
- - architecture: Ampere
120
- cudaCores: 6912
121
- memoryTotal: "85899345920"
122
- name: NVIDIA A100 80GB PCIe
123
- uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0
124
- - architecture: Ampere
125
- cudaCores: 6912
126
- memoryTotal: "85899345920"
127
- name: NVIDIA A100 80GB PCIe
128
- uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044
129
- host: sn4622116170
130
- memory:
131
- total: "4316310355968"
132
- os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35
133
- program: /home/n5huang/dna-tokenizer/BPE_merge/run_mlm_200k.py
134
- python: CPython 3.9.18
135
- root: /data/n5huang/dna_token/output_tokens
136
- startedAt: "2026-04-09T02:42:56.385921Z"
137
- writerId: 8xva522u4d798tgf5m4gfomp910saafd
138
- m:
139
- - "1": train/global_step
140
- "6":
141
- - 3
142
- "7": []
143
- - "2": '*'
144
- "5": 1
145
- "6":
146
- - 1
147
- "7": []
148
- python_version: 3.9.18
149
- t:
150
- "1":
151
- - 1
152
- - 5
153
- - 11
154
- - 49
155
- - 51
156
- - 53
157
- - 71
158
- - 100
159
- "2":
160
- - 1
161
- - 5
162
- - 11
163
- - 49
164
- - 51
165
- - 53
166
- - 71
167
- - 100
168
- "3":
169
- - 7
170
- - 66
171
- "4": 3.9.18
172
- "5": 0.23.1
173
- "6": 4.35.2
174
- "9":
175
- "1": transformers_trainer
176
- "12": 0.23.1
177
- "13": linux-x86_64
178
- adafactor:
179
- value: false
180
- adam_beta1:
181
- value: 0.9
182
- adam_beta2:
183
- value: 0.98
184
- adam_epsilon:
185
- value: 1e-06
186
- add_cross_attention:
187
- value: false
188
- architectures:
189
- value:
190
- - BertForMaskedLM
191
- attention_probs_dropout_prob:
192
- value: 0.1
193
- auto_find_batch_size:
194
- value: false
195
- bad_words_ids:
196
- value: null
197
- begin_suppress_tokens:
198
- value: null
199
- bf16:
200
- value: false
201
- bf16_full_eval:
202
- value: false
203
- bos_token_id:
204
- value: null
205
- cache_dir:
206
- value: /home/n5huang/dna_token/output_tokens/cache
207
- chunk_size_feed_forward:
208
- value: 0
209
- classifier_dropout:
210
- value: null
211
- config_name:
212
- value: /home/n5huang/dna_token/pretrain/models/len2_5120/config.json
213
- config_overrides:
214
- value: null
215
- cross_attention_hidden_size:
216
- value: null
217
- data_seed:
218
- value: null
219
- dataloader_drop_last:
220
- value: false
221
- dataloader_num_workers:
222
- value: 0
223
- dataloader_pin_memory:
224
- value: true
225
- dataset_config_name:
226
- value: null
227
- dataset_name:
228
- value: null
229
- ddp_backend:
230
- value: null
231
- ddp_broadcast_buffers:
232
- value: null
233
- ddp_bucket_cap_mb:
234
- value: null
235
- ddp_find_unused_parameters:
236
- value: null
237
- ddp_timeout:
238
- value: 1800
239
- debug:
240
- value: []
241
- decoder_start_token_id:
242
- value: null
243
- deepspeed:
244
- value: null
245
- deepspeed_plugin:
246
- value: null
247
- disable_tqdm:
248
- value: false
249
- dispatch_batches:
250
- value: null
251
- distributed_state:
252
- value: |
253
- Distributed environment: NO
254
- Num processes: 1
255
- Process index: 0
256
- Local process index: 0
257
- Device: cuda
258
- diversity_penalty:
259
- value: 0
260
- do_eval:
261
- value: true
262
- do_predict:
263
- value: false
264
- do_sample:
265
- value: false
266
- do_train:
267
- value: true
268
- early_stopping:
269
- value: false
270
- encoder_no_repeat_ngram_size:
271
- value: 0
272
- eos_token_id:
273
- value: null
274
- eval_accumulation_steps:
275
- value: null
276
- eval_delay:
277
- value: 0
278
- eval_steps:
279
- value: null
280
- evaluation_strategy:
281
- value: "no"
282
- exponential_decay_length_penalty:
283
- value: null
284
- finetuning_task:
285
- value: null
286
- forced_bos_token_id:
287
- value: null
288
- forced_eos_token_id:
289
- value: null
290
- fp16:
291
- value: false
292
- fp16_backend:
293
- value: auto
294
- fp16_full_eval:
295
- value: false
296
- fp16_opt_level:
297
- value: O1
298
- fsdp:
299
- value: []
300
- fsdp_config:
301
- value:
302
- min_num_params: 0
303
- xla: false
304
- xla_fsdp_grad_ckpt: false
305
- fsdp_min_num_params:
306
- value: 0
307
- fsdp_transformer_layer_cls_to_wrap:
308
- value: null
309
- full_determinism:
310
- value: false
311
- gradient_accumulation_steps:
312
- value: 1
313
- gradient_checkpointing:
314
- value: false
315
- gradient_checkpointing_kwargs:
316
- value: null
317
- greater_is_better:
318
- value: null
319
- group_by_length:
320
- value: false
321
- half_precision_backend:
322
- value: auto
323
- hidden_act:
324
- value: gelu
325
- hidden_dropout_prob:
326
- value: 0.1
327
- hidden_size:
328
- value: 768
329
- hub_always_push:
330
- value: false
331
- hub_model_id:
332
- value: null
333
- hub_private_repo:
334
- value: false
335
- hub_strategy:
336
- value: every_save
337
- hub_token:
338
- value: <HUB_TOKEN>
339
- id2label:
340
- value:
341
- "0": LABEL_0
342
- "1": LABEL_1
343
- ignore_data_skip:
344
- value: false
345
- include_inputs_for_metrics:
346
- value: false
347
- include_tokens_per_second:
348
- value: false
349
- initializer_range:
350
- value: 0.02
351
- intermediate_size:
352
- value: 3072
353
- is_decoder:
354
- value: false
355
- is_encoder_decoder:
356
- value: false
357
- jit_mode_eval:
358
- value: false
359
- label_names:
360
- value: null
361
- label_smoothing_factor:
362
- value: 0
363
- label2id:
364
- value:
365
- LABEL_0: 0
366
- LABEL_1: 1
367
- layer_norm_eps:
368
- value: 1e-12
369
- learning_rate:
370
- value: 4e-05
371
- length_column_name:
372
- value: length
373
- length_penalty:
374
- value: 1
375
- line_by_line:
376
- value: true
377
- load_best_model_at_end:
378
- value: false
379
- local_rank:
380
- value: 0
381
- log_level:
382
- value: passive
383
- log_level_replica:
384
- value: warning
385
- log_on_each_node:
386
- value: true
387
- logging_dir:
388
- value: /home/n5huang/dna_token/pretrain/models/len2_5120/runs/Apr09_02-42-57_sn4622116170
389
- logging_first_step:
390
- value: false
391
- logging_nan_inf_filter:
392
- value: true
393
- logging_steps:
394
- value: 1000
395
- logging_strategy:
396
- value: steps
397
- low_cpu_mem_usage:
398
- value: false
399
- lr_scheduler_type:
400
- value: linear
401
- max_eval_samples:
402
- value: null
403
- max_grad_norm:
404
- value: 1
405
- max_length:
406
- value: 512
407
- max_position_embeddings:
408
- value: 512
409
- max_seq_length:
410
- value: 512
411
- max_steps:
412
- value: 100000
413
- max_train_samples:
414
- value: null
415
- metric_for_best_model:
416
- value: null
417
- min_length:
418
- value: 0
419
- mlm_probability:
420
- value: 0.15
421
- model_max_length:
422
- value: 512
423
- model_name_or_path:
424
- value: null
425
- model_revision:
426
- value: main
427
- model_type:
428
- value: bert
429
- mp_parameters:
430
- value: ""
431
- neftune_noise_alpha:
432
- value: null
433
- no_cuda:
434
- value: false
435
- no_repeat_ngram_size:
436
- value: 0
437
- num_attention_heads:
438
- value: 12
439
- num_beam_groups:
440
- value: 1
441
- num_beams:
442
- value: 1
443
- num_hidden_layers:
444
- value: 12
445
- num_return_sequences:
446
- value: 1
447
- num_train_epochs:
448
- value: 3
449
- optim:
450
- value: adamw_torch
451
- optim_args:
452
- value: null
453
- output_attentions:
454
- value: false
455
- output_dir:
456
- value: /home/n5huang/dna_token/pretrain/models/len2_5120
457
- output_hidden_states:
458
- value: false
459
- output_scores:
460
- value: false
461
- overwrite_cache:
462
- value: false
463
- overwrite_output_dir:
464
- value: false
465
- pad_to_max_length:
466
- value: true
467
- pad_token_id:
468
- value: 0
469
- past_index:
470
- value: -1
471
- per_device_eval_batch_size:
472
- value: 96
473
- per_device_train_batch_size:
474
- value: 96
475
- per_gpu_eval_batch_size:
476
- value: null
477
- per_gpu_train_batch_size:
478
- value: null
479
- position_embedding_type:
480
- value: absolute
481
- prediction_loss_only:
482
- value: false
483
- prefix:
484
- value: null
485
- preprocessing_num_workers:
486
- value: 8
487
- problem_type:
488
- value: null
489
- project_name:
490
- value: token_eval_len2_5120
491
- push_to_hub:
492
- value: false
493
- push_to_hub_model_id:
494
- value: null
495
- push_to_hub_organization:
496
- value: null
497
- push_to_hub_token:
498
- value: <PUSH_TO_HUB_TOKEN>
499
- ray_scope:
500
- value: last
501
- remove_invalid_values:
502
- value: false
503
- remove_unused_columns:
504
- value: true
505
- repetition_penalty:
506
- value: 1
507
- report_to:
508
- value:
509
- - wandb
510
- resume_from_checkpoint:
511
- value: /home/n5huang/dna_token/pretrain/models/len2_5120/checkpoint-100000
512
- return_dict:
513
- value: true
514
- return_dict_in_generate:
515
- value: false
516
- run_name:
517
- value: /home/n5huang/dna_token/pretrain/models/len2_5120
518
- save_on_each_node:
519
- value: false
520
- save_safetensors:
521
- value: true
522
- save_steps:
523
- value: 1000
524
- save_strategy:
525
- value: steps
526
- save_total_limit:
527
- value: 10
528
- seed:
529
- value: 42
530
- sep_token_id:
531
- value: null
532
- skip_memory_metrics:
533
- value: true
534
- split_batches:
535
- value: false
536
- streaming:
537
- value: false
538
- suppress_tokens:
539
- value: null
540
- task_specific_params:
541
- value: null
542
- temperature:
543
- value: 1
544
- tf_legacy_loss:
545
- value: false
546
- tf32:
547
- value: null
548
- tie_encoder_decoder:
549
- value: false
550
- tie_word_embeddings:
551
- value: true
552
- token:
553
- value: null
554
- tokenizer_class:
555
- value: null
556
- tokenizer_name:
557
- value: /home/n5huang/dna_token/tokenizer_evaluation/merge_bpe/vocab_5120/merge_tokenizer_unigram_len2.json
558
- top_k:
559
- value: 50
560
- top_p:
561
- value: 1
562
- torch_compile:
563
- value: false
564
- torch_compile_backend:
565
- value: null
566
- torch_compile_mode:
567
- value: null
568
- torch_dtype:
569
- value: float32
570
- torchdynamo:
571
- value: null
572
- torchscript:
573
- value: false
574
- tpu_metrics_debug:
575
- value: false
576
- tpu_num_cores:
577
- value: null
578
- train_file:
579
- value: /home/n5huang/dna_token/output_tokens/merge_bpe_5120_allchr_all_tokenized_train_chrOnly.tsv
580
- transformers_version:
581
- value: 4.35.2
582
- trust_remote_code:
583
- value: false
584
- type_vocab_size:
585
- value: 2
586
- typical_p:
587
- value: 1
588
- use_bfloat16:
589
- value: false
590
- use_cache:
591
- value: true
592
- use_cpu:
593
- value: false
594
- use_fast_tokenizer:
595
- value: true
596
- use_ipex:
597
- value: false
598
- use_legacy_prediction_loop:
599
- value: false
600
- use_mps_device:
601
- value: false
602
- validation_file:
603
- value: /home/n5huang/dna_token/output_tokens/merge_bpe_5120_allchr_all_tokenized_val_chrOnly.tsv
604
- validation_split_percentage:
605
- value: 5
606
- vocab_size:
607
- value: 5120
608
- warmup_ratio:
609
- value: 0
610
- warmup_steps:
611
- value: 10000
612
- weight_decay:
613
- value: 0.01
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
pretrain_tokens/wandb/run-20260409_024256-4yonu3x2/files/output.log DELETED
@@ -1,268 +0,0 @@
1
- 04/09/2026 02:42:57 - WARNING - __main__ - Process rank: 0, device: cuda:0, n_gpu: 1, distributed training: False, 16-bits training: False
2
- 04/09/2026 02:42:57 - INFO - __main__ - Training/evaluation parameters TrainingArguments(
3
- _n_gpu=1,
4
- adafactor=False,
5
- adam_beta1=0.9,
6
- adam_beta2=0.98,
7
- adam_epsilon=1e-06,
8
- auto_find_batch_size=False,
9
- bf16=False,
10
- bf16_full_eval=False,
11
- data_seed=None,
12
- dataloader_drop_last=False,
13
- dataloader_num_workers=0,
14
- dataloader_pin_memory=True,
15
- ddp_backend=None,
16
- ddp_broadcast_buffers=None,
17
- ddp_bucket_cap_mb=None,
18
- ddp_find_unused_parameters=None,
19
- ddp_timeout=1800,
20
- debug=[],
21
- deepspeed=None,
22
- disable_tqdm=False,
23
- dispatch_batches=None,
24
- do_eval=True,
25
- do_predict=False,
26
- do_train=True,
27
- eval_accumulation_steps=None,
28
- eval_delay=0,
29
- eval_steps=None,
30
- evaluation_strategy=no,
31
- fp16=False,
32
- fp16_backend=auto,
33
- fp16_full_eval=False,
34
- fp16_opt_level=O1,
35
- fsdp=[],
36
- fsdp_config={'min_num_params': 0, 'xla': False, 'xla_fsdp_grad_ckpt': False},
37
- fsdp_min_num_params=0,
38
- fsdp_transformer_layer_cls_to_wrap=None,
39
- full_determinism=False,
40
- gradient_accumulation_steps=1,
41
- gradient_checkpointing=False,
42
- gradient_checkpointing_kwargs=None,
43
- greater_is_better=None,
44
- group_by_length=False,
45
- half_precision_backend=auto,
46
- hub_always_push=False,
47
- hub_model_id=None,
48
- hub_private_repo=False,
49
- hub_strategy=every_save,
50
- hub_token=<HUB_TOKEN>,
51
- ignore_data_skip=False,
52
- include_inputs_for_metrics=False,
53
- include_tokens_per_second=False,
54
- jit_mode_eval=False,
55
- label_names=None,
56
- label_smoothing_factor=0.0,
57
- learning_rate=4e-05,
58
- length_column_name=length,
59
- load_best_model_at_end=False,
60
- local_rank=0,
61
- log_level=passive,
62
- log_level_replica=warning,
63
- log_on_each_node=True,
64
- logging_dir=/home/n5huang/dna_token/pretrain/models/len2_5120/runs/Apr09_02-42-57_sn4622116170,
65
- logging_first_step=False,
66
- logging_nan_inf_filter=True,
67
- logging_steps=1000,
68
- logging_strategy=steps,
69
- lr_scheduler_type=linear,
70
- max_grad_norm=1.0,
71
- max_steps=100000,
72
- metric_for_best_model=None,
73
- mp_parameters=,
74
- neftune_noise_alpha=None,
75
- no_cuda=False,
76
- num_train_epochs=3.0,
77
- optim=adamw_torch,
78
- optim_args=None,
79
- output_dir=/home/n5huang/dna_token/pretrain/models/len2_5120,
80
- overwrite_output_dir=False,
81
- past_index=-1,
82
- per_device_eval_batch_size=96,
83
- per_device_train_batch_size=96,
84
- prediction_loss_only=False,
85
- push_to_hub=False,
86
- push_to_hub_model_id=None,
87
- push_to_hub_organization=None,
88
- push_to_hub_token=<PUSH_TO_HUB_TOKEN>,
89
- ray_scope=last,
90
- remove_unused_columns=True,
91
- report_to=['wandb'],
92
- resume_from_checkpoint=/home/n5huang/dna_token/pretrain/models/len2_5120/checkpoint-100000,
93
- run_name=/home/n5huang/dna_token/pretrain/models/len2_5120,
94
- save_on_each_node=False,
95
- save_safetensors=True,
96
- save_steps=1000,
97
- save_strategy=steps,
98
- save_total_limit=10,
99
- seed=42,
100
- skip_memory_metrics=True,
101
- split_batches=False,
102
- tf32=None,
103
- torch_compile=False,
104
- torch_compile_backend=None,
105
- torch_compile_mode=None,
106
- torchdynamo=None,
107
- tpu_metrics_debug=False,
108
- tpu_num_cores=None,
109
- use_cpu=False,
110
- use_ipex=False,
111
- use_legacy_prediction_loop=False,
112
- use_mps_device=False,
113
- warmup_ratio=0.0,
114
- warmup_steps=10000,
115
- weight_decay=0.01,
116
- )
117
- Using custom data configuration default-9aa68439a1bf4533
118
- 04/09/2026 02:42:58 - INFO - datasets.builder - Using custom data configuration default-9aa68439a1bf4533
119
- Generating dataset csv (/home/n5huang/dna_token/output_tokens/cache/csv/default-9aa68439a1bf4533/0.0.0/a43390c7ecea6519ff2ce9d10005c8750601c9e456069be5efbd2747df45f420)
120
- 04/09/2026 02:42:58 - INFO - datasets.builder - Generating dataset csv (/home/n5huang/dna_token/output_tokens/cache/csv/default-9aa68439a1bf4533/0.0.0/a43390c7ecea6519ff2ce9d10005c8750601c9e456069be5efbd2747df45f420)
121
- Downloading and preparing dataset csv/default to /home/n5huang/dna_token/output_tokens/cache/csv/default-9aa68439a1bf4533/0.0.0/a43390c7ecea6519ff2ce9d10005c8750601c9e456069be5efbd2747df45f420...
122
- 04/09/2026 02:42:58 - INFO - datasets.builder - Downloading and preparing dataset csv/default to /home/n5huang/dna_token/output_tokens/cache/csv/default-9aa68439a1bf4533/0.0.0/a43390c7ecea6519ff2ce9d10005c8750601c9e456069be5efbd2747df45f420...
123
- Downloading took 0.0 min
124
- 04/09/2026 02:42:58 - INFO - datasets.download.download_manager - Downloading took 0.0 min
125
- Checksum Computation took 0.0 min
126
- 04/09/2026 02:42:58 - INFO - datasets.download.download_manager - Checksum Computation took 0.0 min
127
- Generating train split
128
- 04/09/2026 02:42:58 - INFO - datasets.builder - Generating train split
129
- Generating train split: 982503 examples [00:24, 40012.03 examples/s]
130
- Generating validation split
131
- 04/09/2026 02:43:22 - INFO - datasets.builder - Generating validation split
132
- Generating validation split: 109173 examples [00:02, 40132.11 examples/s]
133
- Unable to verify splits sizes.
134
- 04/09/2026 02:43:25 - INFO - datasets.utils.info_utils - Unable to verify splits sizes.
135
- Dataset csv downloaded and prepared to /home/n5huang/dna_token/output_tokens/cache/csv/default-9aa68439a1bf4533/0.0.0/a43390c7ecea6519ff2ce9d10005c8750601c9e456069be5efbd2747df45f420. Subsequent calls will reuse this data.
136
- 04/09/2026 02:43:25 - INFO - datasets.builder - Dataset csv downloaded and prepared to /home/n5huang/dna_token/output_tokens/cache/csv/default-9aa68439a1bf4533/0.0.0/a43390c7ecea6519ff2ce9d10005c8750601c9e456069be5efbd2747df45f420. Subsequent calls will reuse this data.
137
- [INFO|configuration_utils.py:715] 2026-04-09 02:43:25,496 >> loading configuration file /home/n5huang/dna_token/pretrain/models/len2_5120/config.json
138
- [INFO|configuration_utils.py:777] 2026-04-09 02:43:25,497 >> Model config BertConfig {
139
- "architectures": [
140
- "BertForMaskedLM"
141
- ],
142
- "attention_probs_dropout_prob": 0.1,
143
- "classifier_dropout": null,
144
- "hidden_act": "gelu",
145
- "hidden_dropout_prob": 0.1,
146
- "hidden_size": 768,
147
- "initializer_range": 0.02,
148
- "intermediate_size": 3072,
149
- "layer_norm_eps": 1e-12,
150
- "max_length": 512,
151
- "max_position_embeddings": 512,
152
- "model_type": "bert",
153
- "num_attention_heads": 12,
154
- "num_hidden_layers": 12,
155
- "pad_token_id": 0,
156
- "position_embedding_type": "absolute",
157
- "torch_dtype": "float32",
158
- "transformers_version": "4.35.2",
159
- "type_vocab_size": 2,
160
- "use_cache": true,
161
- "vocab_size": 5120
162
- }
163
- 04/09/2026 02:43:25 - INFO - __main__ - Training new model from scratch
164
-
165
- /home/n5huang/miniconda3/envs/bpe/lib/python3.9/site-packages/transformers/utils/generic.py:309: FutureWarning: `torch.utils._pytree._register_pytree_node` is deprecated. Please use `torch.utils._pytree.register_pytree_node` instead.
166
- _torch_pytree._register_pytree_node(
167
- [INFO|configuration_utils.py:791] 2026-04-09 02:43:25,507 >> Generate config GenerationConfig {
168
- "max_length": 512,
169
- "pad_token_id": 0
170
- }
171
-
172
- Process #1 will write at /home/n5huang/dna_token/output_tokens/cache/csv/default-9aa68439a1bf4533/0.0.0/a43390c7ecea6519ff2ce9d10005c8750601c9e456069be5efbd2747df45f420/cache-b7e4e83b1e5bb0f0_00000_of_00008.arrow
173
- 04/09/2026 02:43:41 - INFO - datasets.arrow_dataset - Process #1 will write at /home/n5huang/dna_token/output_tokens/cache/csv/default-9aa68439a1bf4533/0.0.0/a43390c7ecea6519ff2ce9d10005c8750601c9e456069be5efbd2747df45f420/cache-b7e4e83b1e5bb0f0_00000_of_00008.arrow
174
- Process #2 will write at /home/n5huang/dna_token/output_tokens/cache/csv/default-9aa68439a1bf4533/0.0.0/a43390c7ecea6519ff2ce9d10005c8750601c9e456069be5efbd2747df45f420/cache-b7e4e83b1e5bb0f0_00001_of_00008.arrow
175
- 04/09/2026 02:43:41 - INFO - datasets.arrow_dataset - Process #2 will write at /home/n5huang/dna_token/output_tokens/cache/csv/default-9aa68439a1bf4533/0.0.0/a43390c7ecea6519ff2ce9d10005c8750601c9e456069be5efbd2747df45f420/cache-b7e4e83b1e5bb0f0_00001_of_00008.arrow
176
- Process #3 will write at /home/n5huang/dna_token/output_tokens/cache/csv/default-9aa68439a1bf4533/0.0.0/a43390c7ecea6519ff2ce9d10005c8750601c9e456069be5efbd2747df45f420/cache-b7e4e83b1e5bb0f0_00002_of_00008.arrow
177
- 04/09/2026 02:43:41 - INFO - datasets.arrow_dataset - Process #3 will write at /home/n5huang/dna_token/output_tokens/cache/csv/default-9aa68439a1bf4533/0.0.0/a43390c7ecea6519ff2ce9d10005c8750601c9e456069be5efbd2747df45f420/cache-b7e4e83b1e5bb0f0_00002_of_00008.arrow
178
- Process #4 will write at /home/n5huang/dna_token/output_tokens/cache/csv/default-9aa68439a1bf4533/0.0.0/a43390c7ecea6519ff2ce9d10005c8750601c9e456069be5efbd2747df45f420/cache-b7e4e83b1e5bb0f0_00003_of_00008.arrow
179
- 04/09/2026 02:43:41 - INFO - datasets.arrow_dataset - Process #4 will write at /home/n5huang/dna_token/output_tokens/cache/csv/default-9aa68439a1bf4533/0.0.0/a43390c7ecea6519ff2ce9d10005c8750601c9e456069be5efbd2747df45f420/cache-b7e4e83b1e5bb0f0_00003_of_00008.arrow
180
- Process #5 will write at /home/n5huang/dna_token/output_tokens/cache/csv/default-9aa68439a1bf4533/0.0.0/a43390c7ecea6519ff2ce9d10005c8750601c9e456069be5efbd2747df45f420/cache-b7e4e83b1e5bb0f0_00004_of_00008.arrow
181
- 04/09/2026 02:43:41 - INFO - datasets.arrow_dataset - Process #5 will write at /home/n5huang/dna_token/output_tokens/cache/csv/default-9aa68439a1bf4533/0.0.0/a43390c7ecea6519ff2ce9d10005c8750601c9e456069be5efbd2747df45f420/cache-b7e4e83b1e5bb0f0_00004_of_00008.arrow
182
- Process #6 will write at /home/n5huang/dna_token/output_tokens/cache/csv/default-9aa68439a1bf4533/0.0.0/a43390c7ecea6519ff2ce9d10005c8750601c9e456069be5efbd2747df45f420/cache-b7e4e83b1e5bb0f0_00005_of_00008.arrow
183
- 04/09/2026 02:43:41 - INFO - datasets.arrow_dataset - Process #6 will write at /home/n5huang/dna_token/output_tokens/cache/csv/default-9aa68439a1bf4533/0.0.0/a43390c7ecea6519ff2ce9d10005c8750601c9e456069be5efbd2747df45f420/cache-b7e4e83b1e5bb0f0_00005_of_00008.arrow
184
- Process #7 will write at /home/n5huang/dna_token/output_tokens/cache/csv/default-9aa68439a1bf4533/0.0.0/a43390c7ecea6519ff2ce9d10005c8750601c9e456069be5efbd2747df45f420/cache-b7e4e83b1e5bb0f0_00006_of_00008.arrow
185
- 04/09/2026 02:43:41 - INFO - datasets.arrow_dataset - Process #7 will write at /home/n5huang/dna_token/output_tokens/cache/csv/default-9aa68439a1bf4533/0.0.0/a43390c7ecea6519ff2ce9d10005c8750601c9e456069be5efbd2747df45f420/cache-b7e4e83b1e5bb0f0_00006_of_00008.arrow
186
- Process #8 will write at /home/n5huang/dna_token/output_tokens/cache/csv/default-9aa68439a1bf4533/0.0.0/a43390c7ecea6519ff2ce9d10005c8750601c9e456069be5efbd2747df45f420/cache-b7e4e83b1e5bb0f0_00007_of_00008.arrow
187
- 04/09/2026 02:43:41 - INFO - datasets.arrow_dataset - Process #8 will write at /home/n5huang/dna_token/output_tokens/cache/csv/default-9aa68439a1bf4533/0.0.0/a43390c7ecea6519ff2ce9d10005c8750601c9e456069be5efbd2747df45f420/cache-b7e4e83b1e5bb0f0_00007_of_00008.arrow
188
- Running tokenizer on dataset line_by_line (num_proc=8): 0%| | 0/982503 [00:00<?, ? examples/s]Spawning 8 processes
189
- 04/09/2026 02:43:41 - INFO - datasets.arrow_dataset - Spawning 8 processes
190
- Running tokenizer on dataset line_by_line (num_proc=8): 100%|██████████| 982503/982503 [02:32<00:00, 6449.24 examples/s]
191
- Concatenating 8 shards
192
- 04/09/2026 02:46:14 - INFO - datasets.arrow_dataset - Concatenating 8 shards
193
- Process #1 will write at /home/n5huang/dna_token/output_tokens/cache/csv/default-9aa68439a1bf4533/0.0.0/a43390c7ecea6519ff2ce9d10005c8750601c9e456069be5efbd2747df45f420/cache-e09c066770dc1f08_00000_of_00008.arrow
194
- 04/09/2026 02:46:14 - INFO - datasets.arrow_dataset - Process #1 will write at /home/n5huang/dna_token/output_tokens/cache/csv/default-9aa68439a1bf4533/0.0.0/a43390c7ecea6519ff2ce9d10005c8750601c9e456069be5efbd2747df45f420/cache-e09c066770dc1f08_00000_of_00008.arrow
195
- Process #2 will write at /home/n5huang/dna_token/output_tokens/cache/csv/default-9aa68439a1bf4533/0.0.0/a43390c7ecea6519ff2ce9d10005c8750601c9e456069be5efbd2747df45f420/cache-e09c066770dc1f08_00001_of_00008.arrow
196
- 04/09/2026 02:46:14 - INFO - datasets.arrow_dataset - Process #2 will write at /home/n5huang/dna_token/output_tokens/cache/csv/default-9aa68439a1bf4533/0.0.0/a43390c7ecea6519ff2ce9d10005c8750601c9e456069be5efbd2747df45f420/cache-e09c066770dc1f08_00001_of_00008.arrow
197
- Process #3 will write at /home/n5huang/dna_token/output_tokens/cache/csv/default-9aa68439a1bf4533/0.0.0/a43390c7ecea6519ff2ce9d10005c8750601c9e456069be5efbd2747df45f420/cache-e09c066770dc1f08_00002_of_00008.arrow
198
- 04/09/2026 02:46:14 - INFO - datasets.arrow_dataset - Process #3 will write at /home/n5huang/dna_token/output_tokens/cache/csv/default-9aa68439a1bf4533/0.0.0/a43390c7ecea6519ff2ce9d10005c8750601c9e456069be5efbd2747df45f420/cache-e09c066770dc1f08_00002_of_00008.arrow
199
- Process #4 will write at /home/n5huang/dna_token/output_tokens/cache/csv/default-9aa68439a1bf4533/0.0.0/a43390c7ecea6519ff2ce9d10005c8750601c9e456069be5efbd2747df45f420/cache-e09c066770dc1f08_00003_of_00008.arrow
200
- 04/09/2026 02:46:14 - INFO - datasets.arrow_dataset - Process #4 will write at /home/n5huang/dna_token/output_tokens/cache/csv/default-9aa68439a1bf4533/0.0.0/a43390c7ecea6519ff2ce9d10005c8750601c9e456069be5efbd2747df45f420/cache-e09c066770dc1f08_00003_of_00008.arrow
201
- Process #5 will write at /home/n5huang/dna_token/output_tokens/cache/csv/default-9aa68439a1bf4533/0.0.0/a43390c7ecea6519ff2ce9d10005c8750601c9e456069be5efbd2747df45f420/cache-e09c066770dc1f08_00004_of_00008.arrow
202
- 04/09/2026 02:46:14 - INFO - datasets.arrow_dataset - Process #5 will write at /home/n5huang/dna_token/output_tokens/cache/csv/default-9aa68439a1bf4533/0.0.0/a43390c7ecea6519ff2ce9d10005c8750601c9e456069be5efbd2747df45f420/cache-e09c066770dc1f08_00004_of_00008.arrow
203
- Process #6 will write at /home/n5huang/dna_token/output_tokens/cache/csv/default-9aa68439a1bf4533/0.0.0/a43390c7ecea6519ff2ce9d10005c8750601c9e456069be5efbd2747df45f420/cache-e09c066770dc1f08_00005_of_00008.arrow
204
- 04/09/2026 02:46:14 - INFO - datasets.arrow_dataset - Process #6 will write at /home/n5huang/dna_token/output_tokens/cache/csv/default-9aa68439a1bf4533/0.0.0/a43390c7ecea6519ff2ce9d10005c8750601c9e456069be5efbd2747df45f420/cache-e09c066770dc1f08_00005_of_00008.arrow
205
- Process #7 will write at /home/n5huang/dna_token/output_tokens/cache/csv/default-9aa68439a1bf4533/0.0.0/a43390c7ecea6519ff2ce9d10005c8750601c9e456069be5efbd2747df45f420/cache-e09c066770dc1f08_00006_of_00008.arrow
206
- 04/09/2026 02:46:14 - INFO - datasets.arrow_dataset - Process #7 will write at /home/n5huang/dna_token/output_tokens/cache/csv/default-9aa68439a1bf4533/0.0.0/a43390c7ecea6519ff2ce9d10005c8750601c9e456069be5efbd2747df45f420/cache-e09c066770dc1f08_00006_of_00008.arrow
207
- Process #8 will write at /home/n5huang/dna_token/output_tokens/cache/csv/default-9aa68439a1bf4533/0.0.0/a43390c7ecea6519ff2ce9d10005c8750601c9e456069be5efbd2747df45f420/cache-e09c066770dc1f08_00007_of_00008.arrow
208
- 04/09/2026 02:46:14 - INFO - datasets.arrow_dataset - Process #8 will write at /home/n5huang/dna_token/output_tokens/cache/csv/default-9aa68439a1bf4533/0.0.0/a43390c7ecea6519ff2ce9d10005c8750601c9e456069be5efbd2747df45f420/cache-e09c066770dc1f08_00007_of_00008.arrow
209
- Running tokenizer on dataset line_by_line (num_proc=8): 0%| | 0/109173 [00:00<?, ? examples/s]Spawning 8 processes
210
- 04/09/2026 02:46:14 - INFO - datasets.arrow_dataset - Spawning 8 processes
211
- Running tokenizer on dataset line_by_line (num_proc=8): 100%|██████████| 109173/109173 [00:17<00:00, 6162.84 examples/s]
212
- Concatenating 8 shards
213
- 04/09/2026 02:46:31 - INFO - datasets.arrow_dataset - Concatenating 8 shards
214
- [INFO|trainer.py:544] 2026-04-09 02:46:37,686 >> max_steps is given, it will override any value given in num_train_epochs
215
- [INFO|trainer.py:2066] 2026-04-09 02:46:37,688 >> Loading model from /home/n5huang/dna_token/pretrain/models/len2_5120/checkpoint-100000.
216
- [WARNING|trainer.py:2231] 2026-04-09 02:46:37,942 >> There were missing keys in the checkpoint model loaded: ['cls.predictions.decoder.weight', 'cls.predictions.decoder.bias'].
217
- [INFO|trainer.py:738] 2026-04-09 02:46:38,250 >> The following columns in the training set don't have a corresponding argument in `BertForMaskedLM.forward` and have been ignored: special_tokens_mask. If special_tokens_mask are not expected by `BertForMaskedLM.forward`, you can safely ignore this message.
218
- [INFO|trainer.py:1723] 2026-04-09 02:46:38,922 >> ***** Running training *****
219
- [INFO|trainer.py:1724] 2026-04-09 02:46:38,923 >> Num examples = 982,503
220
- [INFO|trainer.py:1725] 2026-04-09 02:46:38,923 >> Num Epochs = 10
221
- [INFO|trainer.py:1726] 2026-04-09 02:46:38,924 >> Instantaneous batch size per device = 96
222
- [INFO|trainer.py:1729] 2026-04-09 02:46:38,924 >> Total train batch size (w. parallel, distributed & accumulation) = 96
223
- [INFO|trainer.py:1730] 2026-04-09 02:46:38,925 >> Gradient Accumulation steps = 1
224
- [INFO|trainer.py:1731] 2026-04-09 02:46:38,925 >> Total optimization steps = 100,000
225
- [INFO|trainer.py:1732] 2026-04-09 02:46:38,926 >> Number of trainable parameters = 89,980,160
226
- [INFO|trainer.py:1752] 2026-04-09 02:46:38,927 >> Continuing training from checkpoint, will skip to saved global_step
227
- [INFO|trainer.py:1753] 2026-04-09 02:46:38,927 >> Continuing training from epoch 9
228
- [INFO|trainer.py:1754] 2026-04-09 02:46:38,927 >> Continuing training from global step 100000
229
- [INFO|trainer.py:1756] 2026-04-09 02:46:38,927 >> Will skip the first 9 epochs then the first 7885 batches in the first epoch.
230
- [INFO|integration_utils.py:718] 2026-04-09 02:46:38,928 >> Automatic Weights & Biases logging enabled, to disable set os.environ["WANDB_DISABLED"] = "true"
231
- 0%| | 0/100000 [00:00<?, ?it/s][WARNING|logging.py:314] 2026-04-09 02:46:40,535 >> You're using a PreTrainedTokenizerFast tokenizer. Please note that with a fast tokenizer, using the `__call__` method is faster than using a method to encode the text followed by a call to the `pad` method to get a padded encoding.
232
- [INFO|trainer.py:2302] 2026-04-09 02:46:41,283 >> Didn't find an RNG file, if you are resuming a training that was launched in a distributed fashion, reproducibility is not guaranteed.
233
- 100001it [00:04, 20981.36it/s] [INFO|trainer.py:1955] 2026-04-09 02:46:43,723 >>
234
-
235
- Training completed. Do not forget to share your model on huggingface.co/models =)
236
-
237
-
238
- 100001it [00:04, 20868.88it/s]
239
- {'train_runtime': 4.7982, 'train_samples_per_second': 2000761.461, 'train_steps_per_second': 20841.265, 'train_loss': 4.9309695196505064e-05, 'epoch': 9.77}
240
- [INFO|trainer.py:2881] 2026-04-09 02:46:43,749 >> Saving model checkpoint to /home/n5huang/dna_token/pretrain/models/len2_5120
241
- [INFO|configuration_utils.py:461] 2026-04-09 02:46:43,751 >> Configuration saved in /home/n5huang/dna_token/pretrain/models/len2_5120/config.json
242
- [INFO|configuration_utils.py:564] 2026-04-09 02:46:43,752 >> Configuration saved in /home/n5huang/dna_token/pretrain/models/len2_5120/generation_config.json
243
- [INFO|modeling_utils.py:2193] 2026-04-09 02:46:44,597 >> Model weights saved in /home/n5huang/dna_token/pretrain/models/len2_5120/pytorch_model.bin
244
- ***** train metrics *****
245
- epoch = 9.77
246
- train_loss = 0.0
247
- train_runtime = 0:00:04.79
248
- train_samples = 982503
249
- train_samples_per_second = 2000761.461
250
- train_steps_per_second = 20841.265
251
- 04/09/2026 02:46:44 - INFO - __main__ - *** Evaluate ***
252
- [INFO|trainer.py:738] 2026-04-09 02:46:44,604 >> The following columns in the evaluation set don't have a corresponding argument in `BertForMaskedLM.forward` and have been ignored: special_tokens_mask. If special_tokens_mask are not expected by `BertForMaskedLM.forward`, you can safely ignore this message.
253
- [INFO|trainer.py:3158] 2026-04-09 02:46:44,623 >> ***** Running Evaluation *****
254
- [INFO|trainer.py:3160] 2026-04-09 02:46:44,623 >> Num examples = 109173
255
- [INFO|trainer.py:3163] 2026-04-09 02:46:44,623 >> Batch size = 96
256
- 100%|██████████| 1138/1138 [20:09<00:00, 1.06s/it]
257
- ***** eval metrics *****
258
- epoch = 9.77
259
- eval_accuracy = 0.2987
260
- eval_loss = 4.9606
261
- eval_runtime = 0:20:10.53
262
- eval_samples = 109173
263
- eval_samples_per_second = 90.186
264
- eval_step = 100001
265
- eval_steps_per_second = 0.94
266
- perplexity = 142.6779
267
- [INFO|modelcard.py:452] 2026-04-09 03:06:55,252 >> Dropping the following result as it does not have all the necessary fields:
268
- {'task': {'name': 'Masked Language Modeling', 'type': 'fill-mask'}, 'metrics': [{'name': 'Accuracy', 'type': 'accuracy', 'value': 0.2987349408299944}]}
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
pretrain_tokens/wandb/run-20260409_024256-4yonu3x2/files/requirements.txt DELETED
@@ -1,148 +0,0 @@
1
- fonttools==4.60.1
2
- mpmath==1.3.0
3
- httpx==0.28.1
4
- yarl==1.22.0
5
- attrs==25.4.0
6
- pydantic_core==2.33.2
7
- nvidia-cusparse-cu12==12.5.8.93
8
- GitPython==3.1.45
9
- PyQt6_sip==13.10.2
10
- nvidia-nvtx-cu12==12.8.90
11
- nest_asyncio==1.6.0
12
- cffi==2.0.0
13
- tqdm==4.67.1
14
- tzdata==2025.2
15
- dill==0.4.0
16
- cycler==0.11.0
17
- aiohttp==3.13.2
18
- pydantic==2.11.7
19
- pickleshare==0.7.5
20
- nvidia-cusparselt-cu12==0.7.1
21
- contourpy==1.2.1
22
- platformdirs==4.3.8
23
- importlib_metadata==8.7.0
24
- biopython==1.85
25
- idna==3.11
26
- stack_data==0.6.3
27
- pycparser==2.23
28
- python-dateutil==2.9.0.post0
29
- wheel==0.45.1
30
- psutil==7.0.0
31
- importlib_resources==6.5.2
32
- pyparsing==3.2.0
33
- exceptiongroup==1.3.0
34
- exceptiongroup==1.3.1
35
- gitdb==4.0.12
36
- pip==25.3
37
- pillow==11.3.0
38
- jupyter_core==5.8.1
39
- transformers==4.29.2
40
- matplotlib-inline==0.1.7
41
- packaging==25.0
42
- nvidia-nccl-cu12==2.27.3
43
- debugpy==1.8.16
44
- ipython==8.18.1
45
- anyio==4.12.0
46
- prompt_toolkit==3.0.51
47
- mkl_fft==1.3.11
48
- httpcore==1.0.9
49
- Jinja2==3.1.6
50
- ply==3.11
51
- zipp==3.23.0
52
- setproctitle==1.3.6
53
- docker-pycreds==0.4.0
54
- nvidia-cuda-nvrtc-cu12==12.8.93
55
- urllib3==2.5.0
56
- kiwisolver==1.4.4
57
- nvidia-curand-cu12==10.3.9.90
58
- llvmlite==0.43.0
59
- six==1.17.0
60
- frozenlist==1.8.0
61
- wcwidth==0.2.13
62
- numexpr==2.10.1
63
- click==8.1.8
64
- multiprocess==0.70.18
65
- threadpoolctl==3.6.0
66
- typing_extensions==4.15.0
67
- decorator==5.2.1
68
- sip==6.7.12
69
- pure_eval==0.2.3
70
- async-timeout==5.0.1
71
- Pygments==2.19.2
72
- mkl-service==2.4.0
73
- transformers==4.35.2
74
- numba==0.60.0
75
- pyzmq==27.0.2
76
- mkl_random==1.2.8
77
- ptyprocess==0.7.0
78
- nvidia-cuda-cupti-cu12==12.8.90
79
- charset-normalizer==3.4.4
80
- nvidia-cublas-cu12==12.8.4.1
81
- PyQt5_sip==12.13.0
82
- Bottleneck==1.4.2
83
- networkx==3.2.1
84
- PySocks==1.7.1
85
- pysam==0.9.1
86
- tornado==6.5.2
87
- pandas==2.3.3
88
- smmap==5.0.2
89
- PyQt5==5.15.10
90
- nvidia-cufft-cu12==11.3.3.83
91
- safetensors==0.7.0
92
- requests==2.32.5
93
- pytz==2025.2
94
- fsspec==2025.7.0
95
- certifi==2025.10.5
96
- sentry-sdk==2.35.0
97
- parso==0.8.4
98
- aiosignal==1.4.0
99
- traitlets==5.14.3
100
- hf-xet==1.1.8
101
- nvidia-cudnn-cu12==9.10.2.21
102
- accelerate==0.25.0
103
- eval_type_backport==0.2.2
104
- datasets==4.4.1
105
- huggingface_hub==0.34.4
106
- wandb==0.23.1
107
- tomli==2.2.1
108
- comm==0.2.3
109
- executing==2.2.0
110
- PyYAML==6.0.2
111
- scipy==1.13.1
112
- pexpect==4.9.0
113
- matplotlib==3.9.2
114
- annotated-types==0.7.0
115
- asttokens==3.0.0
116
- tokenizers==0.15.2
117
- nvidia-cufile-cu12==1.13.1.3
118
- appdirs==1.4.4
119
- h11==0.16.0
120
- numpy==2.0.2
121
- jupyter_client==8.6.3
122
- joblib==1.5.1
123
- joblib==1.5.3
124
- jedi==0.19.2
125
- MarkupSafe==3.0.3
126
- nvidia-nvjitlink-cu12==12.8.93
127
- pyarrow==21.0.0
128
- torch==2.8.0
129
- protobuf==3.20.3
130
- propcache==0.4.1
131
- multidict==6.7.0
132
- nvidia-cusolver-cu12==11.7.3.90
133
- umap-learn==0.5.9.post2
134
- ipykernel==6.30.1
135
- triton==3.4.0
136
- sympy==1.14.0
137
- scikit-learn==1.6.1
138
- brotlicffi==1.0.9.2
139
- xxhash==3.6.0
140
- seaborn==0.13.2
141
- pynndescent==0.5.13
142
- regex==2025.11.3
143
- typing-inspection==0.4.1
144
- evaluate==0.4.6
145
- nvidia-cuda-runtime-cu12==12.8.90
146
- filelock==3.17.0
147
- aiohappyeyeballs==2.6.1
148
- setuptools==80.9.0
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
pretrain_tokens/wandb/run-20260409_024256-4yonu3x2/files/wandb-metadata.json DELETED
@@ -1,149 +0,0 @@
1
- {
2
- "os": "Linux-5.15.0-72-generic-x86_64-with-glibc2.35",
3
- "python": "CPython 3.9.18",
4
- "startedAt": "2026-04-09T02:42:56.385921Z",
5
- "args": [
6
- "--output_dir",
7
- "/home/n5huang/dna_token/pretrain/models/len2_5120",
8
- "--model_type",
9
- "bert",
10
- "--tokenizer_name",
11
- "/home/n5huang/dna_token/tokenizer_evaluation/merge_bpe/vocab_5120/merge_tokenizer_unigram_len2.json",
12
- "--config_name",
13
- "/home/n5huang/dna_token/pretrain/models/len2_5120/config.json",
14
- "--project_name",
15
- "token_eval_len2_5120",
16
- "--do_train",
17
- "True",
18
- "--model_max_length",
19
- "512",
20
- "--max_seq_length",
21
- "512",
22
- "--line_by_line",
23
- "True",
24
- "--pad_to_max_length",
25
- "True",
26
- "--train_file",
27
- "/home/n5huang/dna_token/output_tokens/merge_bpe_5120_allchr_all_tokenized_train_chrOnly.tsv",
28
- "--validation_file",
29
- "/home/n5huang/dna_token/output_tokens/merge_bpe_5120_allchr_all_tokenized_val_chrOnly.tsv",
30
- "--cache_dir",
31
- "/home/n5huang/dna_token/output_tokens/cache",
32
- "--use_fast_tokenizer",
33
- "True",
34
- "--do_eval",
35
- "True",
36
- "--gradient_accumulation_steps",
37
- "1",
38
- "--per_device_train_batch_size",
39
- "96",
40
- "--per_device_eval_batch_size",
41
- "96",
42
- "--save_steps",
43
- "1000",
44
- "--save_total_limit",
45
- "10",
46
- "--max_steps",
47
- "100000",
48
- "--logging_steps",
49
- "1000",
50
- "--learning_rate",
51
- "4e-5",
52
- "--adam_epsilon",
53
- "1e-6",
54
- "--weight_decay",
55
- "0.01",
56
- "--adam_beta1",
57
- "0.9",
58
- "--adam_beta2",
59
- "0.98",
60
- "--mlm_probability",
61
- "0.15",
62
- "--warmup_steps",
63
- "10000",
64
- "--seed",
65
- "42",
66
- "--preprocessing_num_workers",
67
- "8",
68
- "--resume_from_checkpoint",
69
- "/home/n5huang/dna_token/pretrain/models/len2_5120/checkpoint-100000"
70
- ],
71
- "program": "/home/n5huang/dna-tokenizer/BPE_merge/run_mlm_200k.py",
72
- "email": "mtapiapacheco@ucsd.edu",
73
- "root": "/data/n5huang/dna_token/output_tokens",
74
- "host": "sn4622116170",
75
- "executable": "/home/n5huang/miniconda3/envs/bpe/bin/python",
76
- "cpu_count": 128,
77
- "cpu_count_logical": 255,
78
- "gpu": "NVIDIA A100 80GB PCIe",
79
- "gpu_count": 8,
80
- "disk": {
81
- "/": {
82
- "total": "1876350566400",
83
- "used": "405230526464"
84
- }
85
- },
86
- "memory": {
87
- "total": "4316310355968"
88
- },
89
- "gpu_nvidia": [
90
- {
91
- "name": "NVIDIA A100 80GB PCIe",
92
- "memoryTotal": "85899345920",
93
- "cudaCores": 6912,
94
- "architecture": "Ampere",
95
- "uuid": "GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3"
96
- },
97
- {
98
- "name": "NVIDIA A100 80GB PCIe",
99
- "memoryTotal": "85899345920",
100
- "cudaCores": 6912,
101
- "architecture": "Ampere",
102
- "uuid": "GPU-054a4d72-8520-5e4a-5cd3-7519a0966809"
103
- },
104
- {
105
- "name": "NVIDIA A100 80GB PCIe",
106
- "memoryTotal": "85899345920",
107
- "cudaCores": 6912,
108
- "architecture": "Ampere",
109
- "uuid": "GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab"
110
- },
111
- {
112
- "name": "NVIDIA A100 80GB PCIe",
113
- "memoryTotal": "85899345920",
114
- "cudaCores": 6912,
115
- "architecture": "Ampere",
116
- "uuid": "GPU-a18369da-b15a-c8af-72f1-7f6272e479af"
117
- },
118
- {
119
- "name": "NVIDIA A100 80GB PCIe",
120
- "memoryTotal": "85899345920",
121
- "cudaCores": 6912,
122
- "architecture": "Ampere",
123
- "uuid": "GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10"
124
- },
125
- {
126
- "name": "NVIDIA A100 80GB PCIe",
127
- "memoryTotal": "85899345920",
128
- "cudaCores": 6912,
129
- "architecture": "Ampere",
130
- "uuid": "GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e"
131
- },
132
- {
133
- "name": "NVIDIA A100 80GB PCIe",
134
- "memoryTotal": "85899345920",
135
- "cudaCores": 6912,
136
- "architecture": "Ampere",
137
- "uuid": "GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0"
138
- },
139
- {
140
- "name": "NVIDIA A100 80GB PCIe",
141
- "memoryTotal": "85899345920",
142
- "cudaCores": 6912,
143
- "architecture": "Ampere",
144
- "uuid": "GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044"
145
- }
146
- ],
147
- "cudaVersion": "12.2",
148
- "writerId": "8xva522u4d798tgf5m4gfomp910saafd"
149
- }
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
pretrain_tokens/wandb/run-20260409_024256-4yonu3x2/files/wandb-summary.json DELETED
@@ -1 +0,0 @@
1
- {"train/train_steps_per_second":20841.265,"eval_samples":109173,"_wandb":{"runtime":1437},"_timestamp":1.7757040152510617e+09,"train/total_flos":2.020816249744366e+19,"train/train_samples_per_second":2.000761461e+06,"eval_runtime":1210.5316,"epoch":9.77,"train/epoch":9.77,"eval/accuracy":0.2987349408299944,"_step":3,"eval_samples_per_second":90.186,"step":100001,"eval/loss":4.960589408874512,"train/train_loss":4.9309695196505064e-05,"train/global_step":100001,"eval_steps_per_second":0.94,"eval/samples_per_second":90.186,"eval/steps_per_second":0.94,"eval/runtime":1210.5316,"_runtime":1437,"train/train_runtime":4.7982,"eval_accuracy":0.2987349408299944,"eval_step":100001,"accuracy":0.2987349408299944,"perplexity":142.6778667193516,"eval_loss":4.960589408874512,"eval/step":100001}
 
 
pretrain_tokens/wandb/run-20260409_024256-4yonu3x2/logs/debug-core.log DELETED
@@ -1,14 +0,0 @@
1
- {"time":"2026-04-09T02:42:56.481790454Z","level":"INFO","msg":"main: starting server","port-filename":"/tmp/tmpyfmhka5c/port-3530706.txt","pid":3530706,"log-level":0,"disable-analytics":false,"shutdown-on-parent-exit":false,"enable-dcgm-profiling":false}
2
- {"time":"2026-04-09T02:42:56.482516143Z","level":"INFO","msg":"server: will exit if parent process dies","ppid":3530706}
3
- {"time":"2026-04-09T02:42:56.482525493Z","level":"INFO","msg":"server: accepting connections","addr":{"Name":"/tmp/wandb-3530706-3530948-3197655517/socket","Net":"unix"}}
4
- {"time":"2026-04-09T02:42:56.666452772Z","level":"INFO","msg":"connection: ManageConnectionData: new connection created","id":"1(@)"}
5
- {"time":"2026-04-09T02:42:56.697519602Z","level":"INFO","msg":"handleInformInit: received","streamId":"4yonu3x2","id":"1(@)"}
6
- {"time":"2026-04-09T02:42:57.031667181Z","level":"INFO","msg":"handleInformInit: stream started","streamId":"4yonu3x2","id":"1(@)"}
7
- {"time":"2026-04-09T03:06:55.25564144Z","level":"INFO","msg":"handleInformTeardown: server teardown initiated","id":"1(@)"}
8
- {"time":"2026-04-09T03:06:55.25571027Z","level":"INFO","msg":"connection: closing","id":"1(@)"}
9
- {"time":"2026-04-09T03:06:55.25574761Z","level":"INFO","msg":"server is shutting down"}
10
- {"time":"2026-04-09T03:06:55.257595438Z","level":"INFO","msg":"connection: closed successfully","id":"1(@)"}
11
- {"time":"2026-04-09T03:06:55.257720888Z","level":"INFO","msg":"server: listener closed","addr":{"Name":"/tmp/wandb-3530706-3530948-3197655517/socket","Net":"unix"}}
12
- {"time":"2026-04-09T03:06:55.887591019Z","level":"INFO","msg":"handleInformTeardown: server shutdown complete","id":"1(@)"}
13
- {"time":"2026-04-09T03:06:55.887645599Z","level":"INFO","msg":"connection: ManageConnectionData: connection closed","id":"1(@)"}
14
- {"time":"2026-04-09T03:06:55.887670279Z","level":"INFO","msg":"server is closed"}
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
pretrain_tokens/wandb/run-20260409_024256-4yonu3x2/logs/debug-internal.log DELETED
@@ -1,11 +0,0 @@
1
- {"time":"2026-04-09T02:42:56.697651042Z","level":"INFO","msg":"stream: starting","core version":"0.23.1"}
2
- {"time":"2026-04-09T02:42:57.031332971Z","level":"INFO","msg":"stream: created new stream","id":"4yonu3x2"}
3
- {"time":"2026-04-09T02:42:57.031508781Z","level":"INFO","msg":"handler: started","stream_id":"4yonu3x2"}
4
- {"time":"2026-04-09T02:42:57.031644811Z","level":"INFO","msg":"stream: started","id":"4yonu3x2"}
5
- {"time":"2026-04-09T02:42:57.031662631Z","level":"INFO","msg":"sender: started","stream_id":"4yonu3x2"}
6
- {"time":"2026-04-09T02:42:57.031667791Z","level":"INFO","msg":"writer: started","stream_id":"4yonu3x2"}
7
- {"time":"2026-04-09T03:06:55.25572892Z","level":"INFO","msg":"stream: closing","id":"4yonu3x2"}
8
- {"time":"2026-04-09T03:06:55.662561763Z","level":"INFO","msg":"fileTransfer: Close: file transfer manager closed"}
9
- {"time":"2026-04-09T03:06:55.879353875Z","level":"INFO","msg":"handler: closed","stream_id":"4yonu3x2"}
10
- {"time":"2026-04-09T03:06:55.879544965Z","level":"INFO","msg":"sender: closed","stream_id":"4yonu3x2"}
11
- {"time":"2026-04-09T03:06:55.879567205Z","level":"INFO","msg":"stream: closed","id":"4yonu3x2"}
 
 
 
 
 
 
 
 
 
 
 
 
pretrain_tokens/wandb/run-20260409_024256-4yonu3x2/logs/debug.log DELETED
@@ -1,27 +0,0 @@
1
- 2026-04-09 02:42:56,388 INFO MainThread:3530706 [wandb_setup.py:_flush():80] Current SDK version is 0.23.1
2
- 2026-04-09 02:42:56,388 INFO MainThread:3530706 [wandb_setup.py:_flush():80] Configure stats pid to 3530706
3
- 2026-04-09 02:42:56,388 INFO MainThread:3530706 [wandb_setup.py:_flush():80] Loading settings from /home/n5huang/.config/wandb/settings
4
- 2026-04-09 02:42:56,389 INFO MainThread:3530706 [wandb_setup.py:_flush():80] Loading settings from /data/n5huang/dna_token/output_tokens/wandb/settings
5
- 2026-04-09 02:42:56,389 INFO MainThread:3530706 [wandb_setup.py:_flush():80] Loading settings from environment variables
6
- 2026-04-09 02:42:56,389 INFO MainThread:3530706 [wandb_init.py:setup_run_log_directory():714] Logging user logs to /data/n5huang/dna_token/output_tokens/wandb/run-20260409_024256-4yonu3x2/logs/debug.log
7
- 2026-04-09 02:42:56,389 INFO MainThread:3530706 [wandb_init.py:setup_run_log_directory():715] Logging internal logs to /data/n5huang/dna_token/output_tokens/wandb/run-20260409_024256-4yonu3x2/logs/debug-internal.log
8
- 2026-04-09 02:42:56,389 INFO MainThread:3530706 [wandb_init.py:init():841] calling init triggers
9
- 2026-04-09 02:42:56,389 INFO MainThread:3530706 [wandb_init.py:init():846] wandb.init called with sweep_config: {}
10
- config: {'_wandb': {}}
11
- 2026-04-09 02:42:56,389 INFO MainThread:3530706 [wandb_init.py:init():889] starting backend
12
- 2026-04-09 02:42:56,666 INFO MainThread:3530706 [wandb_init.py:init():892] sending inform_init request
13
- 2026-04-09 02:42:56,695 INFO MainThread:3530706 [wandb_init.py:init():900] backend started and connected
14
- 2026-04-09 02:42:56,701 INFO MainThread:3530706 [wandb_init.py:init():970] updated telemetry
15
- 2026-04-09 02:42:56,702 INFO MainThread:3530706 [wandb_init.py:init():994] communicating run to backend with 90.0 second timeout
16
- 2026-04-09 02:42:57,403 INFO MainThread:3530706 [wandb_init.py:init():1041] starting run threads in backend
17
- 2026-04-09 02:42:57,510 INFO MainThread:3530706 [wandb_run.py:_console_start():2521] atexit reg
18
- 2026-04-09 02:42:57,511 INFO MainThread:3530706 [wandb_run.py:_redirect():2369] redirect: wrap_raw
19
- 2026-04-09 02:42:57,511 INFO MainThread:3530706 [wandb_run.py:_redirect():2438] Wrapping output streams.
20
- 2026-04-09 02:42:57,511 INFO MainThread:3530706 [wandb_run.py:_redirect():2461] Redirects installed.
21
- 2026-04-09 02:42:57,515 INFO MainThread:3530706 [wandb_init.py:init():1081] run started, returning control to user process
22
- 2026-04-09 02:42:57,824 INFO MainThread:3530706 [wandb_run.py:_config_callback():1396] config_cb None None {'output_dir': '/home/n5huang/dna_token/pretrain/models/len2_5120', 'overwrite_output_dir': False, 'do_train': True, 'do_eval': True, 'do_predict': False, 'evaluation_strategy': 'NO', 'prediction_loss_only': False, 'per_device_train_batch_size': 96, 'per_device_eval_batch_size': 96, 'per_gpu_train_batch_size': None, 'per_gpu_eval_batch_size': None, 'gradient_accumulation_steps': 1, 'eval_accumulation_steps': None, 'eval_delay': 0, 'learning_rate': 4e-05, 'weight_decay': 0.01, 'adam_beta1': 0.9, 'adam_beta2': 0.98, 'adam_epsilon': 1e-06, 'max_grad_norm': 1.0, 'num_train_epochs': 3.0, 'max_steps': 100000, 'lr_scheduler_type': 'LINEAR', 'warmup_ratio': 0.0, 'warmup_steps': 10000, 'log_level': 'passive', 'log_level_replica': 'warning', 'log_on_each_node': True, 'logging_dir': '/home/n5huang/dna_token/pretrain/models/len2_5120/runs/Apr09_02-42-57_sn4622116170', 'logging_strategy': 'STEPS', 'logging_first_step': False, 'logging_steps': 1000, 'logging_nan_inf_filter': True, 'save_strategy': 'STEPS', 'save_steps': 1000, 'save_total_limit': 10, 'save_safetensors': True, 'save_on_each_node': False, 'no_cuda': False, 'use_cpu': False, 'use_mps_device': False, 'seed': 42, 'data_seed': None, 'jit_mode_eval': False, 'use_ipex': False, 'bf16': False, 'fp16': False, 'fp16_opt_level': 'O1', 'half_precision_backend': 'auto', 'bf16_full_eval': False, 'fp16_full_eval': False, 'tf32': None, 'local_rank': 0, 'ddp_backend': None, 'tpu_num_cores': None, 'tpu_metrics_debug': False, 'debug': [], 'dataloader_drop_last': False, 'eval_steps': None, 'dataloader_num_workers': 0, 'past_index': -1, 'run_name': '/home/n5huang/dna_token/pretrain/models/len2_5120', 'disable_tqdm': False, 'remove_unused_columns': True, 'label_names': None, 'load_best_model_at_end': False, 'metric_for_best_model': None, 'greater_is_better': None, 'ignore_data_skip': False, 'fsdp': [], 'fsdp_min_num_params': 0, 'fsdp_config': {'min_num_params': 0, 'xla': False, 'xla_fsdp_grad_ckpt': False}, 'fsdp_transformer_layer_cls_to_wrap': None, 'deepspeed': None, 'label_smoothing_factor': 0.0, 'optim': 'ADAMW_TORCH', 'optim_args': None, 'adafactor': False, 'group_by_length': False, 'length_column_name': 'length', 'report_to': ['wandb'], 'ddp_find_unused_parameters': None, 'ddp_bucket_cap_mb': None, 'ddp_broadcast_buffers': None, 'dataloader_pin_memory': True, 'skip_memory_metrics': True, 'use_legacy_prediction_loop': False, 'push_to_hub': False, 'resume_from_checkpoint': '/home/n5huang/dna_token/pretrain/models/len2_5120/checkpoint-100000', 'hub_model_id': None, 'hub_strategy': 'EVERY_SAVE', 'hub_token': None, 'hub_private_repo': False, 'hub_always_push': False, 'gradient_checkpointing': False, 'gradient_checkpointing_kwargs': None, 'include_inputs_for_metrics': False, 'fp16_backend': 'auto', 'push_to_hub_model_id': None, 'push_to_hub_organization': None, 'push_to_hub_token': None, 'mp_parameters': '', 'auto_find_batch_size': False, 'full_determinism': False, 'torchdynamo': None, 'ray_scope': 'last', 'ddp_timeout': 1800, 'torch_compile': False, 'torch_compile_backend': None, 'torch_compile_mode': None, 'dispatch_batches': None, 'split_batches': False, 'include_tokens_per_second': False, 'neftune_noise_alpha': None, 'distributed_state': 'Distributed environment: NO\nNum processes: 1\nProcess index: 0\nLocal process index: 0\nDevice: cuda\n', '_n_gpu': 1, '__cached__setup_devices': 'cuda:0', 'deepspeed_plugin': None}
23
- 2026-04-09 02:42:57,826 INFO MainThread:3530706 [wandb_run.py:_config_callback():1396] config_cb None None {'model_name_or_path': None, 'model_type': 'bert', 'config_overrides': None, 'config_name': '/home/n5huang/dna_token/pretrain/models/len2_5120/config.json', 'tokenizer_name': '/home/n5huang/dna_token/tokenizer_evaluation/merge_bpe/vocab_5120/merge_tokenizer_unigram_len2.json', 'cache_dir': '/home/n5huang/dna_token/output_tokens/cache', 'use_fast_tokenizer': True, 'model_revision': 'main', 'token': None, 'trust_remote_code': False, 'torch_dtype': None, 'low_cpu_mem_usage': False, 'model_max_length': 512}
24
- 2026-04-09 02:42:57,826 INFO MainThread:3530706 [wandb_run.py:_config_callback():1396] config_cb None None {'dataset_name': None, 'dataset_config_name': None, 'train_file': '/home/n5huang/dna_token/output_tokens/merge_bpe_5120_allchr_all_tokenized_train_chrOnly.tsv', 'validation_file': '/home/n5huang/dna_token/output_tokens/merge_bpe_5120_allchr_all_tokenized_val_chrOnly.tsv', 'overwrite_cache': False, 'validation_split_percentage': 5, 'max_seq_length': 512, 'preprocessing_num_workers': 8, 'mlm_probability': 0.15, 'line_by_line': True, 'pad_to_max_length': True, 'max_train_samples': None, 'max_eval_samples': None, 'project_name': 'token_eval_len2_5120', 'streaming': False}
25
- 2026-04-09 02:46:38,931 INFO MainThread:3530706 [wandb_run.py:_config_callback():1396] config_cb None None {'return_dict': True, 'output_hidden_states': False, 'output_attentions': False, 'torchscript': False, 'torch_dtype': 'float32', 'use_bfloat16': False, 'tf_legacy_loss': False, 'pruned_heads': {}, 'tie_word_embeddings': True, 'is_encoder_decoder': False, 'is_decoder': False, 'cross_attention_hidden_size': None, 'add_cross_attention': False, 'tie_encoder_decoder': False, 'max_length': 512, 'min_length': 0, 'do_sample': False, 'early_stopping': False, 'num_beams': 1, 'num_beam_groups': 1, 'diversity_penalty': 0.0, 'temperature': 1.0, 'top_k': 50, 'top_p': 1.0, 'typical_p': 1.0, 'repetition_penalty': 1.0, 'length_penalty': 1.0, 'no_repeat_ngram_size': 0, 'encoder_no_repeat_ngram_size': 0, 'bad_words_ids': None, 'num_return_sequences': 1, 'chunk_size_feed_forward': 0, 'output_scores': False, 'return_dict_in_generate': False, 'forced_bos_token_id': None, 'forced_eos_token_id': None, 'remove_invalid_values': False, 'exponential_decay_length_penalty': None, 'suppress_tokens': None, 'begin_suppress_tokens': None, 'architectures': ['BertForMaskedLM'], 'finetuning_task': None, 'id2label': {0: 'LABEL_0', 1: 'LABEL_1'}, 'label2id': {'LABEL_0': 0, 'LABEL_1': 1}, 'tokenizer_class': None, 'prefix': None, 'bos_token_id': None, 'pad_token_id': 0, 'eos_token_id': None, 'sep_token_id': None, 'decoder_start_token_id': None, 'task_specific_params': None, 'problem_type': None, '_name_or_path': '', 'transformers_version': '4.35.2', 'model_type': 'bert', 'vocab_size': 5120, 'hidden_size': 768, 'num_hidden_layers': 12, 'num_attention_heads': 12, 'hidden_act': 'gelu', 'intermediate_size': 3072, 'hidden_dropout_prob': 0.1, 'attention_probs_dropout_prob': 0.1, 'max_position_embeddings': 512, 'type_vocab_size': 2, 'initializer_range': 0.02, 'layer_norm_eps': 1e-12, 'position_embedding_type': 'absolute', 'use_cache': True, 'classifier_dropout': None, 'output_dir': '/home/n5huang/dna_token/pretrain/models/len2_5120', 'overwrite_output_dir': False, 'do_train': True, 'do_eval': True, 'do_predict': False, 'evaluation_strategy': 'no', 'prediction_loss_only': False, 'per_device_train_batch_size': 96, 'per_device_eval_batch_size': 96, 'per_gpu_train_batch_size': None, 'per_gpu_eval_batch_size': None, 'gradient_accumulation_steps': 1, 'eval_accumulation_steps': None, 'eval_delay': 0, 'learning_rate': 4e-05, 'weight_decay': 0.01, 'adam_beta1': 0.9, 'adam_beta2': 0.98, 'adam_epsilon': 1e-06, 'max_grad_norm': 1.0, 'num_train_epochs': 3.0, 'max_steps': 100000, 'lr_scheduler_type': 'linear', 'warmup_ratio': 0.0, 'warmup_steps': 10000, 'log_level': 'passive', 'log_level_replica': 'warning', 'log_on_each_node': True, 'logging_dir': '/home/n5huang/dna_token/pretrain/models/len2_5120/runs/Apr09_02-42-57_sn4622116170', 'logging_strategy': 'steps', 'logging_first_step': False, 'logging_steps': 1000, 'logging_nan_inf_filter': True, 'save_strategy': 'steps', 'save_steps': 1000, 'save_total_limit': 10, 'save_safetensors': True, 'save_on_each_node': False, 'no_cuda': False, 'use_cpu': False, 'use_mps_device': False, 'seed': 42, 'data_seed': None, 'jit_mode_eval': False, 'use_ipex': False, 'bf16': False, 'fp16': False, 'fp16_opt_level': 'O1', 'half_precision_backend': 'auto', 'bf16_full_eval': False, 'fp16_full_eval': False, 'tf32': None, 'local_rank': 0, 'ddp_backend': None, 'tpu_num_cores': None, 'tpu_metrics_debug': False, 'debug': [], 'dataloader_drop_last': False, 'eval_steps': None, 'dataloader_num_workers': 0, 'past_index': -1, 'run_name': '/home/n5huang/dna_token/pretrain/models/len2_5120', 'disable_tqdm': False, 'remove_unused_columns': True, 'label_names': None, 'load_best_model_at_end': False, 'metric_for_best_model': None, 'greater_is_better': None, 'ignore_data_skip': False, 'fsdp': [], 'fsdp_min_num_params': 0, 'fsdp_config': {'min_num_params': 0, 'xla': False, 'xla_fsdp_grad_ckpt': False}, 'fsdp_transformer_layer_cls_to_wrap': None, 'deepspeed': None, 'label_smoothing_factor': 0.0, 'optim': 'adamw_torch', 'optim_args': None, 'adafactor': False, 'group_by_length': False, 'length_column_name': 'length', 'report_to': ['wandb'], 'ddp_find_unused_parameters': None, 'ddp_bucket_cap_mb': None, 'ddp_broadcast_buffers': None, 'dataloader_pin_memory': True, 'skip_memory_metrics': True, 'use_legacy_prediction_loop': False, 'push_to_hub': False, 'resume_from_checkpoint': '/home/n5huang/dna_token/pretrain/models/len2_5120/checkpoint-100000', 'hub_model_id': None, 'hub_strategy': 'every_save', 'hub_token': '<HUB_TOKEN>', 'hub_private_repo': False, 'hub_always_push': False, 'gradient_checkpointing': False, 'gradient_checkpointing_kwargs': None, 'include_inputs_for_metrics': False, 'fp16_backend': 'auto', 'push_to_hub_model_id': None, 'push_to_hub_organization': None, 'push_to_hub_token': '<PUSH_TO_HUB_TOKEN>', 'mp_parameters': '', 'auto_find_batch_size': False, 'full_determinism': False, 'torchdynamo': None, 'ray_scope': 'last', 'ddp_timeout': 1800, 'torch_compile': False, 'torch_compile_backend': None, 'torch_compile_mode': None, 'dispatch_batches': None, 'split_batches': False, 'include_tokens_per_second': False, 'neftune_noise_alpha': None}
26
- 2026-04-09 03:06:55,255 INFO wandb-AsyncioManager-main:3530706 [service_client.py:_forward_responses():80] Reached EOF.
27
- 2026-04-09 03:06:55,256 INFO wandb-AsyncioManager-main:3530706 [mailbox.py:close():137] Closing mailbox, abandoning 1 handles.
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
pretrain_tokens/wandb/run-20260409_024256-4yonu3x2/run-4yonu3x2.wandb DELETED
@@ -1,3 +0,0 @@
1
- version https://git-lfs.github.com/spec/v1
2
- oid sha256:a6fde69b4759a75921e2f130844047a1d47447c38793aa29a667115e10523544
3
- size 639410
 
 
 
 
pretrain_tokens/wandb/run-20260409_031927-9ph1pkcx/files/config.yaml DELETED
@@ -1,613 +0,0 @@
1
- __cached__setup_devices:
2
- value: cuda:0
3
- _n_gpu:
4
- value: 1
5
- _name_or_path:
6
- value: ""
7
- _wandb:
8
- value:
9
- cli_version: 0.23.1
10
- e:
11
- shyl6ozoxin31qqkhj4f84yadhwytjka:
12
- args:
13
- - --output_dir
14
- - /home/n5huang/dna_token/pretrain/models/len2_5120
15
- - --model_type
16
- - bert
17
- - --tokenizer_name
18
- - /home/n5huang/dna_token/tokenizer_evaluation/merge_bpe/vocab_5120/merge_tokenizer_unigram_len2.json
19
- - --config_name
20
- - /home/n5huang/dna_token/pretrain/models/len2_5120/config.json
21
- - --project_name
22
- - token_eval_len2_5120
23
- - --do_train
24
- - "True"
25
- - --model_max_length
26
- - "512"
27
- - --max_seq_length
28
- - "512"
29
- - --line_by_line
30
- - "True"
31
- - --pad_to_max_length
32
- - "True"
33
- - --train_file
34
- - /home/n5huang/dna_token/output_tokens/merge_bpe_5120_allchr_all_tokenized_train_chrOnly.tsv
35
- - --validation_file
36
- - /home/n5huang/dna_token/output_tokens/merge_bpe_5120_allchr_all_tokenized_val_chrOnly.tsv
37
- - --cache_dir
38
- - /home/n5huang/dna_token/output_tokens/cache
39
- - --use_fast_tokenizer
40
- - "True"
41
- - --do_eval
42
- - "True"
43
- - --gradient_accumulation_steps
44
- - "1"
45
- - --per_device_train_batch_size
46
- - "96"
47
- - --per_device_eval_batch_size
48
- - "96"
49
- - --save_steps
50
- - "1000"
51
- - --save_total_limit
52
- - "10"
53
- - --max_steps
54
- - "200000"
55
- - --logging_steps
56
- - "1000"
57
- - --learning_rate
58
- - "4e-5"
59
- - --adam_epsilon
60
- - "1e-6"
61
- - --weight_decay
62
- - "0.01"
63
- - --adam_beta1
64
- - "0.9"
65
- - --adam_beta2
66
- - "0.98"
67
- - --mlm_probability
68
- - "0.15"
69
- - --warmup_steps
70
- - "10000"
71
- - --seed
72
- - "42"
73
- - --preprocessing_num_workers
74
- - "8"
75
- - --resume_from_checkpoint
76
- - /home/n5huang/dna_token/pretrain/models/len2_5120/checkpoint-100000
77
- cpu_count: 128
78
- cpu_count_logical: 255
79
- cudaVersion: "12.2"
80
- disk:
81
- /:
82
- total: "1876350566400"
83
- used: "405397532672"
84
- email: mtapiapacheco@ucsd.edu
85
- executable: /home/n5huang/miniconda3/envs/bpe/bin/python
86
- gpu: NVIDIA A100 80GB PCIe
87
- gpu_count: 8
88
- gpu_nvidia:
89
- - architecture: Ampere
90
- cudaCores: 6912
91
- memoryTotal: "85899345920"
92
- name: NVIDIA A100 80GB PCIe
93
- uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3
94
- - architecture: Ampere
95
- cudaCores: 6912
96
- memoryTotal: "85899345920"
97
- name: NVIDIA A100 80GB PCIe
98
- uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809
99
- - architecture: Ampere
100
- cudaCores: 6912
101
- memoryTotal: "85899345920"
102
- name: NVIDIA A100 80GB PCIe
103
- uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab
104
- - architecture: Ampere
105
- cudaCores: 6912
106
- memoryTotal: "85899345920"
107
- name: NVIDIA A100 80GB PCIe
108
- uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af
109
- - architecture: Ampere
110
- cudaCores: 6912
111
- memoryTotal: "85899345920"
112
- name: NVIDIA A100 80GB PCIe
113
- uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10
114
- - architecture: Ampere
115
- cudaCores: 6912
116
- memoryTotal: "85899345920"
117
- name: NVIDIA A100 80GB PCIe
118
- uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e
119
- - architecture: Ampere
120
- cudaCores: 6912
121
- memoryTotal: "85899345920"
122
- name: NVIDIA A100 80GB PCIe
123
- uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0
124
- - architecture: Ampere
125
- cudaCores: 6912
126
- memoryTotal: "85899345920"
127
- name: NVIDIA A100 80GB PCIe
128
- uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044
129
- host: sn4622116170
130
- memory:
131
- total: "4316310355968"
132
- os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35
133
- program: /home/n5huang/dna-tokenizer/BPE_merge/run_mlm_200k.py
134
- python: CPython 3.9.18
135
- root: /data/n5huang/dna_token/output_tokens
136
- startedAt: "2026-04-09T03:19:27.923698Z"
137
- writerId: shyl6ozoxin31qqkhj4f84yadhwytjka
138
- m:
139
- - "1": train/global_step
140
- "6":
141
- - 3
142
- "7": []
143
- - "2": '*'
144
- "5": 1
145
- "6":
146
- - 1
147
- "7": []
148
- python_version: 3.9.18
149
- t:
150
- "1":
151
- - 1
152
- - 5
153
- - 11
154
- - 49
155
- - 51
156
- - 53
157
- - 71
158
- - 100
159
- "2":
160
- - 1
161
- - 5
162
- - 11
163
- - 49
164
- - 51
165
- - 53
166
- - 71
167
- - 100
168
- "3":
169
- - 7
170
- - 66
171
- "4": 3.9.18
172
- "5": 0.23.1
173
- "6": 4.35.2
174
- "9":
175
- "1": transformers_trainer
176
- "12": 0.23.1
177
- "13": linux-x86_64
178
- adafactor:
179
- value: false
180
- adam_beta1:
181
- value: 0.9
182
- adam_beta2:
183
- value: 0.98
184
- adam_epsilon:
185
- value: 1e-06
186
- add_cross_attention:
187
- value: false
188
- architectures:
189
- value:
190
- - BertForMaskedLM
191
- attention_probs_dropout_prob:
192
- value: 0.1
193
- auto_find_batch_size:
194
- value: false
195
- bad_words_ids:
196
- value: null
197
- begin_suppress_tokens:
198
- value: null
199
- bf16:
200
- value: false
201
- bf16_full_eval:
202
- value: false
203
- bos_token_id:
204
- value: null
205
- cache_dir:
206
- value: /home/n5huang/dna_token/output_tokens/cache
207
- chunk_size_feed_forward:
208
- value: 0
209
- classifier_dropout:
210
- value: null
211
- config_name:
212
- value: /home/n5huang/dna_token/pretrain/models/len2_5120/config.json
213
- config_overrides:
214
- value: null
215
- cross_attention_hidden_size:
216
- value: null
217
- data_seed:
218
- value: null
219
- dataloader_drop_last:
220
- value: false
221
- dataloader_num_workers:
222
- value: 0
223
- dataloader_pin_memory:
224
- value: true
225
- dataset_config_name:
226
- value: null
227
- dataset_name:
228
- value: null
229
- ddp_backend:
230
- value: null
231
- ddp_broadcast_buffers:
232
- value: null
233
- ddp_bucket_cap_mb:
234
- value: null
235
- ddp_find_unused_parameters:
236
- value: null
237
- ddp_timeout:
238
- value: 1800
239
- debug:
240
- value: []
241
- decoder_start_token_id:
242
- value: null
243
- deepspeed:
244
- value: null
245
- deepspeed_plugin:
246
- value: null
247
- disable_tqdm:
248
- value: false
249
- dispatch_batches:
250
- value: null
251
- distributed_state:
252
- value: |
253
- Distributed environment: NO
254
- Num processes: 1
255
- Process index: 0
256
- Local process index: 0
257
- Device: cuda
258
- diversity_penalty:
259
- value: 0
260
- do_eval:
261
- value: true
262
- do_predict:
263
- value: false
264
- do_sample:
265
- value: false
266
- do_train:
267
- value: true
268
- early_stopping:
269
- value: false
270
- encoder_no_repeat_ngram_size:
271
- value: 0
272
- eos_token_id:
273
- value: null
274
- eval_accumulation_steps:
275
- value: null
276
- eval_delay:
277
- value: 0
278
- eval_steps:
279
- value: null
280
- evaluation_strategy:
281
- value: "no"
282
- exponential_decay_length_penalty:
283
- value: null
284
- finetuning_task:
285
- value: null
286
- forced_bos_token_id:
287
- value: null
288
- forced_eos_token_id:
289
- value: null
290
- fp16:
291
- value: false
292
- fp16_backend:
293
- value: auto
294
- fp16_full_eval:
295
- value: false
296
- fp16_opt_level:
297
- value: O1
298
- fsdp:
299
- value: []
300
- fsdp_config:
301
- value:
302
- min_num_params: 0
303
- xla: false
304
- xla_fsdp_grad_ckpt: false
305
- fsdp_min_num_params:
306
- value: 0
307
- fsdp_transformer_layer_cls_to_wrap:
308
- value: null
309
- full_determinism:
310
- value: false
311
- gradient_accumulation_steps:
312
- value: 1
313
- gradient_checkpointing:
314
- value: false
315
- gradient_checkpointing_kwargs:
316
- value: null
317
- greater_is_better:
318
- value: null
319
- group_by_length:
320
- value: false
321
- half_precision_backend:
322
- value: auto
323
- hidden_act:
324
- value: gelu
325
- hidden_dropout_prob:
326
- value: 0.1
327
- hidden_size:
328
- value: 768
329
- hub_always_push:
330
- value: false
331
- hub_model_id:
332
- value: null
333
- hub_private_repo:
334
- value: false
335
- hub_strategy:
336
- value: every_save
337
- hub_token:
338
- value: <HUB_TOKEN>
339
- id2label:
340
- value:
341
- "0": LABEL_0
342
- "1": LABEL_1
343
- ignore_data_skip:
344
- value: false
345
- include_inputs_for_metrics:
346
- value: false
347
- include_tokens_per_second:
348
- value: false
349
- initializer_range:
350
- value: 0.02
351
- intermediate_size:
352
- value: 3072
353
- is_decoder:
354
- value: false
355
- is_encoder_decoder:
356
- value: false
357
- jit_mode_eval:
358
- value: false
359
- label_names:
360
- value: null
361
- label_smoothing_factor:
362
- value: 0
363
- label2id:
364
- value:
365
- LABEL_0: 0
366
- LABEL_1: 1
367
- layer_norm_eps:
368
- value: 1e-12
369
- learning_rate:
370
- value: 4e-05
371
- length_column_name:
372
- value: length
373
- length_penalty:
374
- value: 1
375
- line_by_line:
376
- value: true
377
- load_best_model_at_end:
378
- value: false
379
- local_rank:
380
- value: 0
381
- log_level:
382
- value: passive
383
- log_level_replica:
384
- value: warning
385
- log_on_each_node:
386
- value: true
387
- logging_dir:
388
- value: /home/n5huang/dna_token/pretrain/models/len2_5120/runs/Apr09_03-19-29_sn4622116170
389
- logging_first_step:
390
- value: false
391
- logging_nan_inf_filter:
392
- value: true
393
- logging_steps:
394
- value: 1000
395
- logging_strategy:
396
- value: steps
397
- low_cpu_mem_usage:
398
- value: false
399
- lr_scheduler_type:
400
- value: linear
401
- max_eval_samples:
402
- value: null
403
- max_grad_norm:
404
- value: 1
405
- max_length:
406
- value: 512
407
- max_position_embeddings:
408
- value: 512
409
- max_seq_length:
410
- value: 512
411
- max_steps:
412
- value: 200000
413
- max_train_samples:
414
- value: null
415
- metric_for_best_model:
416
- value: null
417
- min_length:
418
- value: 0
419
- mlm_probability:
420
- value: 0.15
421
- model_max_length:
422
- value: 512
423
- model_name_or_path:
424
- value: null
425
- model_revision:
426
- value: main
427
- model_type:
428
- value: bert
429
- mp_parameters:
430
- value: ""
431
- neftune_noise_alpha:
432
- value: null
433
- no_cuda:
434
- value: false
435
- no_repeat_ngram_size:
436
- value: 0
437
- num_attention_heads:
438
- value: 12
439
- num_beam_groups:
440
- value: 1
441
- num_beams:
442
- value: 1
443
- num_hidden_layers:
444
- value: 12
445
- num_return_sequences:
446
- value: 1
447
- num_train_epochs:
448
- value: 3
449
- optim:
450
- value: adamw_torch
451
- optim_args:
452
- value: null
453
- output_attentions:
454
- value: false
455
- output_dir:
456
- value: /home/n5huang/dna_token/pretrain/models/len2_5120
457
- output_hidden_states:
458
- value: false
459
- output_scores:
460
- value: false
461
- overwrite_cache:
462
- value: false
463
- overwrite_output_dir:
464
- value: false
465
- pad_to_max_length:
466
- value: true
467
- pad_token_id:
468
- value: 0
469
- past_index:
470
- value: -1
471
- per_device_eval_batch_size:
472
- value: 96
473
- per_device_train_batch_size:
474
- value: 96
475
- per_gpu_eval_batch_size:
476
- value: null
477
- per_gpu_train_batch_size:
478
- value: null
479
- position_embedding_type:
480
- value: absolute
481
- prediction_loss_only:
482
- value: false
483
- prefix:
484
- value: null
485
- preprocessing_num_workers:
486
- value: 8
487
- problem_type:
488
- value: null
489
- project_name:
490
- value: token_eval_len2_5120
491
- push_to_hub:
492
- value: false
493
- push_to_hub_model_id:
494
- value: null
495
- push_to_hub_organization:
496
- value: null
497
- push_to_hub_token:
498
- value: <PUSH_TO_HUB_TOKEN>
499
- ray_scope:
500
- value: last
501
- remove_invalid_values:
502
- value: false
503
- remove_unused_columns:
504
- value: true
505
- repetition_penalty:
506
- value: 1
507
- report_to:
508
- value:
509
- - wandb
510
- resume_from_checkpoint:
511
- value: /home/n5huang/dna_token/pretrain/models/len2_5120/checkpoint-100000
512
- return_dict:
513
- value: true
514
- return_dict_in_generate:
515
- value: false
516
- run_name:
517
- value: /home/n5huang/dna_token/pretrain/models/len2_5120
518
- save_on_each_node:
519
- value: false
520
- save_safetensors:
521
- value: true
522
- save_steps:
523
- value: 1000
524
- save_strategy:
525
- value: steps
526
- save_total_limit:
527
- value: 10
528
- seed:
529
- value: 42
530
- sep_token_id:
531
- value: null
532
- skip_memory_metrics:
533
- value: true
534
- split_batches:
535
- value: false
536
- streaming:
537
- value: false
538
- suppress_tokens:
539
- value: null
540
- task_specific_params:
541
- value: null
542
- temperature:
543
- value: 1
544
- tf_legacy_loss:
545
- value: false
546
- tf32:
547
- value: null
548
- tie_encoder_decoder:
549
- value: false
550
- tie_word_embeddings:
551
- value: true
552
- token:
553
- value: null
554
- tokenizer_class:
555
- value: null
556
- tokenizer_name:
557
- value: /home/n5huang/dna_token/tokenizer_evaluation/merge_bpe/vocab_5120/merge_tokenizer_unigram_len2.json
558
- top_k:
559
- value: 50
560
- top_p:
561
- value: 1
562
- torch_compile:
563
- value: false
564
- torch_compile_backend:
565
- value: null
566
- torch_compile_mode:
567
- value: null
568
- torch_dtype:
569
- value: float32
570
- torchdynamo:
571
- value: null
572
- torchscript:
573
- value: false
574
- tpu_metrics_debug:
575
- value: false
576
- tpu_num_cores:
577
- value: null
578
- train_file:
579
- value: /home/n5huang/dna_token/output_tokens/merge_bpe_5120_allchr_all_tokenized_train_chrOnly.tsv
580
- transformers_version:
581
- value: 4.35.2
582
- trust_remote_code:
583
- value: false
584
- type_vocab_size:
585
- value: 2
586
- typical_p:
587
- value: 1
588
- use_bfloat16:
589
- value: false
590
- use_cache:
591
- value: true
592
- use_cpu:
593
- value: false
594
- use_fast_tokenizer:
595
- value: true
596
- use_ipex:
597
- value: false
598
- use_legacy_prediction_loop:
599
- value: false
600
- use_mps_device:
601
- value: false
602
- validation_file:
603
- value: /home/n5huang/dna_token/output_tokens/merge_bpe_5120_allchr_all_tokenized_val_chrOnly.tsv
604
- validation_split_percentage:
605
- value: 5
606
- vocab_size:
607
- value: 5120
608
- warmup_ratio:
609
- value: 0
610
- warmup_steps:
611
- value: 10000
612
- weight_decay:
613
- value: 0.01
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
pretrain_tokens/wandb/run-20260409_031927-9ph1pkcx/files/output.log DELETED
The diff for this file is too large to render. See raw diff
 
pretrain_tokens/wandb/run-20260409_031927-9ph1pkcx/files/requirements.txt DELETED
@@ -1,148 +0,0 @@
1
- fonttools==4.60.1
2
- mpmath==1.3.0
3
- httpx==0.28.1
4
- yarl==1.22.0
5
- attrs==25.4.0
6
- pydantic_core==2.33.2
7
- nvidia-cusparse-cu12==12.5.8.93
8
- GitPython==3.1.45
9
- PyQt6_sip==13.10.2
10
- nvidia-nvtx-cu12==12.8.90
11
- nest_asyncio==1.6.0
12
- cffi==2.0.0
13
- tqdm==4.67.1
14
- tzdata==2025.2
15
- dill==0.4.0
16
- cycler==0.11.0
17
- aiohttp==3.13.2
18
- pydantic==2.11.7
19
- pickleshare==0.7.5
20
- nvidia-cusparselt-cu12==0.7.1
21
- contourpy==1.2.1
22
- platformdirs==4.3.8
23
- importlib_metadata==8.7.0
24
- biopython==1.85
25
- idna==3.11
26
- stack_data==0.6.3
27
- pycparser==2.23
28
- python-dateutil==2.9.0.post0
29
- wheel==0.45.1
30
- psutil==7.0.0
31
- importlib_resources==6.5.2
32
- pyparsing==3.2.0
33
- exceptiongroup==1.3.0
34
- exceptiongroup==1.3.1
35
- gitdb==4.0.12
36
- pip==25.3
37
- pillow==11.3.0
38
- jupyter_core==5.8.1
39
- transformers==4.29.2
40
- matplotlib-inline==0.1.7
41
- packaging==25.0
42
- nvidia-nccl-cu12==2.27.3
43
- debugpy==1.8.16
44
- ipython==8.18.1
45
- anyio==4.12.0
46
- prompt_toolkit==3.0.51
47
- mkl_fft==1.3.11
48
- httpcore==1.0.9
49
- Jinja2==3.1.6
50
- ply==3.11
51
- zipp==3.23.0
52
- setproctitle==1.3.6
53
- docker-pycreds==0.4.0
54
- nvidia-cuda-nvrtc-cu12==12.8.93
55
- urllib3==2.5.0
56
- kiwisolver==1.4.4
57
- nvidia-curand-cu12==10.3.9.90
58
- llvmlite==0.43.0
59
- six==1.17.0
60
- frozenlist==1.8.0
61
- wcwidth==0.2.13
62
- numexpr==2.10.1
63
- click==8.1.8
64
- multiprocess==0.70.18
65
- threadpoolctl==3.6.0
66
- typing_extensions==4.15.0
67
- decorator==5.2.1
68
- sip==6.7.12
69
- pure_eval==0.2.3
70
- async-timeout==5.0.1
71
- Pygments==2.19.2
72
- mkl-service==2.4.0
73
- transformers==4.35.2
74
- numba==0.60.0
75
- pyzmq==27.0.2
76
- mkl_random==1.2.8
77
- ptyprocess==0.7.0
78
- nvidia-cuda-cupti-cu12==12.8.90
79
- charset-normalizer==3.4.4
80
- nvidia-cublas-cu12==12.8.4.1
81
- PyQt5_sip==12.13.0
82
- Bottleneck==1.4.2
83
- networkx==3.2.1
84
- PySocks==1.7.1
85
- pysam==0.9.1
86
- tornado==6.5.2
87
- pandas==2.3.3
88
- smmap==5.0.2
89
- PyQt5==5.15.10
90
- nvidia-cufft-cu12==11.3.3.83
91
- safetensors==0.7.0
92
- requests==2.32.5
93
- pytz==2025.2
94
- fsspec==2025.7.0
95
- certifi==2025.10.5
96
- sentry-sdk==2.35.0
97
- parso==0.8.4
98
- aiosignal==1.4.0
99
- traitlets==5.14.3
100
- hf-xet==1.1.8
101
- nvidia-cudnn-cu12==9.10.2.21
102
- accelerate==0.25.0
103
- eval_type_backport==0.2.2
104
- datasets==4.4.1
105
- huggingface_hub==0.34.4
106
- wandb==0.23.1
107
- tomli==2.2.1
108
- comm==0.2.3
109
- executing==2.2.0
110
- PyYAML==6.0.2
111
- scipy==1.13.1
112
- pexpect==4.9.0
113
- matplotlib==3.9.2
114
- annotated-types==0.7.0
115
- asttokens==3.0.0
116
- tokenizers==0.15.2
117
- nvidia-cufile-cu12==1.13.1.3
118
- appdirs==1.4.4
119
- h11==0.16.0
120
- numpy==2.0.2
121
- jupyter_client==8.6.3
122
- joblib==1.5.1
123
- joblib==1.5.3
124
- jedi==0.19.2
125
- MarkupSafe==3.0.3
126
- nvidia-nvjitlink-cu12==12.8.93
127
- pyarrow==21.0.0
128
- torch==2.8.0
129
- protobuf==3.20.3
130
- propcache==0.4.1
131
- multidict==6.7.0
132
- nvidia-cusolver-cu12==11.7.3.90
133
- umap-learn==0.5.9.post2
134
- ipykernel==6.30.1
135
- triton==3.4.0
136
- sympy==1.14.0
137
- scikit-learn==1.6.1
138
- brotlicffi==1.0.9.2
139
- xxhash==3.6.0
140
- seaborn==0.13.2
141
- pynndescent==0.5.13
142
- regex==2025.11.3
143
- typing-inspection==0.4.1
144
- evaluate==0.4.6
145
- nvidia-cuda-runtime-cu12==12.8.90
146
- filelock==3.17.0
147
- aiohappyeyeballs==2.6.1
148
- setuptools==80.9.0
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
pretrain_tokens/wandb/run-20260409_031927-9ph1pkcx/files/wandb-metadata.json DELETED
@@ -1,149 +0,0 @@
1
- {
2
- "os": "Linux-5.15.0-72-generic-x86_64-with-glibc2.35",
3
- "python": "CPython 3.9.18",
4
- "startedAt": "2026-04-09T03:19:27.923698Z",
5
- "args": [
6
- "--output_dir",
7
- "/home/n5huang/dna_token/pretrain/models/len2_5120",
8
- "--model_type",
9
- "bert",
10
- "--tokenizer_name",
11
- "/home/n5huang/dna_token/tokenizer_evaluation/merge_bpe/vocab_5120/merge_tokenizer_unigram_len2.json",
12
- "--config_name",
13
- "/home/n5huang/dna_token/pretrain/models/len2_5120/config.json",
14
- "--project_name",
15
- "token_eval_len2_5120",
16
- "--do_train",
17
- "True",
18
- "--model_max_length",
19
- "512",
20
- "--max_seq_length",
21
- "512",
22
- "--line_by_line",
23
- "True",
24
- "--pad_to_max_length",
25
- "True",
26
- "--train_file",
27
- "/home/n5huang/dna_token/output_tokens/merge_bpe_5120_allchr_all_tokenized_train_chrOnly.tsv",
28
- "--validation_file",
29
- "/home/n5huang/dna_token/output_tokens/merge_bpe_5120_allchr_all_tokenized_val_chrOnly.tsv",
30
- "--cache_dir",
31
- "/home/n5huang/dna_token/output_tokens/cache",
32
- "--use_fast_tokenizer",
33
- "True",
34
- "--do_eval",
35
- "True",
36
- "--gradient_accumulation_steps",
37
- "1",
38
- "--per_device_train_batch_size",
39
- "96",
40
- "--per_device_eval_batch_size",
41
- "96",
42
- "--save_steps",
43
- "1000",
44
- "--save_total_limit",
45
- "10",
46
- "--max_steps",
47
- "200000",
48
- "--logging_steps",
49
- "1000",
50
- "--learning_rate",
51
- "4e-5",
52
- "--adam_epsilon",
53
- "1e-6",
54
- "--weight_decay",
55
- "0.01",
56
- "--adam_beta1",
57
- "0.9",
58
- "--adam_beta2",
59
- "0.98",
60
- "--mlm_probability",
61
- "0.15",
62
- "--warmup_steps",
63
- "10000",
64
- "--seed",
65
- "42",
66
- "--preprocessing_num_workers",
67
- "8",
68
- "--resume_from_checkpoint",
69
- "/home/n5huang/dna_token/pretrain/models/len2_5120/checkpoint-100000"
70
- ],
71
- "program": "/home/n5huang/dna-tokenizer/BPE_merge/run_mlm_200k.py",
72
- "email": "mtapiapacheco@ucsd.edu",
73
- "root": "/data/n5huang/dna_token/output_tokens",
74
- "host": "sn4622116170",
75
- "executable": "/home/n5huang/miniconda3/envs/bpe/bin/python",
76
- "cpu_count": 128,
77
- "cpu_count_logical": 255,
78
- "gpu": "NVIDIA A100 80GB PCIe",
79
- "gpu_count": 8,
80
- "disk": {
81
- "/": {
82
- "total": "1876350566400",
83
- "used": "405397532672"
84
- }
85
- },
86
- "memory": {
87
- "total": "4316310355968"
88
- },
89
- "gpu_nvidia": [
90
- {
91
- "name": "NVIDIA A100 80GB PCIe",
92
- "memoryTotal": "85899345920",
93
- "cudaCores": 6912,
94
- "architecture": "Ampere",
95
- "uuid": "GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3"
96
- },
97
- {
98
- "name": "NVIDIA A100 80GB PCIe",
99
- "memoryTotal": "85899345920",
100
- "cudaCores": 6912,
101
- "architecture": "Ampere",
102
- "uuid": "GPU-054a4d72-8520-5e4a-5cd3-7519a0966809"
103
- },
104
- {
105
- "name": "NVIDIA A100 80GB PCIe",
106
- "memoryTotal": "85899345920",
107
- "cudaCores": 6912,
108
- "architecture": "Ampere",
109
- "uuid": "GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab"
110
- },
111
- {
112
- "name": "NVIDIA A100 80GB PCIe",
113
- "memoryTotal": "85899345920",
114
- "cudaCores": 6912,
115
- "architecture": "Ampere",
116
- "uuid": "GPU-a18369da-b15a-c8af-72f1-7f6272e479af"
117
- },
118
- {
119
- "name": "NVIDIA A100 80GB PCIe",
120
- "memoryTotal": "85899345920",
121
- "cudaCores": 6912,
122
- "architecture": "Ampere",
123
- "uuid": "GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10"
124
- },
125
- {
126
- "name": "NVIDIA A100 80GB PCIe",
127
- "memoryTotal": "85899345920",
128
- "cudaCores": 6912,
129
- "architecture": "Ampere",
130
- "uuid": "GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e"
131
- },
132
- {
133
- "name": "NVIDIA A100 80GB PCIe",
134
- "memoryTotal": "85899345920",
135
- "cudaCores": 6912,
136
- "architecture": "Ampere",
137
- "uuid": "GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0"
138
- },
139
- {
140
- "name": "NVIDIA A100 80GB PCIe",
141
- "memoryTotal": "85899345920",
142
- "cudaCores": 6912,
143
- "architecture": "Ampere",
144
- "uuid": "GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044"
145
- }
146
- ],
147
- "cudaVersion": "12.2",
148
- "writerId": "shyl6ozoxin31qqkhj4f84yadhwytjka"
149
- }
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
pretrain_tokens/wandb/run-20260409_031927-9ph1pkcx/files/wandb-summary.json DELETED
@@ -1 +0,0 @@
1
- {"train/train_samples_per_second":74.262,"train/total_flos":2.2734004322427208e+19,"train/train_runtime":258545.0504,"train/global_step":200000,"perplexity":134.40830833002153,"step":200000,"eval_samples_per_second":86.657,"epoch":19.54,"eval_step":200000,"eval_steps_per_second":0.903,"eval/runtime":1259.8218,"eval/step":200000,"eval/accuracy":0.30433709022367145,"eval/steps_per_second":0.903,"train/epoch":19.54,"train/train_steps_per_second":0.774,"eval_samples":109173,"_step":103,"_wandb":{"runtime":259827},"eval_accuracy":0.30433709022367145,"train/loss":4.9315,"eval/samples_per_second":86.657,"eval/loss":4.900882244110107,"eval_loss":4.900882244110107,"train/train_loss":2.48521353515625,"_timestamp":1.7759645965117583e+09,"eval_runtime":1259.8218,"train/learning_rate":0,"accuracy":0.30433709022367145,"_runtime":259827}
 
 
pretrain_tokens/wandb/run-20260409_031927-9ph1pkcx/logs/debug-core.log DELETED
@@ -1,14 +0,0 @@
1
- {"time":"2026-04-09T03:19:28.031871423Z","level":"INFO","msg":"main: starting server","port-filename":"/tmp/tmpfnra4150/port-3566905.txt","pid":3566905,"log-level":0,"disable-analytics":false,"shutdown-on-parent-exit":false,"enable-dcgm-profiling":false}
2
- {"time":"2026-04-09T03:19:28.034677991Z","level":"INFO","msg":"server: will exit if parent process dies","ppid":3566905}
3
- {"time":"2026-04-09T03:19:28.034672701Z","level":"INFO","msg":"server: accepting connections","addr":{"Name":"/tmp/wandb-3566905-3567158-744466961/socket","Net":"unix"}}
4
- {"time":"2026-04-09T03:19:28.217201312Z","level":"INFO","msg":"connection: ManageConnectionData: new connection created","id":"1(@)"}
5
- {"time":"2026-04-09T03:19:28.253049116Z","level":"INFO","msg":"handleInformInit: received","streamId":"9ph1pkcx","id":"1(@)"}
6
- {"time":"2026-04-09T03:19:28.588618726Z","level":"INFO","msg":"handleInformInit: stream started","streamId":"9ph1pkcx","id":"1(@)"}
7
- {"time":"2026-04-12T03:29:56.515958294Z","level":"INFO","msg":"handleInformTeardown: server teardown initiated","id":"1(@)"}
8
- {"time":"2026-04-12T03:29:56.516759323Z","level":"INFO","msg":"connection: closing","id":"1(@)"}
9
- {"time":"2026-04-12T03:29:56.516809293Z","level":"INFO","msg":"connection: closed successfully","id":"1(@)"}
10
- {"time":"2026-04-12T03:29:56.516769743Z","level":"INFO","msg":"server is shutting down"}
11
- {"time":"2026-04-12T03:29:56.516898183Z","level":"INFO","msg":"server: listener closed","addr":{"Name":"/tmp/wandb-3566905-3567158-744466961/socket","Net":"unix"}}
12
- {"time":"2026-04-12T03:29:57.223915447Z","level":"INFO","msg":"handleInformTeardown: server shutdown complete","id":"1(@)"}
13
- {"time":"2026-04-12T03:29:57.223965837Z","level":"INFO","msg":"connection: ManageConnectionData: connection closed","id":"1(@)"}
14
- {"time":"2026-04-12T03:29:57.223990097Z","level":"INFO","msg":"server is closed"}
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
pretrain_tokens/wandb/run-20260409_031927-9ph1pkcx/logs/debug-internal.log DELETED
@@ -1,15 +0,0 @@
1
- {"time":"2026-04-09T03:19:28.253252886Z","level":"INFO","msg":"stream: starting","core version":"0.23.1"}
2
- {"time":"2026-04-09T03:19:28.588342136Z","level":"INFO","msg":"stream: created new stream","id":"9ph1pkcx"}
3
- {"time":"2026-04-09T03:19:28.588502646Z","level":"INFO","msg":"handler: started","stream_id":"9ph1pkcx"}
4
- {"time":"2026-04-09T03:19:28.588564816Z","level":"INFO","msg":"stream: started","id":"9ph1pkcx"}
5
- {"time":"2026-04-09T03:19:28.588589346Z","level":"INFO","msg":"writer: started","stream_id":"9ph1pkcx"}
6
- {"time":"2026-04-09T03:19:28.588586606Z","level":"INFO","msg":"sender: started","stream_id":"9ph1pkcx"}
7
- {"time":"2026-04-09T07:38:54.243251922Z","level":"INFO","msg":"api: retrying error","error":"Post \"https://api.wandb.ai/files/mtapiapacheco-university-of-california-san-diego/uncategorized/9ph1pkcx/file_stream\": dial tcp: lookup api.wandb.ai on 127.0.0.53:53: read udp 127.0.0.1:46273->127.0.0.53:53: i/o timeout"}
8
- {"time":"2026-04-10T15:10:52.177204385Z","level":"INFO","msg":"api: retrying error","error":"Post \"https://api.wandb.ai/files/mtapiapacheco-university-of-california-san-diego/uncategorized/9ph1pkcx/file_stream\": context deadline exceeded (Client.Timeout exceeded while awaiting headers)"}
9
- {"time":"2026-04-10T17:40:21.310822834Z","level":"INFO","msg":"api: retrying error","error":"Post \"https://api.wandb.ai/files/mtapiapacheco-university-of-california-san-diego/uncategorized/9ph1pkcx/file_stream\": context deadline exceeded (Client.Timeout exceeded while awaiting headers)"}
10
- {"time":"2026-04-10T18:17:02.326710103Z","level":"INFO","msg":"api: retrying error","error":"Post \"https://api.wandb.ai/files/mtapiapacheco-university-of-california-san-diego/uncategorized/9ph1pkcx/file_stream\": context deadline exceeded (Client.Timeout exceeded while awaiting headers)"}
11
- {"time":"2026-04-12T03:29:56.516755613Z","level":"INFO","msg":"stream: closing","id":"9ph1pkcx"}
12
- {"time":"2026-04-12T03:29:56.970094158Z","level":"INFO","msg":"fileTransfer: Close: file transfer manager closed"}
13
- {"time":"2026-04-12T03:29:57.220807579Z","level":"INFO","msg":"handler: closed","stream_id":"9ph1pkcx"}
14
- {"time":"2026-04-12T03:29:57.220969499Z","level":"INFO","msg":"sender: closed","stream_id":"9ph1pkcx"}
15
- {"time":"2026-04-12T03:29:57.220985529Z","level":"INFO","msg":"stream: closed","id":"9ph1pkcx"}
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
pretrain_tokens/wandb/run-20260409_031927-9ph1pkcx/logs/debug.log DELETED
@@ -1,27 +0,0 @@
1
- 2026-04-09 03:19:27,927 INFO MainThread:3566905 [wandb_setup.py:_flush():80] Current SDK version is 0.23.1
2
- 2026-04-09 03:19:27,927 INFO MainThread:3566905 [wandb_setup.py:_flush():80] Configure stats pid to 3566905
3
- 2026-04-09 03:19:27,927 INFO MainThread:3566905 [wandb_setup.py:_flush():80] Loading settings from /home/n5huang/.config/wandb/settings
4
- 2026-04-09 03:19:27,927 INFO MainThread:3566905 [wandb_setup.py:_flush():80] Loading settings from /data/n5huang/dna_token/output_tokens/wandb/settings
5
- 2026-04-09 03:19:27,927 INFO MainThread:3566905 [wandb_setup.py:_flush():80] Loading settings from environment variables
6
- 2026-04-09 03:19:27,927 INFO MainThread:3566905 [wandb_init.py:setup_run_log_directory():714] Logging user logs to /data/n5huang/dna_token/output_tokens/wandb/run-20260409_031927-9ph1pkcx/logs/debug.log
7
- 2026-04-09 03:19:27,927 INFO MainThread:3566905 [wandb_init.py:setup_run_log_directory():715] Logging internal logs to /data/n5huang/dna_token/output_tokens/wandb/run-20260409_031927-9ph1pkcx/logs/debug-internal.log
8
- 2026-04-09 03:19:27,927 INFO MainThread:3566905 [wandb_init.py:init():841] calling init triggers
9
- 2026-04-09 03:19:27,927 INFO MainThread:3566905 [wandb_init.py:init():846] wandb.init called with sweep_config: {}
10
- config: {'_wandb': {}}
11
- 2026-04-09 03:19:27,927 INFO MainThread:3566905 [wandb_init.py:init():889] starting backend
12
- 2026-04-09 03:19:28,217 INFO MainThread:3566905 [wandb_init.py:init():892] sending inform_init request
13
- 2026-04-09 03:19:28,251 INFO MainThread:3566905 [wandb_init.py:init():900] backend started and connected
14
- 2026-04-09 03:19:28,254 INFO MainThread:3566905 [wandb_init.py:init():970] updated telemetry
15
- 2026-04-09 03:19:28,256 INFO MainThread:3566905 [wandb_init.py:init():994] communicating run to backend with 90.0 second timeout
16
- 2026-04-09 03:19:28,885 INFO MainThread:3566905 [wandb_init.py:init():1041] starting run threads in backend
17
- 2026-04-09 03:19:28,994 INFO MainThread:3566905 [wandb_run.py:_console_start():2521] atexit reg
18
- 2026-04-09 03:19:28,994 INFO MainThread:3566905 [wandb_run.py:_redirect():2369] redirect: wrap_raw
19
- 2026-04-09 03:19:28,994 INFO MainThread:3566905 [wandb_run.py:_redirect():2438] Wrapping output streams.
20
- 2026-04-09 03:19:28,995 INFO MainThread:3566905 [wandb_run.py:_redirect():2461] Redirects installed.
21
- 2026-04-09 03:19:29,000 INFO MainThread:3566905 [wandb_init.py:init():1081] run started, returning control to user process
22
- 2026-04-09 03:19:29,346 INFO MainThread:3566905 [wandb_run.py:_config_callback():1396] config_cb None None {'output_dir': '/home/n5huang/dna_token/pretrain/models/len2_5120', 'overwrite_output_dir': False, 'do_train': True, 'do_eval': True, 'do_predict': False, 'evaluation_strategy': 'NO', 'prediction_loss_only': False, 'per_device_train_batch_size': 96, 'per_device_eval_batch_size': 96, 'per_gpu_train_batch_size': None, 'per_gpu_eval_batch_size': None, 'gradient_accumulation_steps': 1, 'eval_accumulation_steps': None, 'eval_delay': 0, 'learning_rate': 4e-05, 'weight_decay': 0.01, 'adam_beta1': 0.9, 'adam_beta2': 0.98, 'adam_epsilon': 1e-06, 'max_grad_norm': 1.0, 'num_train_epochs': 3.0, 'max_steps': 200000, 'lr_scheduler_type': 'LINEAR', 'warmup_ratio': 0.0, 'warmup_steps': 10000, 'log_level': 'passive', 'log_level_replica': 'warning', 'log_on_each_node': True, 'logging_dir': '/home/n5huang/dna_token/pretrain/models/len2_5120/runs/Apr09_03-19-29_sn4622116170', 'logging_strategy': 'STEPS', 'logging_first_step': False, 'logging_steps': 1000, 'logging_nan_inf_filter': True, 'save_strategy': 'STEPS', 'save_steps': 1000, 'save_total_limit': 10, 'save_safetensors': True, 'save_on_each_node': False, 'no_cuda': False, 'use_cpu': False, 'use_mps_device': False, 'seed': 42, 'data_seed': None, 'jit_mode_eval': False, 'use_ipex': False, 'bf16': False, 'fp16': False, 'fp16_opt_level': 'O1', 'half_precision_backend': 'auto', 'bf16_full_eval': False, 'fp16_full_eval': False, 'tf32': None, 'local_rank': 0, 'ddp_backend': None, 'tpu_num_cores': None, 'tpu_metrics_debug': False, 'debug': [], 'dataloader_drop_last': False, 'eval_steps': None, 'dataloader_num_workers': 0, 'past_index': -1, 'run_name': '/home/n5huang/dna_token/pretrain/models/len2_5120', 'disable_tqdm': False, 'remove_unused_columns': True, 'label_names': None, 'load_best_model_at_end': False, 'metric_for_best_model': None, 'greater_is_better': None, 'ignore_data_skip': False, 'fsdp': [], 'fsdp_min_num_params': 0, 'fsdp_config': {'min_num_params': 0, 'xla': False, 'xla_fsdp_grad_ckpt': False}, 'fsdp_transformer_layer_cls_to_wrap': None, 'deepspeed': None, 'label_smoothing_factor': 0.0, 'optim': 'ADAMW_TORCH', 'optim_args': None, 'adafactor': False, 'group_by_length': False, 'length_column_name': 'length', 'report_to': ['wandb'], 'ddp_find_unused_parameters': None, 'ddp_bucket_cap_mb': None, 'ddp_broadcast_buffers': None, 'dataloader_pin_memory': True, 'skip_memory_metrics': True, 'use_legacy_prediction_loop': False, 'push_to_hub': False, 'resume_from_checkpoint': '/home/n5huang/dna_token/pretrain/models/len2_5120/checkpoint-100000', 'hub_model_id': None, 'hub_strategy': 'EVERY_SAVE', 'hub_token': None, 'hub_private_repo': False, 'hub_always_push': False, 'gradient_checkpointing': False, 'gradient_checkpointing_kwargs': None, 'include_inputs_for_metrics': False, 'fp16_backend': 'auto', 'push_to_hub_model_id': None, 'push_to_hub_organization': None, 'push_to_hub_token': None, 'mp_parameters': '', 'auto_find_batch_size': False, 'full_determinism': False, 'torchdynamo': None, 'ray_scope': 'last', 'ddp_timeout': 1800, 'torch_compile': False, 'torch_compile_backend': None, 'torch_compile_mode': None, 'dispatch_batches': None, 'split_batches': False, 'include_tokens_per_second': False, 'neftune_noise_alpha': None, 'distributed_state': 'Distributed environment: NO\nNum processes: 1\nProcess index: 0\nLocal process index: 0\nDevice: cuda\n', '_n_gpu': 1, '__cached__setup_devices': 'cuda:0', 'deepspeed_plugin': None}
23
- 2026-04-09 03:19:29,348 INFO MainThread:3566905 [wandb_run.py:_config_callback():1396] config_cb None None {'model_name_or_path': None, 'model_type': 'bert', 'config_overrides': None, 'config_name': '/home/n5huang/dna_token/pretrain/models/len2_5120/config.json', 'tokenizer_name': '/home/n5huang/dna_token/tokenizer_evaluation/merge_bpe/vocab_5120/merge_tokenizer_unigram_len2.json', 'cache_dir': '/home/n5huang/dna_token/output_tokens/cache', 'use_fast_tokenizer': True, 'model_revision': 'main', 'token': None, 'trust_remote_code': False, 'torch_dtype': None, 'low_cpu_mem_usage': False, 'model_max_length': 512}
24
- 2026-04-09 03:19:29,349 INFO MainThread:3566905 [wandb_run.py:_config_callback():1396] config_cb None None {'dataset_name': None, 'dataset_config_name': None, 'train_file': '/home/n5huang/dna_token/output_tokens/merge_bpe_5120_allchr_all_tokenized_train_chrOnly.tsv', 'validation_file': '/home/n5huang/dna_token/output_tokens/merge_bpe_5120_allchr_all_tokenized_val_chrOnly.tsv', 'overwrite_cache': False, 'validation_split_percentage': 5, 'max_seq_length': 512, 'preprocessing_num_workers': 8, 'mlm_probability': 0.15, 'line_by_line': True, 'pad_to_max_length': True, 'max_train_samples': None, 'max_eval_samples': None, 'project_name': 'token_eval_len2_5120', 'streaming': False}
25
- 2026-04-09 03:19:50,773 INFO MainThread:3566905 [wandb_run.py:_config_callback():1396] config_cb None None {'return_dict': True, 'output_hidden_states': False, 'output_attentions': False, 'torchscript': False, 'torch_dtype': 'float32', 'use_bfloat16': False, 'tf_legacy_loss': False, 'pruned_heads': {}, 'tie_word_embeddings': True, 'is_encoder_decoder': False, 'is_decoder': False, 'cross_attention_hidden_size': None, 'add_cross_attention': False, 'tie_encoder_decoder': False, 'max_length': 512, 'min_length': 0, 'do_sample': False, 'early_stopping': False, 'num_beams': 1, 'num_beam_groups': 1, 'diversity_penalty': 0.0, 'temperature': 1.0, 'top_k': 50, 'top_p': 1.0, 'typical_p': 1.0, 'repetition_penalty': 1.0, 'length_penalty': 1.0, 'no_repeat_ngram_size': 0, 'encoder_no_repeat_ngram_size': 0, 'bad_words_ids': None, 'num_return_sequences': 1, 'chunk_size_feed_forward': 0, 'output_scores': False, 'return_dict_in_generate': False, 'forced_bos_token_id': None, 'forced_eos_token_id': None, 'remove_invalid_values': False, 'exponential_decay_length_penalty': None, 'suppress_tokens': None, 'begin_suppress_tokens': None, 'architectures': ['BertForMaskedLM'], 'finetuning_task': None, 'id2label': {0: 'LABEL_0', 1: 'LABEL_1'}, 'label2id': {'LABEL_0': 0, 'LABEL_1': 1}, 'tokenizer_class': None, 'prefix': None, 'bos_token_id': None, 'pad_token_id': 0, 'eos_token_id': None, 'sep_token_id': None, 'decoder_start_token_id': None, 'task_specific_params': None, 'problem_type': None, '_name_or_path': '', 'transformers_version': '4.35.2', 'model_type': 'bert', 'vocab_size': 5120, 'hidden_size': 768, 'num_hidden_layers': 12, 'num_attention_heads': 12, 'hidden_act': 'gelu', 'intermediate_size': 3072, 'hidden_dropout_prob': 0.1, 'attention_probs_dropout_prob': 0.1, 'max_position_embeddings': 512, 'type_vocab_size': 2, 'initializer_range': 0.02, 'layer_norm_eps': 1e-12, 'position_embedding_type': 'absolute', 'use_cache': True, 'classifier_dropout': None, 'output_dir': '/home/n5huang/dna_token/pretrain/models/len2_5120', 'overwrite_output_dir': False, 'do_train': True, 'do_eval': True, 'do_predict': False, 'evaluation_strategy': 'no', 'prediction_loss_only': False, 'per_device_train_batch_size': 96, 'per_device_eval_batch_size': 96, 'per_gpu_train_batch_size': None, 'per_gpu_eval_batch_size': None, 'gradient_accumulation_steps': 1, 'eval_accumulation_steps': None, 'eval_delay': 0, 'learning_rate': 4e-05, 'weight_decay': 0.01, 'adam_beta1': 0.9, 'adam_beta2': 0.98, 'adam_epsilon': 1e-06, 'max_grad_norm': 1.0, 'num_train_epochs': 3.0, 'max_steps': 200000, 'lr_scheduler_type': 'linear', 'warmup_ratio': 0.0, 'warmup_steps': 10000, 'log_level': 'passive', 'log_level_replica': 'warning', 'log_on_each_node': True, 'logging_dir': '/home/n5huang/dna_token/pretrain/models/len2_5120/runs/Apr09_03-19-29_sn4622116170', 'logging_strategy': 'steps', 'logging_first_step': False, 'logging_steps': 1000, 'logging_nan_inf_filter': True, 'save_strategy': 'steps', 'save_steps': 1000, 'save_total_limit': 10, 'save_safetensors': True, 'save_on_each_node': False, 'no_cuda': False, 'use_cpu': False, 'use_mps_device': False, 'seed': 42, 'data_seed': None, 'jit_mode_eval': False, 'use_ipex': False, 'bf16': False, 'fp16': False, 'fp16_opt_level': 'O1', 'half_precision_backend': 'auto', 'bf16_full_eval': False, 'fp16_full_eval': False, 'tf32': None, 'local_rank': 0, 'ddp_backend': None, 'tpu_num_cores': None, 'tpu_metrics_debug': False, 'debug': [], 'dataloader_drop_last': False, 'eval_steps': None, 'dataloader_num_workers': 0, 'past_index': -1, 'run_name': '/home/n5huang/dna_token/pretrain/models/len2_5120', 'disable_tqdm': False, 'remove_unused_columns': True, 'label_names': None, 'load_best_model_at_end': False, 'metric_for_best_model': None, 'greater_is_better': None, 'ignore_data_skip': False, 'fsdp': [], 'fsdp_min_num_params': 0, 'fsdp_config': {'min_num_params': 0, 'xla': False, 'xla_fsdp_grad_ckpt': False}, 'fsdp_transformer_layer_cls_to_wrap': None, 'deepspeed': None, 'label_smoothing_factor': 0.0, 'optim': 'adamw_torch', 'optim_args': None, 'adafactor': False, 'group_by_length': False, 'length_column_name': 'length', 'report_to': ['wandb'], 'ddp_find_unused_parameters': None, 'ddp_bucket_cap_mb': None, 'ddp_broadcast_buffers': None, 'dataloader_pin_memory': True, 'skip_memory_metrics': True, 'use_legacy_prediction_loop': False, 'push_to_hub': False, 'resume_from_checkpoint': '/home/n5huang/dna_token/pretrain/models/len2_5120/checkpoint-100000', 'hub_model_id': None, 'hub_strategy': 'every_save', 'hub_token': '<HUB_TOKEN>', 'hub_private_repo': False, 'hub_always_push': False, 'gradient_checkpointing': False, 'gradient_checkpointing_kwargs': None, 'include_inputs_for_metrics': False, 'fp16_backend': 'auto', 'push_to_hub_model_id': None, 'push_to_hub_organization': None, 'push_to_hub_token': '<PUSH_TO_HUB_TOKEN>', 'mp_parameters': '', 'auto_find_batch_size': False, 'full_determinism': False, 'torchdynamo': None, 'ray_scope': 'last', 'ddp_timeout': 1800, 'torch_compile': False, 'torch_compile_backend': None, 'torch_compile_mode': None, 'dispatch_batches': None, 'split_batches': False, 'include_tokens_per_second': False, 'neftune_noise_alpha': None}
26
- 2026-04-12 03:29:56,516 INFO wandb-AsyncioManager-main:3566905 [service_client.py:_forward_responses():80] Reached EOF.
27
- 2026-04-12 03:29:56,516 INFO wandb-AsyncioManager-main:3566905 [mailbox.py:close():137] Closing mailbox, abandoning 1 handles.
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
pretrain_tokens/wandb/run-20260409_031927-9ph1pkcx/run-9ph1pkcx.wandb DELETED
@@ -1,3 +0,0 @@
1
- version https://git-lfs.github.com/spec/v1
2
- oid sha256:17de86abcebc0cebad76a935509a91336050962a6dc0b95a9b32cdc20dd73663
3
- size 72483299