Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

error :replicating biobert exactly with NCbI dataset #190

Open
ayodejioogunseye opened this issue Jul 24, 2023 · 1 comment
Open

error :replicating biobert exactly with NCbI dataset #190

ayodejioogunseye opened this issue Jul 24, 2023 · 1 comment

Comments

@ayodejioogunseye
Copy link

Hello, pls i tried to replicate the trainig as specified aand using same NCIB dataset buut got stalked here .

this code line"
$ python run_ner.py --do_train=true --do_eval=true --vocab_file=$BIOBERT_DIR/vocab.txt --bert_config_file=$BIOBERT_DIR/bert_config.json --init_checkpoint=$BIOBERT_DIR/model.ckpt-1000000 --num_train_epochs=10.0 --data_dir=$NER_DIR --output_dir=$OUTPUT_DIr "

(tf15) C:\Users\Ayodee\biobert>python run_ner.py --do_train=true --do_eval=true --vocab_file$BIOBERT_DIR/vocab.txt --bert_config_file=BIOBERT_DIR/bert_config.json --init_checkpoint=BIOBERT_DIR/model.ckpt-1000000 --num_train_epochs=10.0 --data_dir=NER_DIR --output_dir=OUTPUT_DIR
WARNING:tensorflow:From C:\Users\Ayodee\biobert\optimization.py:87: The name tf.train.Optimizer is deprecated. Please use tf.compat.v1.train.Optimizer instead.

C:\Users\Ayodee\anaconda3\envs\tf15\lib\site-packages\absl\flags_validators.py:206: UserWarning: Flag --task_name has a non-None default value; therefore, mark_flag_as_required will pass even if flag is not specified in the command line!
'command line!' % flag_name)
WARNING:tensorflow:From run_ner.py:651: The name tf.app.run is deprecated. Please use tf.compat.v1.app.run instead.

Traceback (most recent call last):
File "run_ner.py", line 651, in
tf.app.run()
File "C:\Users\Ayodee\anaconda3\envs\tf15\lib\site-packages\tensorflow_core\python\platform\app.py", line 40, in run
_run(main=main, argv=argv, flags_parser=_parse_flags_tolerate_undef)
File "C:\Users\Ayodee\anaconda3\envs\tf15\lib\site-packages\absl\app.py", line 306, in run
flags_parser,
File "C:\Users\Ayodee\anaconda3\envs\tf15\lib\site-packages\absl\app.py", line 375, in _run_init
flags_parser=flags_parser,
File "C:\Users\Ayodee\anaconda3\envs\tf15\lib\site-packages\absl\app.py", line 220, in _register_and_parse_flags_with_usage
args_to_main = flags_parser(original_argv)
File "C:\Users\Ayodee\anaconda3\envs\tf15\lib\site-packages\tensorflow_core\python\platform\app.py", line 31, in _parse_flags_tolerate_undef
return flags.FLAGS(_sys.argv if argv is None else argv, known_only=True)
File "C:\Users\Ayodee\anaconda3\envs\tf15\lib\site-packages\tensorflow_core\python\platform\flags.py", line 112, in call
return self.dict['__wrapped'].call(*args, **kwargs)
File "C:\Users\Ayodee\anaconda3\envs\tf15\lib\site-packages\absl\flags_flagvalues.py", line 673, in call
self.validate_all_flags()
File "C:\Users\Ayodee\anaconda3\envs\tf15\lib\site-packages\absl\flags_flagvalues.py", line 533, in validate_all_flags
self._assert_validators(all_validators)
File "C:\Users\Ayodee\anaconda3\envs\tf15\lib\site-packages\absl\flags_flagvalues.py", line 568, in _assert_validators
raise _exceptions.IllegalFlagValueError('\n'.join(messages))
absl.flags._exceptions.IllegalFlagValueError: flag --vocab_file=None: Flag --vocab_file must have a value other than None.

@ayodejioogunseye ayodejioogunseye changed the title error :replicating bibert exactly with NCbI dataset error :replicating biobert exactly with NCbI dataset Jul 24, 2023
@ayodejioogunseye
Copy link
Author

used tenforflow 1.15.2 as per instruction in requirement.txt
WARNING:tensorflow:From C:\Users\Ayodee\biobert\optimization.py:87: The name tf.train.Optimizer is deprecated. Please use tf.compat.v1.train.Optimizer instead.

C:\Users\Ayodee\anaconda3\envs\tf15\lib\site-packages\absl\flags_validators.py:206: UserWarning: Flag --task_name has a non-None default value; therefore, mark_flag_as_required will pass even if flag is not specified in the command line!
'command line!' % flag_name)
WARNING:tensorflow:From C:\Users\Ayodee\biobert\run_ner.py:651: The name tf.app.run is deprecated. Please use tf.compat.v1.app.run instead.

WARNING:tensorflow:From C:\Users\Ayodee\biobert\run_ner.py:466: The name tf.logging.set_verbosity is deprecated. Please use tf.compat.v1.logging.set_verbosity instead.

W0724 16:58:51.533188 12640 module_wrapper.py:139] From C:\Users\Ayodee\biobert\run_ner.py:466: The name tf.logging.set_verbosity is deprecated. Please use tf.compat.v1.logging.set_verbosity instead.

WARNING:tensorflow:From C:\Users\Ayodee\biobert\run_ner.py:466: The name tf.logging.INFO is deprecated. Please use tf.compat.v1.logging.INFO instead.

W0724 16:58:51.534185 12640 module_wrapper.py:139] From C:\Users\Ayodee\biobert\run_ner.py:466: The name tf.logging.INFO is deprecated. Please use tf.compat.v1.logging.INFO instead.

WARNING:tensorflow:From C:\Users\Ayodee\biobert\modeling.py:92: The name tf.gfile.GFile is deprecated. Please use tf.io.gfile.GFile instead.

W0724 16:58:51.534185 12640 module_wrapper.py:139] From C:\Users\Ayodee\biobert\modeling.py:92: The name tf.gfile.GFile is deprecated. Please use tf.io.gfile.GFile instead.

Traceback (most recent call last):
File "C:\Users\Ayodee\biobert\run_ner.py", line 651, in
tf.app.run()
File "C:\Users\Ayodee\anaconda3\envs\tf15\lib\site-packages\tensorflow_core\python\platform\app.py", line 40, in run
_run(main=main, argv=argv, flags_parser=_parse_flags_tolerate_undef)
File "C:\Users\Ayodee\anaconda3\envs\tf15\lib\site-packages\absl\app.py", line 312, in run
_run_main(main, args)
File "C:\Users\Ayodee\anaconda3\envs\tf15\lib\site-packages\absl\app.py", line 258, in _run_main
sys.exit(main(argv))
File "C:\Users\Ayodee\biobert\run_ner.py", line 473, in main
bert_config = modeling.BertConfig.from_json_file(FLAGS.bert_config_file)
File "C:\Users\Ayodee\biobert\modeling.py", line 93, in from_json_file
text = reader.read()
File "C:\Users\Ayodee\anaconda3\envs\tf15\lib\site-packages\tensorflow_core\python\lib\io\file_io.py", line 122, in read
self._preread_check()
File "C:\Users\Ayodee\anaconda3\envs\tf15\lib\site-packages\tensorflow_core\python\lib\io\file_io.py", line 84, in _preread_check
compat.as_bytes(self.__name), 1024 * 512)
tensorflow.python.framework.errors_impl.NotFoundError: NewRandomAccessFile failed to Create/Open: BIOBERT_DIR/bert_config.json : The system cannot find the path specified.

; No such process

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant