Error loading weights

[rederyang]

When I ran this code in the reproducing results colab notebook:

!allennlp evaluate "$pretrained_model_url" "$preprocessed_data_dir/test.tsv" \
    --output-file "$output_dir/test_metrics.jsonl" \
    --cuda-device 0 \
    --predictions-output-file "$output_dir/test_predictions.jsonl" \
    --include-package "seq2rel"

I got this Error:

2024-04-12 10:27:06,782 - INFO - allennlp.common.plugins - Plugin allennlp_models available
2024-04-12 10:27:08,988 - INFO - cached_path - cache of https://github.com/JohnGiorgi/seq2rel/releases/download/pretrained-models/cdr_hints.tar.gz is up-to-date
2024-04-12 10:27:08,989 - INFO - allennlp.models.archival - loading archive file https://github.com/JohnGiorgi/seq2rel/releases/download/pretrained-models/cdr_hints.tar.gz from cache at /root/.allennlp/cache/5d845bebc5887213bab7c90a311e51d6dff9a03fb60648a6498d58be8397166c.82548b1687f75978154d471c6ead95e2dd4d865a01baaba9fa7873d62232ffbe
2024-04-12 10:27:08,990 - INFO - allennlp.models.archival - extracting archive file /root/.allennlp/cache/5d845bebc5887213bab7c90a311e51d6dff9a03fb60648a6498d58be8397166c.82548b1687f75978154d471c6ead95e2dd4d865a01baaba9fa7873d62232ffbe to temp dir /tmp/tmp0mo17roo
2024-04-12 10:27:15,245 - INFO - allennlp.models.archival - removing temporary unarchived model dir at /tmp/tmp0mo17roo
Traceback (most recent call last):
  File "/usr/local/lib/python3.8/site-packages/transformers/configuration_utils.py", line 616, in _get_config_dict
    resolved_config_file = cached_path(
  File "/usr/local/lib/python3.8/site-packages/transformers/utils/hub.py", line 284, in cached_path
    output_path = get_from_cache(
  File "/usr/local/lib/python3.8/site-packages/transformers/utils/hub.py", line 508, in get_from_cache
    raise OSError(
OSError: Distant resource does not have an ETag, we won't be able to reliably ensure reproducibility.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/local/bin/allennlp", line 8, in <module>
    sys.exit(run())
  File "/usr/local/lib/python3.8/site-packages/allennlp/__main__.py", line 39, in run
    main(prog="allennlp")
  File "/usr/local/lib/python3.8/site-packages/allennlp/commands/__init__.py", line 120, in main
    args.func(args)
  File "/usr/local/lib/python3.8/site-packages/allennlp/commands/evaluate.py", line 135, in evaluate_from_args
    return evaluate_from_archive(
  File "/usr/local/lib/python3.8/site-packages/allennlp/commands/evaluate.py", line 242, in evaluate_from_archive
    archive = load_archive(
  File "/usr/local/lib/python3.8/site-packages/allennlp/models/archival.py", line 232, in load_archive
    dataset_reader, validation_dataset_reader = _load_dataset_readers(
  File "/usr/local/lib/python3.8/site-packages/allennlp/models/archival.py", line 268, in _load_dataset_readers
    dataset_reader = DatasetReader.from_params(
  File "/usr/local/lib/python3.8/site-packages/allennlp/common/from_params.py", line 604, in from_params
    return retyped_subclass.from_params(
  File "/usr/local/lib/python3.8/site-packages/allennlp/common/from_params.py", line 636, in from_params
    kwargs = create_kwargs(constructor_to_inspect, cls, params, **extras)
  File "/usr/local/lib/python3.8/site-packages/allennlp/common/from_params.py", line 206, in create_kwargs
    constructed_arg = pop_and_construct_arg(
  File "/usr/local/lib/python3.8/site-packages/allennlp/common/from_params.py", line 314, in pop_and_construct_arg
    return construct_arg(class_name, name, popped_params, annotation, default, **extras)
  File "/usr/local/lib/python3.8/site-packages/allennlp/common/from_params.py", line 348, in construct_arg
    result = annotation.from_params(params=popped_params, **subextras)
  File "/usr/local/lib/python3.8/site-packages/allennlp/common/from_params.py", line 604, in from_params
    return retyped_subclass.from_params(
  File "/usr/local/lib/python3.8/site-packages/allennlp/common/from_params.py", line 638, in from_params
    return constructor_to_call(**kwargs)  # type: ignore
  File "/usr/local/lib/python3.8/site-packages/allennlp/data/tokenizers/pretrained_transformer_tokenizer.py", line 72, in __init__
    self.tokenizer = cached_transformers.get_tokenizer(
  File "/usr/local/lib/python3.8/site-packages/allennlp/common/cached_transformers.py", line 204, in get_tokenizer
    tokenizer = transformers.AutoTokenizer.from_pretrained(
  File "/usr/local/lib/python3.8/site-packages/transformers/models/auto/tokenization_auto.py", line 547, in from_pretrained
    config = AutoConfig.from_pretrained(
  File "/usr/local/lib/python3.8/site-packages/transformers/models/auto/configuration_auto.py", line 725, in from_pretrained
    config_dict, _ = PretrainedConfig.get_config_dict(pretrained_model_name_or_path, **kwargs)
  File "/usr/local/lib/python3.8/site-packages/transformers/configuration_utils.py", line 561, in get_config_dict
    config_dict, kwargs = cls._get_config_dict(pretrained_model_name_or_path, **kwargs)
  File "/usr/local/lib/python3.8/site-packages/transformers/configuration_utils.py", line 656, in _get_config_dict
    raise EnvironmentError(
OSError: Can't load config for 'microsoft/BiomedNLP-PubMedBERT-base-uncased-abstract-fulltext'. If you were trying to load it from 'https://huggingface.co/models', make sure you don't have a local directory with the same name. Otherwise, make sure 'microsoft/BiomedNLP-PubMedBERT-base-uncased-abstract-fulltext' is the correct path to a directory containing a config.json file

After upgrading to the latest version of transformers(4.39.3), this error is solved, but I got a new error:

2024-04-12 10:30:32,153 - INFO - allennlp.common.plugins - Plugin allennlp_models available
2024-04-12 10:30:34,344 - INFO - cached_path - cache of https://github.com/JohnGiorgi/seq2rel/releases/download/pretrained-models/cdr_hints.tar.gz is up-to-date
2024-04-12 10:30:34,345 - INFO - allennlp.models.archival - loading archive file https://github.com/JohnGiorgi/seq2rel/releases/download/pretrained-models/cdr_hints.tar.gz from cache at /root/.allennlp/cache/5d845bebc5887213bab7c90a311e51d6dff9a03fb60648a6498d58be8397166c.82548b1687f75978154d471c6ead95e2dd4d865a01baaba9fa7873d62232ffbe
2024-04-12 10:30:34,345 - INFO - allennlp.models.archival - extracting archive file /root/.allennlp/cache/5d845bebc5887213bab7c90a311e51d6dff9a03fb60648a6498d58be8397166c.82548b1687f75978154d471c6ead95e2dd4d865a01baaba9fa7873d62232ffbe to temp dir /tmp/tmpq6ecqnkx
2024-04-12 10:30:41,043 - INFO - allennlp.data.vocabulary - Loading token dictionary from /tmp/tmpq6ecqnkx/vocabulary.
2024-04-12 10:30:43,684 - INFO - allennlp.modules.token_embedders.embedding - Loading a model trained before embedding extension was implemented; pass an explicit vocab namespace if you want to extend the vocabulary.
2024-04-12 10:30:44,093 - INFO - allennlp.models.archival - removing temporary unarchived model dir at /tmp/tmpq6ecqnkx
Traceback (most recent call last):
  File "/usr/local/bin/allennlp", line 8, in <module>
    sys.exit(run())
  File "/usr/local/lib/python3.8/site-packages/allennlp/__main__.py", line 39, in run
    main(prog="allennlp")
  File "/usr/local/lib/python3.8/site-packages/allennlp/commands/__init__.py", line 120, in main
    args.func(args)
  File "/usr/local/lib/python3.8/site-packages/allennlp/commands/evaluate.py", line 135, in evaluate_from_args
    return evaluate_from_archive(
  File "/usr/local/lib/python3.8/site-packages/allennlp/commands/evaluate.py", line 242, in evaluate_from_archive
    archive = load_archive(
  File "/usr/local/lib/python3.8/site-packages/allennlp/models/archival.py", line 235, in load_archive
    model = _load_model(config.duplicate(), weights_path, serialization_dir, cuda_device)
  File "/usr/local/lib/python3.8/site-packages/allennlp/models/archival.py", line 279, in _load_model
    return Model.load(
  File "/usr/local/lib/python3.8/site-packages/allennlp/models/model.py", line 438, in load
    return model_class._load(config, serialization_dir, weights_file, cuda_device)
  File "/usr/local/lib/python3.8/site-packages/allennlp/models/model.py", line 380, in _load
    raise RuntimeError(
RuntimeError: Error loading state dict for CopyNetSeq2Rel
	Missing keys: []
	Unexpected keys: ['_source_embedder.token_embedder_tokens.transformer_model.embeddings.position_ids']

Could you please help fix this problem? Thanks for your great work!

[TingheZhang]

Model name was changed to BiomedNLP-BiomedBERT-base-uncased-abstract-fulltext https://huggingface.co/microsoft/BiomedNLP-BiomedBERT-base-uncased-abstract-fulltext

[rederyang]

@TingheZhang Thanks.

[JohnGiorgi]

Thanks @TingheZhang! @rederxz I have a PR open to fix this on the fly so you don't have to mess with the pre-trained models config files: #392