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2024-09-05 22:43:35.221687: I tensorflow/core/util/port.cc:153] oneDNN custom operations are on. You may see slightly different numerical results due to floating-point round-off errors from different computation orders. To turn them off, set the environment variable `TF_ENABLE_ONEDNN_OPTS=0`.
2024-09-05 22:43:35.239699: E external/local_xla/xla/stream_executor/cuda/cuda_fft.cc:485] Unable to register cuFFT factory: Attempting to register factory for plugin cuFFT when one has already been registered
2024-09-05 22:43:35.261393: E external/local_xla/xla/stream_executor/cuda/cuda_dnn.cc:8454] Unable to register cuDNN factory: Attempting to register factory for plugin cuDNN when one has already been registered
2024-09-05 22:43:35.267947: E external/local_xla/xla/stream_executor/cuda/cuda_blas.cc:1452] Unable to register cuBLAS factory: Attempting to register factory for plugin cuBLAS when one has already been registered
2024-09-05 22:43:35.283519: I tensorflow/core/platform/cpu_feature_guard.cc:210] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations.
To enable the following instructions: AVX2 AVX512F AVX512_VNNI FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags.
2024-09-05 22:43:36.568969: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not find TensorRT
/usr/local/lib/python3.10/dist-packages/transformers/training_args.py:1525: FutureWarning: `evaluation_strategy` is deprecated and will be removed in version 4.46 of 🤗 Transformers. Use `eval_strategy` instead
warnings.warn(
09/05/2024 22:43:38 - WARNING - __main__ - Process rank: 0, device: cuda:0, n_gpu: 1distributed training: True, 16-bits training: False
09/05/2024 22:43:38 - INFO - __main__ - Training/evaluation parameters TrainingArguments(
_n_gpu=1,
accelerator_config={'split_batches': False, 'dispatch_batches': None, 'even_batches': True, 'use_seedable_sampler': True, 'non_blocking': False, 'gradient_accumulation_kwargs': None, 'use_configured_state': False},
adafactor=False,
adam_beta1=0.9,
adam_beta2=0.999,
adam_epsilon=1e-08,
auto_find_batch_size=False,
batch_eval_metrics=False,
bf16=False,
bf16_full_eval=False,
data_seed=None,
dataloader_drop_last=False,
dataloader_num_workers=0,
dataloader_persistent_workers=False,
dataloader_pin_memory=True,
dataloader_prefetch_factor=None,
ddp_backend=None,
ddp_broadcast_buffers=None,
ddp_bucket_cap_mb=None,
ddp_find_unused_parameters=None,
ddp_timeout=1800,
debug=[],
deepspeed=None,
disable_tqdm=False,
dispatch_batches=None,
do_eval=True,
do_predict=True,
do_train=True,
eval_accumulation_steps=None,
eval_delay=0,
eval_do_concat_batches=True,
eval_on_start=False,
eval_steps=None,
eval_strategy=epoch,
eval_use_gather_object=False,
evaluation_strategy=epoch,
fp16=False,
fp16_backend=auto,
fp16_full_eval=False,
fp16_opt_level=O1,
fsdp=[],
fsdp_config={'min_num_params': 0, 'xla': False, 'xla_fsdp_v2': False, 'xla_fsdp_grad_ckpt': False},
fsdp_min_num_params=0,
fsdp_transformer_layer_cls_to_wrap=None,
full_determinism=False,
gradient_accumulation_steps=2,
gradient_checkpointing=False,
gradient_checkpointing_kwargs=None,
greater_is_better=True,
group_by_length=False,
half_precision_backend=auto,
hub_always_push=False,
hub_model_id=None,
hub_private_repo=False,
hub_strategy=every_save,
hub_token=<HUB_TOKEN>,
ignore_data_skip=False,
include_inputs_for_metrics=False,
include_num_input_tokens_seen=False,
include_tokens_per_second=False,
jit_mode_eval=False,
label_names=None,
label_smoothing_factor=0.0,
learning_rate=5e-05,
length_column_name=length,
load_best_model_at_end=True,
local_rank=0,
log_level=passive,
log_level_replica=warning,
log_on_each_node=True,
logging_dir=/content/dissertation/scripts/ner/output/tb,
logging_first_step=False,
logging_nan_inf_filter=True,
logging_steps=500,
logging_strategy=steps,
lr_scheduler_kwargs={},
lr_scheduler_type=linear,
max_grad_norm=1.0,
max_steps=-1,
metric_for_best_model=f1,
mp_parameters=,
neftune_noise_alpha=None,
no_cuda=False,
num_train_epochs=10.0,
optim=adamw_torch,
optim_args=None,
optim_target_modules=None,
output_dir=/content/dissertation/scripts/ner/output,
overwrite_output_dir=True,
past_index=-1,
per_device_eval_batch_size=8,
per_device_train_batch_size=32,
prediction_loss_only=False,
push_to_hub=True,
push_to_hub_model_id=None,
push_to_hub_organization=None,
push_to_hub_token=<PUSH_TO_HUB_TOKEN>,
ray_scope=last,
remove_unused_columns=True,
report_to=['tensorboard'],
restore_callback_states_from_checkpoint=False,
resume_from_checkpoint=None,
run_name=/content/dissertation/scripts/ner/output,
save_on_each_node=False,
save_only_model=False,
save_safetensors=True,
save_steps=500,
save_strategy=epoch,
save_total_limit=None,
seed=42,
skip_memory_metrics=True,
split_batches=None,
tf32=None,
torch_compile=False,
torch_compile_backend=None,
torch_compile_mode=None,
torch_empty_cache_steps=None,
torchdynamo=None,
tpu_metrics_debug=False,
tpu_num_cores=None,
use_cpu=False,
use_ipex=False,
use_legacy_prediction_loop=False,
use_mps_device=False,
warmup_ratio=0.0,
warmup_steps=0,
weight_decay=0.0,
)
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[INFO|configuration_utils.py:733] 2024-09-05 22:43:57,301 >> loading configuration file config.json from cache at /root/.cache/huggingface/hub/models--PlanTL-GOB-ES--bsc-bio-ehr-es/snapshots/1e543adb2d21f19d85a89305eebdbd64ab656b99/config.json
[INFO|configuration_utils.py:800] 2024-09-05 22:43:57,310 >> Model config RobertaConfig {
"_name_or_path": "PlanTL-GOB-ES/bsc-bio-ehr-es",
"architectures": [
"RobertaForMaskedLM"
],
"attention_probs_dropout_prob": 0.1,
"bos_token_id": 0,
"classifier_dropout": null,
"eos_token_id": 2,
"finetuning_task": "ner",
"gradient_checkpointing": false,
"hidden_act": "gelu",
"hidden_dropout_prob": 0.1,
"hidden_size": 768,
"id2label": {
"0": "O",
"1": "B-ENFERMEDAD",
"2": "I-ENFERMEDAD"
},
"initializer_range": 0.02,
"intermediate_size": 3072,
"label2id": {
"B-ENFERMEDAD": 1,
"I-ENFERMEDAD": 2,
"O": 0
},
"layer_norm_eps": 1e-05,
"max_position_embeddings": 514,
"model_type": "roberta",
"num_attention_heads": 12,
"num_hidden_layers": 12,
"pad_token_id": 1,
"position_embedding_type": "absolute",
"transformers_version": "4.44.2",
"type_vocab_size": 1,
"use_cache": true,
"vocab_size": 50262
}
[INFO|configuration_utils.py:733] 2024-09-05 22:43:57,806 >> loading configuration file config.json from cache at /root/.cache/huggingface/hub/models--PlanTL-GOB-ES--bsc-bio-ehr-es/snapshots/1e543adb2d21f19d85a89305eebdbd64ab656b99/config.json
[INFO|configuration_utils.py:800] 2024-09-05 22:43:57,808 >> Model config RobertaConfig {
"_name_or_path": "PlanTL-GOB-ES/bsc-bio-ehr-es",
"architectures": [
"RobertaForMaskedLM"
],
"attention_probs_dropout_prob": 0.1,
"bos_token_id": 0,
"classifier_dropout": null,
"eos_token_id": 2,
"gradient_checkpointing": false,
"hidden_act": "gelu",
"hidden_dropout_prob": 0.1,
"hidden_size": 768,
"initializer_range": 0.02,
"intermediate_size": 3072,
"layer_norm_eps": 1e-05,
"max_position_embeddings": 514,
"model_type": "roberta",
"num_attention_heads": 12,
"num_hidden_layers": 12,
"pad_token_id": 1,
"position_embedding_type": "absolute",
"transformers_version": "4.44.2",
"type_vocab_size": 1,
"use_cache": true,
"vocab_size": 50262
}
[INFO|tokenization_utils_base.py:2269] 2024-09-05 22:44:00,154 >> loading file vocab.json from cache at /root/.cache/huggingface/hub/models--PlanTL-GOB-ES--bsc-bio-ehr-es/snapshots/1e543adb2d21f19d85a89305eebdbd64ab656b99/vocab.json
[INFO|tokenization_utils_base.py:2269] 2024-09-05 22:44:00,154 >> loading file merges.txt from cache at /root/.cache/huggingface/hub/models--PlanTL-GOB-ES--bsc-bio-ehr-es/snapshots/1e543adb2d21f19d85a89305eebdbd64ab656b99/merges.txt
[INFO|tokenization_utils_base.py:2269] 2024-09-05 22:44:00,154 >> loading file tokenizer.json from cache at None
[INFO|tokenization_utils_base.py:2269] 2024-09-05 22:44:00,154 >> loading file added_tokens.json from cache at None
[INFO|tokenization_utils_base.py:2269] 2024-09-05 22:44:00,154 >> loading file special_tokens_map.json from cache at /root/.cache/huggingface/hub/models--PlanTL-GOB-ES--bsc-bio-ehr-es/snapshots/1e543adb2d21f19d85a89305eebdbd64ab656b99/special_tokens_map.json
[INFO|tokenization_utils_base.py:2269] 2024-09-05 22:44:00,154 >> loading file tokenizer_config.json from cache at /root/.cache/huggingface/hub/models--PlanTL-GOB-ES--bsc-bio-ehr-es/snapshots/1e543adb2d21f19d85a89305eebdbd64ab656b99/tokenizer_config.json
[INFO|configuration_utils.py:733] 2024-09-05 22:44:00,155 >> loading configuration file config.json from cache at /root/.cache/huggingface/hub/models--PlanTL-GOB-ES--bsc-bio-ehr-es/snapshots/1e543adb2d21f19d85a89305eebdbd64ab656b99/config.json
[INFO|configuration_utils.py:800] 2024-09-05 22:44:00,156 >> Model config RobertaConfig {
"_name_or_path": "PlanTL-GOB-ES/bsc-bio-ehr-es",
"architectures": [
"RobertaForMaskedLM"
],
"attention_probs_dropout_prob": 0.1,
"bos_token_id": 0,
"classifier_dropout": null,
"eos_token_id": 2,
"gradient_checkpointing": false,
"hidden_act": "gelu",
"hidden_dropout_prob": 0.1,
"hidden_size": 768,
"initializer_range": 0.02,
"intermediate_size": 3072,
"layer_norm_eps": 1e-05,
"max_position_embeddings": 514,
"model_type": "roberta",
"num_attention_heads": 12,
"num_hidden_layers": 12,
"pad_token_id": 1,
"position_embedding_type": "absolute",
"transformers_version": "4.44.2",
"type_vocab_size": 1,
"use_cache": true,
"vocab_size": 50262
}
/usr/local/lib/python3.10/dist-packages/transformers/tokenization_utils_base.py:1601: FutureWarning: `clean_up_tokenization_spaces` was not set. It will be set to `True` by default. This behavior will be depracted in transformers v4.45, and will be then set to `False` by default. For more details check this issue: https://github.com/huggingface/transformers/issues/31884
warnings.warn(
[INFO|configuration_utils.py:733] 2024-09-05 22:44:00,243 >> loading configuration file config.json from cache at /root/.cache/huggingface/hub/models--PlanTL-GOB-ES--bsc-bio-ehr-es/snapshots/1e543adb2d21f19d85a89305eebdbd64ab656b99/config.json
[INFO|configuration_utils.py:800] 2024-09-05 22:44:00,244 >> Model config RobertaConfig {
"_name_or_path": "PlanTL-GOB-ES/bsc-bio-ehr-es",
"architectures": [
"RobertaForMaskedLM"
],
"attention_probs_dropout_prob": 0.1,
"bos_token_id": 0,
"classifier_dropout": null,
"eos_token_id": 2,
"gradient_checkpointing": false,
"hidden_act": "gelu",
"hidden_dropout_prob": 0.1,
"hidden_size": 768,
"initializer_range": 0.02,
"intermediate_size": 3072,
"layer_norm_eps": 1e-05,
"max_position_embeddings": 514,
"model_type": "roberta",
"num_attention_heads": 12,
"num_hidden_layers": 12,
"pad_token_id": 1,
"position_embedding_type": "absolute",
"transformers_version": "4.44.2",
"type_vocab_size": 1,
"use_cache": true,
"vocab_size": 50262
}
[INFO|modeling_utils.py:3678] 2024-09-05 22:44:31,232 >> loading weights file pytorch_model.bin from cache at /root/.cache/huggingface/hub/models--PlanTL-GOB-ES--bsc-bio-ehr-es/snapshots/1e543adb2d21f19d85a89305eebdbd64ab656b99/pytorch_model.bin
[INFO|modeling_utils.py:4497] 2024-09-05 22:44:31,384 >> Some weights of the model checkpoint at PlanTL-GOB-ES/bsc-bio-ehr-es were not used when initializing RobertaForTokenClassification: ['lm_head.bias', 'lm_head.decoder.bias', 'lm_head.decoder.weight', 'lm_head.dense.bias', 'lm_head.dense.weight', 'lm_head.layer_norm.bias', 'lm_head.layer_norm.weight']
- This IS expected if you are initializing RobertaForTokenClassification from the checkpoint of a model trained on another task or with another architecture (e.g. initializing a BertForSequenceClassification model from a BertForPreTraining model).
- This IS NOT expected if you are initializing RobertaForTokenClassification from the checkpoint of a model that you expect to be exactly identical (initializing a BertForSequenceClassification model from a BertForSequenceClassification model).
[WARNING|modeling_utils.py:4509] 2024-09-05 22:44:31,384 >> Some weights of RobertaForTokenClassification were not initialized from the model checkpoint at PlanTL-GOB-ES/bsc-bio-ehr-es and are newly initialized: ['classifier.bias', 'classifier.weight']
You should probably TRAIN this model on a down-stream task to be able to use it for predictions and inference.
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/content/dissertation/scripts/ner/run_ner_train.py:397: FutureWarning: load_metric is deprecated and will be removed in the next major version of datasets. Use 'evaluate.load' instead, from the new library 🤗 Evaluate: https://huggingface.co/docs/evaluate
metric = load_metric("seqeval", trust_remote_code=True)
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[INFO|trainer.py:811] 2024-09-05 22:44:38,444 >> The following columns in the training set don't have a corresponding argument in `RobertaForTokenClassification.forward` and have been ignored: id, ner_tags, tokens. If id, ner_tags, tokens are not expected by `RobertaForTokenClassification.forward`, you can safely ignore this message.
[INFO|trainer.py:2134] 2024-09-05 22:44:39,141 >> ***** Running training *****
[INFO|trainer.py:2135] 2024-09-05 22:44:39,141 >> Num examples = 31,947
[INFO|trainer.py:2136] 2024-09-05 22:44:39,141 >> Num Epochs = 10
[INFO|trainer.py:2137] 2024-09-05 22:44:39,141 >> Instantaneous batch size per device = 32
[INFO|trainer.py:2140] 2024-09-05 22:44:39,141 >> Total train batch size (w. parallel, distributed & accumulation) = 64
[INFO|trainer.py:2141] 2024-09-05 22:44:39,141 >> Gradient Accumulation steps = 2
[INFO|trainer.py:2142] 2024-09-05 22:44:39,141 >> Total optimization steps = 4,990
[INFO|trainer.py:2143] 2024-09-05 22:44:39,142 >> Number of trainable parameters = 124,055,043
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10%|█ | 499/4990 [02:01<18:19, 4.08it/s][INFO|trainer.py:811] 2024-09-05 22:46:40,950 >> The following columns in the evaluation set don't have a corresponding argument in `RobertaForTokenClassification.forward` and have been ignored: id, ner_tags, tokens. If id, ner_tags, tokens are not expected by `RobertaForTokenClassification.forward`, you can safely ignore this message.
[INFO|trainer.py:3819] 2024-09-05 22:46:40,953 >>
***** Running Evaluation *****
[INFO|trainer.py:3821] 2024-09-05 22:46:40,953 >> Num examples = 6810
[INFO|trainer.py:3824] 2024-09-05 22:46:40,953 >> Batch size = 8
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[A
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[A[INFO|trainer.py:3503] 2024-09-05 22:46:55,159 >> Saving model checkpoint to /content/dissertation/scripts/ner/output/checkpoint-499
[INFO|configuration_utils.py:472] 2024-09-05 22:46:55,160 >> Configuration saved in /content/dissertation/scripts/ner/output/checkpoint-499/config.json
[INFO|modeling_utils.py:2799] 2024-09-05 22:46:56,182 >> Model weights saved in /content/dissertation/scripts/ner/output/checkpoint-499/model.safetensors
[INFO|tokenization_utils_base.py:2684] 2024-09-05 22:46:56,183 >> tokenizer config file saved in /content/dissertation/scripts/ner/output/checkpoint-499/tokenizer_config.json
[INFO|tokenization_utils_base.py:2693] 2024-09-05 22:46:56,183 >> Special tokens file saved in /content/dissertation/scripts/ner/output/checkpoint-499/special_tokens_map.json
[INFO|tokenization_utils_base.py:2684] 2024-09-05 22:46:58,215 >> tokenizer config file saved in /content/dissertation/scripts/ner/output/tokenizer_config.json
[INFO|tokenization_utils_base.py:2693] 2024-09-05 22:46:58,215 >> Special tokens file saved in /content/dissertation/scripts/ner/output/special_tokens_map.json
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