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ncbi-nlp / bluebert

BlueBERT, pre-trained on PubMed abstracts and clinical notes (MIMIC-III).
https://arxiv.org/abs/1906.05474
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ValueError: model_dir should be non-empty. #24

Closed ding-si-han closed 4 years ago

ding-si-han commented 4 years ago

While running the inference task using the following command on MedNLI, I encounterred the following issue displayed below. Have downloaded the BlueBERT-Base, Uncased, PubMed+MIMIC-III model for this inference. Kindly appreciate advice on this error and how to run the inference on a custom NLI example (ie from a .txt file)

Command python bluebert/run_bluebert.py \ --do_train=true \ --do_eval=false \ --do_predict=true \ --task_name="mednli" \ --vocab_file=$BlueBERT_DIR/vocab.txt \ --bert_config_file=$BlueBERT_DIR/bert_config.json \ --init_checkpoint=$BlueBERT_DIR/bert_model.ckpt \ --num_train_epochs=10.0 \ --data_dir=$DATASET_DIR \ --output_dir=$OUTPUT_DIR \ --do_lower_case=true

Logs Traceback (most recent call last): File "bluebert/run_bluebert.py", line 912, in tf.app.run() File "/home/dingsihan/.local/lib/python3.6/site-packages/tensorflow_core/python/platform/app.py", line 40, in run _run(main=main, argv=argv, flags_parser=_parse_flags_tolerate_undef) File "/home/dingsihan/.local/lib/python3.6/site-packages/absl/app.py", line 299, in run _run_main(main, args) File "/home/dingsihan/.local/lib/python3.6/site-packages/absl/app.py", line 250, in _run_main sys.exit(main(argv)) File "bluebert/run_bluebert.py", line 762, in main per_host_input_for_training=is_per_host)) File "/home/dingsihan/.local/lib/python3.6/site-packages/tensorflow_estimator/python/estimator/tpu/tpu_config.py", line 233, in init super(RunConfig, self).init(**kwargs) File "/home/dingsihan/.local/lib/python3.6/site-packages/tensorflow_estimator/python/estimator/run_config.py", line 538, in init compat_internal.path_to_str(model_dir)) File "/home/dingsihan/.local/lib/python3.6/site-packages/tensorflow_estimator/python/estimator/run_config.py", line 944, in _get_model_dir raise ValueError('model_dir should be non-empty.') ValueError: model_dir should be non-empty.

Environment Platform: Ubuntu 18.04 Tensorflow Version: 1.15.2

yfpeng commented 4 years ago

Please check if the variable $OUTPUT_DIR is an empty string.