Delete pretrain_tokens/wandb
Browse files- pretrain_tokens/wandb/debug-internal.log +0 -15
- pretrain_tokens/wandb/debug.log +0 -27
- pretrain_tokens/wandb/run-20260409_024256-4yonu3x2/files/config.yaml +0 -613
- pretrain_tokens/wandb/run-20260409_024256-4yonu3x2/files/output.log +0 -268
- pretrain_tokens/wandb/run-20260409_024256-4yonu3x2/files/requirements.txt +0 -148
- pretrain_tokens/wandb/run-20260409_024256-4yonu3x2/files/wandb-metadata.json +0 -149
- pretrain_tokens/wandb/run-20260409_024256-4yonu3x2/files/wandb-summary.json +0 -1
- pretrain_tokens/wandb/run-20260409_024256-4yonu3x2/logs/debug-core.log +0 -14
- pretrain_tokens/wandb/run-20260409_024256-4yonu3x2/logs/debug-internal.log +0 -11
- pretrain_tokens/wandb/run-20260409_024256-4yonu3x2/logs/debug.log +0 -27
- pretrain_tokens/wandb/run-20260409_024256-4yonu3x2/run-4yonu3x2.wandb +0 -3
- pretrain_tokens/wandb/run-20260409_031927-9ph1pkcx/files/config.yaml +0 -613
- pretrain_tokens/wandb/run-20260409_031927-9ph1pkcx/files/output.log +0 -0
- pretrain_tokens/wandb/run-20260409_031927-9ph1pkcx/files/requirements.txt +0 -148
- pretrain_tokens/wandb/run-20260409_031927-9ph1pkcx/files/wandb-metadata.json +0 -149
- pretrain_tokens/wandb/run-20260409_031927-9ph1pkcx/files/wandb-summary.json +0 -1
- pretrain_tokens/wandb/run-20260409_031927-9ph1pkcx/logs/debug-core.log +0 -14
- pretrain_tokens/wandb/run-20260409_031927-9ph1pkcx/logs/debug-internal.log +0 -15
- pretrain_tokens/wandb/run-20260409_031927-9ph1pkcx/logs/debug.log +0 -27
- pretrain_tokens/wandb/run-20260409_031927-9ph1pkcx/run-9ph1pkcx.wandb +0 -3
pretrain_tokens/wandb/debug-internal.log
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{"time":"2026-04-09T03:19:28.253252886Z","level":"INFO","msg":"stream: starting","core version":"0.23.1"}
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{"time":"2026-04-09T03:19:28.588342136Z","level":"INFO","msg":"stream: created new stream","id":"9ph1pkcx"}
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{"time":"2026-04-09T03:19:28.588502646Z","level":"INFO","msg":"handler: started","stream_id":"9ph1pkcx"}
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{"time":"2026-04-09T03:19:28.588564816Z","level":"INFO","msg":"stream: started","id":"9ph1pkcx"}
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{"time":"2026-04-09T03:19:28.588589346Z","level":"INFO","msg":"writer: started","stream_id":"9ph1pkcx"}
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{"time":"2026-04-09T03:19:28.588586606Z","level":"INFO","msg":"sender: started","stream_id":"9ph1pkcx"}
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{"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"}
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{"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)"}
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{"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)"}
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{"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)"}
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{"time":"2026-04-12T03:29:56.516755613Z","level":"INFO","msg":"stream: closing","id":"9ph1pkcx"}
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{"time":"2026-04-12T03:29:56.970094158Z","level":"INFO","msg":"fileTransfer: Close: file transfer manager closed"}
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{"time":"2026-04-12T03:29:57.220807579Z","level":"INFO","msg":"handler: closed","stream_id":"9ph1pkcx"}
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{"time":"2026-04-12T03:29:57.220969499Z","level":"INFO","msg":"sender: closed","stream_id":"9ph1pkcx"}
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{"time":"2026-04-12T03:29:57.220985529Z","level":"INFO","msg":"stream: closed","id":"9ph1pkcx"}
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pretrain_tokens/wandb/debug.log
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2026-04-09 03:19:27,927 INFO MainThread:3566905 [wandb_setup.py:_flush():80] Current SDK version is 0.23.1
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2026-04-09 03:19:27,927 INFO MainThread:3566905 [wandb_setup.py:_flush():80] Configure stats pid to 3566905
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2026-04-09 03:19:27,927 INFO MainThread:3566905 [wandb_setup.py:_flush():80] Loading settings from /home/n5huang/.config/wandb/settings
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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
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2026-04-09 03:19:27,927 INFO MainThread:3566905 [wandb_setup.py:_flush():80] Loading settings from environment variables
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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
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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
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2026-04-09 03:19:27,927 INFO MainThread:3566905 [wandb_init.py:init():841] calling init triggers
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2026-04-09 03:19:27,927 INFO MainThread:3566905 [wandb_init.py:init():846] wandb.init called with sweep_config: {}
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config: {'_wandb': {}}
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2026-04-09 03:19:27,927 INFO MainThread:3566905 [wandb_init.py:init():889] starting backend
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2026-04-09 03:19:28,217 INFO MainThread:3566905 [wandb_init.py:init():892] sending inform_init request
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2026-04-09 03:19:28,251 INFO MainThread:3566905 [wandb_init.py:init():900] backend started and connected
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2026-04-09 03:19:28,254 INFO MainThread:3566905 [wandb_init.py:init():970] updated telemetry
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2026-04-09 03:19:28,256 INFO MainThread:3566905 [wandb_init.py:init():994] communicating run to backend with 90.0 second timeout
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2026-04-09 03:19:28,885 INFO MainThread:3566905 [wandb_init.py:init():1041] starting run threads in backend
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2026-04-09 03:19:28,994 INFO MainThread:3566905 [wandb_run.py:_console_start():2521] atexit reg
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2026-04-09 03:19:28,994 INFO MainThread:3566905 [wandb_run.py:_redirect():2369] redirect: wrap_raw
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2026-04-09 03:19:28,994 INFO MainThread:3566905 [wandb_run.py:_redirect():2438] Wrapping output streams.
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2026-04-09 03:19:28,995 INFO MainThread:3566905 [wandb_run.py:_redirect():2461] Redirects installed.
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2026-04-09 03:19:29,000 INFO MainThread:3566905 [wandb_init.py:init():1081] run started, returning control to user process
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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}
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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}
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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}
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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}
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2026-04-12 03:29:56,516 INFO wandb-AsyncioManager-main:3566905 [service_client.py:_forward_responses():80] Reached EOF.
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2026-04-12 03:29:56,516 INFO wandb-AsyncioManager-main:3566905 [mailbox.py:close():137] Closing mailbox, abandoning 1 handles.
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pretrain_tokens/wandb/run-20260409_024256-4yonu3x2/files/config.yaml
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__cached__setup_devices:
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value: cuda:0
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_n_gpu:
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value: 1
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_name_or_path:
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value: ""
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_wandb:
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value:
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cli_version: 0.23.1
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e:
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8xva522u4d798tgf5m4gfomp910saafd:
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args:
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- --output_dir
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- /home/n5huang/dna_token/pretrain/models/len2_5120
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- --model_type
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- bert
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- --tokenizer_name
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- /home/n5huang/dna_token/tokenizer_evaluation/merge_bpe/vocab_5120/merge_tokenizer_unigram_len2.json
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- --config_name
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- /home/n5huang/dna_token/pretrain/models/len2_5120/config.json
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- --project_name
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- token_eval_len2_5120
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- --do_train
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- "True"
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- --model_max_length
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- "512"
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- --max_seq_length
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- "512"
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- --line_by_line
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- "True"
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pretrain_tokens/wandb/run-20260409_024256-4yonu3x2/files/output.log
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04/09/2026 02:42:57 - WARNING - __main__ - Process rank: 0, device: cuda:0, n_gpu: 1, distributed training: False, 16-bits training: False
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04/09/2026 02:42:57 - INFO - __main__ - Training/evaluation parameters TrainingArguments(
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_n_gpu=1,
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adafactor=False,
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adam_beta1=0.9,
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adam_beta2=0.98,
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adam_epsilon=1e-06,
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auto_find_batch_size=False,
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bf16=False,
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bf16_full_eval=False,
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data_seed=None,
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dataloader_drop_last=False,
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dataloader_num_workers=0,
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dataloader_pin_memory=True,
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ddp_backend=None,
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ddp_broadcast_buffers=None,
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ddp_bucket_cap_mb=None,
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ddp_find_unused_parameters=None,
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ddp_timeout=1800,
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debug=[],
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deepspeed=None,
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disable_tqdm=False,
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dispatch_batches=None,
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do_eval=True,
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do_predict=False,
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do_train=True,
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eval_accumulation_steps=None,
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eval_steps=None,
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evaluation_strategy=no,
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fp16=False,
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fp16_backend=auto,
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fp16_full_eval=False,
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fp16_opt_level=O1,
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fsdp=[],
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fsdp_config={'min_num_params': 0, 'xla': False, 'xla_fsdp_grad_ckpt': False},
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fsdp_min_num_params=0,
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fsdp_transformer_layer_cls_to_wrap=None,
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full_determinism=False,
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gradient_accumulation_steps=1,
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gradient_checkpointing=False,
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gradient_checkpointing_kwargs=None,
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greater_is_better=None,
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group_by_length=False,
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half_precision_backend=auto,
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hub_always_push=False,
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hub_private_repo=False,
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hub_strategy=every_save,
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hub_token=<HUB_TOKEN>,
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ignore_data_skip=False,
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include_inputs_for_metrics=False,
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include_tokens_per_second=False,
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jit_mode_eval=False,
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label_names=None,
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label_smoothing_factor=0.0,
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learning_rate=4e-05,
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length_column_name=length,
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load_best_model_at_end=False,
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local_rank=0,
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log_level=passive,
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log_level_replica=warning,
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log_on_each_node=True,
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logging_dir=/home/n5huang/dna_token/pretrain/models/len2_5120/runs/Apr09_02-42-57_sn4622116170,
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logging_first_step=False,
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logging_nan_inf_filter=True,
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logging_steps=1000,
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logging_strategy=steps,
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lr_scheduler_type=linear,
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max_grad_norm=1.0,
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max_steps=100000,
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metric_for_best_model=None,
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mp_parameters=,
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neftune_noise_alpha=None,
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no_cuda=False,
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num_train_epochs=3.0,
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optim=adamw_torch,
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optim_args=None,
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output_dir=/home/n5huang/dna_token/pretrain/models/len2_5120,
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overwrite_output_dir=False,
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past_index=-1,
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per_device_eval_batch_size=96,
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per_device_train_batch_size=96,
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prediction_loss_only=False,
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push_to_hub=False,
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push_to_hub_model_id=None,
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push_to_hub_organization=None,
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push_to_hub_token=<PUSH_TO_HUB_TOKEN>,
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ray_scope=last,
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remove_unused_columns=True,
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report_to=['wandb'],
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resume_from_checkpoint=/home/n5huang/dna_token/pretrain/models/len2_5120/checkpoint-100000,
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run_name=/home/n5huang/dna_token/pretrain/models/len2_5120,
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save_on_each_node=False,
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save_safetensors=True,
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skip_memory_metrics=True,
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split_batches=False,
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tf32=None,
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torch_compile=False,
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tpu_metrics_debug=False,
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tpu_num_cores=None,
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use_cpu=False,
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use_ipex=False,
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use_legacy_prediction_loop=False,
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use_mps_device=False,
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warmup_ratio=0.0,
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warmup_steps=10000,
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weight_decay=0.01,
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)
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Using custom data configuration default-9aa68439a1bf4533
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04/09/2026 02:42:58 - INFO - datasets.builder - Using custom data configuration default-9aa68439a1bf4533
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| 119 |
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Generating dataset csv (/home/n5huang/dna_token/output_tokens/cache/csv/default-9aa68439a1bf4533/0.0.0/a43390c7ecea6519ff2ce9d10005c8750601c9e456069be5efbd2747df45f420)
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| 120 |
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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)
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| 121 |
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Downloading and preparing dataset csv/default to /home/n5huang/dna_token/output_tokens/cache/csv/default-9aa68439a1bf4533/0.0.0/a43390c7ecea6519ff2ce9d10005c8750601c9e456069be5efbd2747df45f420...
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| 122 |
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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...
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Downloading took 0.0 min
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04/09/2026 02:42:58 - INFO - datasets.download.download_manager - Downloading took 0.0 min
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Checksum Computation took 0.0 min
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04/09/2026 02:42:58 - INFO - datasets.download.download_manager - Checksum Computation took 0.0 min
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Generating train split
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04/09/2026 02:42:58 - INFO - datasets.builder - Generating train split
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Generating train split: 982503 examples [00:24, 40012.03 examples/s]
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Generating validation split
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04/09/2026 02:43:22 - INFO - datasets.builder - Generating validation split
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Generating validation split: 109173 examples [00:02, 40132.11 examples/s]
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Unable to verify splits sizes.
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04/09/2026 02:43:25 - INFO - datasets.utils.info_utils - Unable to verify splits sizes.
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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.
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| 136 |
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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.
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[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
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[INFO|configuration_utils.py:777] 2026-04-09 02:43:25,497 >> Model config BertConfig {
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"architectures": [
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"BertForMaskedLM"
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],
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"attention_probs_dropout_prob": 0.1,
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"classifier_dropout": null,
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"hidden_act": "gelu",
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"hidden_dropout_prob": 0.1,
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"hidden_size": 768,
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"initializer_range": 0.02,
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"intermediate_size": 3072,
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"layer_norm_eps": 1e-12,
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"max_length": 512,
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"max_position_embeddings": 512,
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"model_type": "bert",
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"num_attention_heads": 12,
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"num_hidden_layers": 12,
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"pad_token_id": 0,
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"position_embedding_type": "absolute",
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"torch_dtype": "float32",
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"transformers_version": "4.35.2",
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"type_vocab_size": 2,
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"use_cache": true,
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"vocab_size": 5120
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}
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04/09/2026 02:43:25 - INFO - __main__ - Training new model from scratch
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| 164 |
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| 165 |
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/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.
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_torch_pytree._register_pytree_node(
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[INFO|configuration_utils.py:791] 2026-04-09 02:43:25,507 >> Generate config GenerationConfig {
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"max_length": 512,
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"pad_token_id": 0
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}
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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Running tokenizer on dataset line_by_line (num_proc=8): 0%| | 0/982503 [00:00<?, ? examples/s]Spawning 8 processes
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04/09/2026 02:43:41 - INFO - datasets.arrow_dataset - Spawning 8 processes
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Running tokenizer on dataset line_by_line (num_proc=8): 100%|██████████| 982503/982503 [02:32<00:00, 6449.24 examples/s]
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Concatenating 8 shards
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04/09/2026 02:46:14 - INFO - datasets.arrow_dataset - Concatenating 8 shards
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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
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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
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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
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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 |
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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}]}
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|
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
|
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networkx==3.2.1
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PySocks==1.7.1
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tornado==6.5.2
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smmap==5.0.2
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PyQt5==5.15.10
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nvidia-cufft-cu12==11.3.3.83
|
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safetensors==0.7.0
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requests==2.32.5
|
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pytz==2025.2
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| 94 |
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fsspec==2025.7.0
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certifi==2025.10.5
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sentry-sdk==2.35.0
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parso==0.8.4
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hf-xet==1.1.8
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nvidia-cudnn-cu12==9.10.2.21
|
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accelerate==0.25.0
|
| 103 |
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eval_type_backport==0.2.2
|
| 104 |
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datasets==4.4.1
|
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huggingface_hub==0.34.4
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wandb==0.23.1
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tomli==2.2.1
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comm==0.2.3
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executing==2.2.0
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PyYAML==6.0.2
|
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scipy==1.13.1
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pexpect==4.9.0
|
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matplotlib==3.9.2
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annotated-types==0.7.0
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asttokens==3.0.0
|
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tokenizers==0.15.2
|
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nvidia-cufile-cu12==1.13.1.3
|
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h11==0.16.0
|
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numpy==2.0.2
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joblib==1.5.3
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MarkupSafe==3.0.3
|
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nvidia-nvjitlink-cu12==12.8.93
|
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pyarrow==21.0.0
|
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torch==2.8.0
|
| 129 |
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protobuf==3.20.3
|
| 130 |
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propcache==0.4.1
|
| 131 |
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multidict==6.7.0
|
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nvidia-cusolver-cu12==11.7.3.90
|
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umap-learn==0.5.9.post2
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ipykernel==6.30.1
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sympy==1.14.0
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pynndescent==0.5.13
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|
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typing-inspection==0.4.1
|
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evaluate==0.4.6
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nvidia-cuda-runtime-cu12==12.8.90
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filelock==3.17.0
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aiohappyeyeballs==2.6.1
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setuptools==80.9.0
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pretrain_tokens/wandb/run-20260409_024256-4yonu3x2/files/wandb-metadata.json
DELETED
|
@@ -1,149 +0,0 @@
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| 6 |
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| 8 |
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| 9 |
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| 10 |
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| 11 |
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| 12 |
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"--config_name",
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| 13 |
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"/home/n5huang/dna_token/pretrain/models/len2_5120/config.json",
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| 14 |
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| 15 |
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| 16 |
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| 17 |
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|
| 18 |
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|
| 19 |
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"512",
|
| 20 |
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|
| 21 |
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"512",
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| 22 |
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| 23 |
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| 24 |
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|
| 25 |
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| 26 |
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| 27 |
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| 28 |
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|
| 29 |
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| 30 |
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| 31 |
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| 32 |
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| 33 |
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"True",
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| 34 |
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|
| 35 |
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| 36 |
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"--gradient_accumulation_steps",
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| 37 |
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| 38 |
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| 39 |
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| 40 |
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| 41 |
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| 42 |
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| 43 |
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| 44 |
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| 45 |
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| 46 |
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| 47 |
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| 48 |
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|
| 49 |
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| 50 |
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| 51 |
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| 52 |
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| 53 |
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| 54 |
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| 55 |
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| 56 |
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| 70 |
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| 71 |
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pretrain_tokens/wandb/run-20260409_024256-4yonu3x2/files/wandb-summary.json
DELETED
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@@ -1 +0,0 @@
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pretrain_tokens/wandb/run-20260409_024256-4yonu3x2/logs/debug-core.log
DELETED
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@@ -1,14 +0,0 @@
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pretrain_tokens/wandb/run-20260409_031927-9ph1pkcx/files/output.log
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|
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|
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|
pretrain_tokens/wandb/run-20260409_031927-9ph1pkcx/files/requirements.txt
DELETED
|
@@ -1,148 +0,0 @@
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| 1 |
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nvidia-cusparse-cu12==12.5.8.93
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nest_asyncio==1.6.0
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nvidia-cusparselt-cu12==0.7.1
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contourpy==1.2.1
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idna==3.11
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pycparser==2.23
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python-dateutil==2.9.0.post0
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wheel==0.45.1
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importlib_resources==6.5.2
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exceptiongroup==1.3.0
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exceptiongroup==1.3.1
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gitdb==4.0.12
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pip==25.3
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pillow==11.3.0
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jupyter_core==5.8.1
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packaging==25.0
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nvidia-nccl-cu12==2.27.3
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ipython==8.18.1
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anyio==4.12.0
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prompt_toolkit==3.0.51
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mkl_fft==1.3.11
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httpcore==1.0.9
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Jinja2==3.1.6
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ply==3.11
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setproctitle==1.3.6
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docker-pycreds==0.4.0
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nvidia-cuda-nvrtc-cu12==12.8.93
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urllib3==2.5.0
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nvidia-curand-cu12==10.3.9.90
|
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llvmlite==0.43.0
|
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six==1.17.0
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| 60 |
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frozenlist==1.8.0
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wcwidth==0.2.13
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numexpr==2.10.1
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click==8.1.8
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multiprocess==0.70.18
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threadpoolctl==3.6.0
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typing_extensions==4.15.0
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decorator==5.2.1
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sip==6.7.12
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pure_eval==0.2.3
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async-timeout==5.0.1
|
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Pygments==2.19.2
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| 72 |
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mkl-service==2.4.0
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transformers==4.35.2
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numba==0.60.0
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pyzmq==27.0.2
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mkl_random==1.2.8
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ptyprocess==0.7.0
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nvidia-cuda-cupti-cu12==12.8.90
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charset-normalizer==3.4.4
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nvidia-cublas-cu12==12.8.4.1
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PyQt5_sip==12.13.0
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Bottleneck==1.4.2
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networkx==3.2.1
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PySocks==1.7.1
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pysam==0.9.1
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tornado==6.5.2
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pandas==2.3.3
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smmap==5.0.2
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PyQt5==5.15.10
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nvidia-cufft-cu12==11.3.3.83
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safetensors==0.7.0
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requests==2.32.5
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pytz==2025.2
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fsspec==2025.7.0
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certifi==2025.10.5
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parso==0.8.4
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traitlets==5.14.3
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hf-xet==1.1.8
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nvidia-cudnn-cu12==9.10.2.21
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accelerate==0.25.0
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eval_type_backport==0.2.2
|
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datasets==4.4.1
|
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huggingface_hub==0.34.4
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wandb==0.23.1
|
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tomli==2.2.1
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comm==0.2.3
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executing==2.2.0
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PyYAML==6.0.2
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scipy==1.13.1
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pexpect==4.9.0
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matplotlib==3.9.2
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| 114 |
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annotated-types==0.7.0
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asttokens==3.0.0
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tokenizers==0.15.2
|
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nvidia-cufile-cu12==1.13.1.3
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appdirs==1.4.4
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MarkupSafe==3.0.3
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nvidia-nvjitlink-cu12==12.8.93
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pyarrow==21.0.0
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torch==2.8.0
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protobuf==3.20.3
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propcache==0.4.1
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nvidia-cusolver-cu12==11.7.3.90
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umap-learn==0.5.9.post2
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|
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",
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| 3 |
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"python": "CPython 3.9.18",
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| 4 |
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"startedAt": "2026-04-09T03:19:27.923698Z",
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| 5 |
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"args": [
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| 6 |
-
"--output_dir",
|
| 7 |
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"/home/n5huang/dna_token/pretrain/models/len2_5120",
|
| 8 |
-
"--model_type",
|
| 9 |
-
"bert",
|
| 10 |
-
"--tokenizer_name",
|
| 11 |
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"/home/n5huang/dna_token/tokenizer_evaluation/merge_bpe/vocab_5120/merge_tokenizer_unigram_len2.json",
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| 12 |
-
"--config_name",
|
| 13 |
-
"/home/n5huang/dna_token/pretrain/models/len2_5120/config.json",
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| 14 |
-
"--project_name",
|
| 15 |
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"token_eval_len2_5120",
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| 16 |
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"--do_train",
|
| 17 |
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"True",
|
| 18 |
-
"--model_max_length",
|
| 19 |
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"512",
|
| 20 |
-
"--max_seq_length",
|
| 21 |
-
"512",
|
| 22 |
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"--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 |
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"/home/n5huang/dna_token/output_tokens/cache",
|
| 32 |
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"--use_fast_tokenizer",
|
| 33 |
-
"True",
|
| 34 |
-
"--do_eval",
|
| 35 |
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"True",
|
| 36 |
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"--gradient_accumulation_steps",
|
| 37 |
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"1",
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| 38 |
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"--per_device_train_batch_size",
|
| 39 |
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"96",
|
| 40 |
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"--per_device_eval_batch_size",
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| 41 |
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"96",
|
| 42 |
-
"--save_steps",
|
| 43 |
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"1000",
|
| 44 |
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"--save_total_limit",
|
| 45 |
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"10",
|
| 46 |
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"--max_steps",
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| 47 |
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"200000",
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| 48 |
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"--logging_steps",
|
| 49 |
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"1000",
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| 50 |
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"--learning_rate",
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| 51 |
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"4e-5",
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| 52 |
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"--adam_epsilon",
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| 53 |
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"1e-6",
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| 54 |
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"--weight_decay",
|
| 55 |
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"0.01",
|
| 56 |
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"--adam_beta1",
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| 57 |
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"0.9",
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| 58 |
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"--adam_beta2",
|
| 59 |
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| 60 |
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"--mlm_probability",
|
| 61 |
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| 62 |
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"--warmup_steps",
|
| 63 |
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| 64 |
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"--seed",
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| 65 |
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| 66 |
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| 67 |
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| 68 |
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| 69 |
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| 70 |
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],
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| 71 |
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"program": "/home/n5huang/dna-tokenizer/BPE_merge/run_mlm_200k.py",
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| 72 |
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| 73 |
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| 136 |
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"architecture": "Ampere",
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"uuid": "GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0"
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{
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"memoryTotal": "85899345920",
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"cudaCores": 6912,
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"architecture": "Ampere",
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"uuid": "GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044"
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"cudaVersion": "12.2",
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"writerId": "shyl6ozoxin31qqkhj4f84yadhwytjka"
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pretrain_tokens/wandb/run-20260409_031927-9ph1pkcx/files/wandb-summary.json
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@@ -1 +0,0 @@
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pretrain_tokens/wandb/run-20260409_031927-9ph1pkcx/logs/debug-core.log
DELETED
|
@@ -1,14 +0,0 @@
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| 1 |
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{"time":"2026-04-09T03:19:28.217201312Z","level":"INFO","msg":"connection: ManageConnectionData: new connection created","id":"1(@)"}
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| 10 |
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| 11 |
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| 12 |
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{"time":"2026-04-12T03:29:57.223915447Z","level":"INFO","msg":"handleInformTeardown: server shutdown complete","id":"1(@)"}
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{"time":"2026-04-12T03:29:57.223965837Z","level":"INFO","msg":"connection: ManageConnectionData: connection closed","id":"1(@)"}
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| 14 |
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{"time":"2026-04-12T03:29:57.223990097Z","level":"INFO","msg":"server is closed"}
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pretrain_tokens/wandb/run-20260409_031927-9ph1pkcx/logs/debug-internal.log
DELETED
|
@@ -1,15 +0,0 @@
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|
| 1 |
-
{"time":"2026-04-09T03:19:28.253252886Z","level":"INFO","msg":"stream: starting","core version":"0.23.1"}
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{"time":"2026-04-09T03:19:28.588502646Z","level":"INFO","msg":"handler: started","stream_id":"9ph1pkcx"}
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{"time":"2026-04-09T03:19:28.588589346Z","level":"INFO","msg":"writer: started","stream_id":"9ph1pkcx"}
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{"time":"2026-04-09T03:19:28.588586606Z","level":"INFO","msg":"sender: started","stream_id":"9ph1pkcx"}
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| 8 |
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{"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 |
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|
| 10 |
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|
| 11 |
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{"time":"2026-04-12T03:29:56.516755613Z","level":"INFO","msg":"stream: closing","id":"9ph1pkcx"}
|
| 12 |
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|
| 13 |
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{"time":"2026-04-12T03:29:57.220807579Z","level":"INFO","msg":"handler: closed","stream_id":"9ph1pkcx"}
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| 14 |
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{"time":"2026-04-12T03:29:57.220969499Z","level":"INFO","msg":"sender: closed","stream_id":"9ph1pkcx"}
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| 15 |
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{"time":"2026-04-12T03:29:57.220985529Z","level":"INFO","msg":"stream: closed","id":"9ph1pkcx"}
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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
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| 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 |
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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 |
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2026-04-09 03:19:28,217 INFO MainThread:3566905 [wandb_init.py:init():892] sending inform_init request
|
| 13 |
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2026-04-09 03:19:28,251 INFO MainThread:3566905 [wandb_init.py:init():900] backend started and connected
|
| 14 |
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2026-04-09 03:19:28,254 INFO MainThread:3566905 [wandb_init.py:init():970] updated telemetry
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| 15 |
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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 |
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2026-04-09 03:19:28,885 INFO MainThread:3566905 [wandb_init.py:init():1041] starting run threads in backend
|
| 17 |
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2026-04-09 03:19:28,994 INFO MainThread:3566905 [wandb_run.py:_console_start():2521] atexit reg
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| 18 |
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2026-04-09 03:19:28,994 INFO MainThread:3566905 [wandb_run.py:_redirect():2369] redirect: wrap_raw
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| 19 |
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2026-04-09 03:19:28,994 INFO MainThread:3566905 [wandb_run.py:_redirect():2438] Wrapping output streams.
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| 20 |
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2026-04-09 03:19:28,995 INFO MainThread:3566905 [wandb_run.py:_redirect():2461] Redirects installed.
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| 21 |
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2026-04-09 03:19:29,000 INFO MainThread:3566905 [wandb_init.py:init():1081] run started, returning control to user process
|
| 22 |
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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 |
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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 |
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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 |
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2026-04-12 03:29:56,516 INFO wandb-AsyncioManager-main:3566905 [mailbox.py:close():137] Closing mailbox, abandoning 1 handles.
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