I'm using the following code out of the box from this url: https://lightning-transformers.readthedocs.io/en/latest/tasks/nlp/question_answering.html
import pytorch_lightning as pl
from transformers import AutoTokenizer
from lightning_transformers.task.nlp.question_answering import (
QuestionAnsweringTransformer,
SquadDataModule,
)
tokenizer = AutoTokenizer.from_pretrained(pretrained_model_name_or_path="bert-base-uncased")
model = QuestionAnsweringTransformer(pretrained_model_name_or_path="bert-base-uncased")
dm = SquadDataModule(
batch_size=1,
dataset_config_name="plain_text",
max_length=384,
version_2_with_negative=False,
null_score_diff_threshold=0.0,
doc_stride=128,
n_best_size=20,
max_answer_length=30,
tokenizer=tokenizer,
)
trainer = pl.Trainer(accelerator="auto", devices="auto", max_epochs=1)
trainer.fit(model, dm)
which throws this error
AssertionError Traceback (most recent call last)
<ipython-input-2-0b608c02a52e> in <module>
14 trainer = pl.Trainer(accelerator="auto", devices="auto", max_epochs=1)
15
---> 16 trainer.fit(model, dm)
16 frames
/usr/local/lib/python3.8/dist-packages/lightning_transformers/task/nlp/question_answering/datasets/squad/processing.py in postprocess_qa_predictions(examples, features, predictions, version_2_with_negative, n_best_size, max_answer_length, null_score_diff_threshold, output_dir, prefix)
245 all_start_logits, all_end_logits, example_ids = predictions
246
--> 247 assert len(predictions[0]) == len(features), f"Got {len(predictions[0])} predictions and {len(features)} features."
248
249 # Build a map example to its corresponding features.
AssertionError: Got 2 predictions and 10784 features.
I was simply trying to get a single example from the documentation to run within google colab before investigating further if this would meet my use case, but I see an error when I try to use the example as is, which is disheartening to consider investigating it. Nothing comes up when I google "AssertionError: Got 2 predictions and 10784 features."
When saving a version in Kaggle, I get StdinNotImplementedError: getpass was called, but this frontend does not support input requests whenever I use the Transformers.Trainer class. The general code I use:
from transformers import Trainer, TrainingArguments
training_args = TrainingArguments(params)
trainer = Trainer(params)
trainer.train()
And the specific cell I am running now:
from transformers import Trainer, TrainingArguments,EarlyStoppingCallback
early_stopping = EarlyStoppingCallback()
training_args = TrainingArguments(
output_dir=OUT_FINETUNED_MODEL_PATH,
num_train_epochs=20,
per_device_train_batch_size=16,
per_device_eval_batch_size=16,
warmup_steps=0,
weight_decay=0.01,
logging_dir='./logs',
logging_steps=100,
evaluation_strategy="steps",
eval_steps=100,
load_best_model_at_end=True,
metric_for_best_model="eval_loss",
greater_is_better=False
)
trainer = Trainer(
model=model,
args=training_args,
train_dataset=train_dataset,
eval_dataset=val_dataset,
callbacks=[early_stopping]
)
trainer.train()
When trainer.train() is called, I get the error below, which I do not get if I train with native PyTorch. I understood that the error arises since I am asked to input a password, but no password is asked when using native PyTorch code, nor when using the same code with trainer.train() on Google Colab.
Any solution would be ok, like:
Avoid being asked the password.
Enable input requests when saving a notebook on Kaggle. After that, if I understood correctly, I would need to go to https://wandb.ai/authorize (after having created an account) and copy the generated key to console. However, I do not understand why wandb should be necessary since I never explicitly used it so far.
wandb: You can find your API key in your browser here: https://wandb.ai/authorize
Traceback (most recent call last):
File "/opt/conda/lib/python3.7/site-packages/wandb/sdk/wandb_init.py", line 741, in init
wi.setup(kwargs)
File "/opt/conda/lib/python3.7/site-packages/wandb/sdk/wandb_init.py", line 155, in setup
wandb_login._login(anonymous=anonymous, force=force, _disable_warning=True)
File "/opt/conda/lib/python3.7/site-packages/wandb/sdk/wandb_login.py", line 210, in _login
wlogin.prompt_api_key()
File "/opt/conda/lib/python3.7/site-packages/wandb/sdk/wandb_login.py", line 144, in prompt_api_key
no_create=self._settings.force,
File "/opt/conda/lib/python3.7/site-packages/wandb/sdk/lib/apikey.py", line 135, in prompt_api_key
key = input_callback(api_ask).strip()
File "/opt/conda/lib/python3.7/site-packages/ipykernel/kernelbase.py", line 825, in getpass
"getpass was called, but this frontend does not support input requests."
IPython.core.error.StdinNotImplementedError: getpass was called, but this frontend does not support input requests.
wandb: ERROR Abnormal program exit
---------------------------------------------------------------------------
StdinNotImplementedError Traceback (most recent call last)
/opt/conda/lib/python3.7/site-packages/wandb/sdk/wandb_init.py in init(job_type, dir, config, project, entity, reinit, tags, group, name, notes, magic, config_exclude_keys, config_include_keys, anonymous, mode, allow_val_change, resume, force, tensorboard, sync_tensorboard, monitor_gym, save_code, id, settings)
740 wi = _WandbInit()
--> 741 wi.setup(kwargs)
742 except_exit = wi.settings._except_exit
/opt/conda/lib/python3.7/site-packages/wandb/sdk/wandb_init.py in setup(self, kwargs)
154 if not settings._offline and not settings._noop:
--> 155 wandb_login._login(anonymous=anonymous, force=force, _disable_warning=True)
156
/opt/conda/lib/python3.7/site-packages/wandb/sdk/wandb_login.py in _login(anonymous, key, relogin, host, force, _backend, _silent, _disable_warning)
209 if not key:
--> 210 wlogin.prompt_api_key()
211
/opt/conda/lib/python3.7/site-packages/wandb/sdk/wandb_login.py in prompt_api_key(self)
143 no_offline=self._settings.force,
--> 144 no_create=self._settings.force,
145 )
/opt/conda/lib/python3.7/site-packages/wandb/sdk/lib/apikey.py in prompt_api_key(settings, api, input_callback, browser_callback, no_offline, no_create, local)
134 )
--> 135 key = input_callback(api_ask).strip()
136 write_key(settings, key, api=api)
/opt/conda/lib/python3.7/site-packages/ipykernel/kernelbase.py in getpass(self, prompt, stream)
824 raise StdinNotImplementedError(
--> 825 "getpass was called, but this frontend does not support input requests."
826 )
StdinNotImplementedError: getpass was called, but this frontend does not support input requests.
The above exception was the direct cause of the following exception:
Exception Traceback (most recent call last)
<ipython-input-82-4d1046ab80b8> in <module>
42 )
43
---> 44 trainer.train()
/opt/conda/lib/python3.7/site-packages/transformers/trainer.py in train(self, resume_from_checkpoint, trial, **kwargs)
1067 model.zero_grad()
1068
-> 1069 self.control = self.callback_handler.on_train_begin(self.args, self.state, self.control)
1070
1071 # Skip the first epochs_trained epochs to get the random state of the dataloader at the right point.
/opt/conda/lib/python3.7/site-packages/transformers/trainer_callback.py in on_train_begin(self, args, state, control)
338 def on_train_begin(self, args: TrainingArguments, state: TrainerState, control: TrainerControl):
339 control.should_training_stop = False
--> 340 return self.call_event("on_train_begin", args, state, control)
341
342 def on_train_end(self, args: TrainingArguments, state: TrainerState, control: TrainerControl):
/opt/conda/lib/python3.7/site-packages/transformers/trainer_callback.py in call_event(self, event, args, state, control, **kwargs)
386 train_dataloader=self.train_dataloader,
387 eval_dataloader=self.eval_dataloader,
--> 388 **kwargs,
389 )
390 # A Callback can skip the return of `control` if it doesn't change it.
/opt/conda/lib/python3.7/site-packages/transformers/integrations.py in on_train_begin(self, args, state, control, model, **kwargs)
627 self._wandb.finish()
628 if not self._initialized:
--> 629 self.setup(args, state, model, **kwargs)
630
631 def on_train_end(self, args, state, control, model=None, tokenizer=None, **kwargs):
/opt/conda/lib/python3.7/site-packages/transformers/integrations.py in setup(self, args, state, model, **kwargs)
604 project=os.getenv("WANDB_PROJECT", "huggingface"),
605 name=run_name,
--> 606 **init_args,
607 )
608 # add config parameters (run may have been created manually)
/opt/conda/lib/python3.7/site-packages/wandb/sdk/wandb_init.py in init(job_type, dir, config, project, entity, reinit, tags, group, name, notes, magic, config_exclude_keys, config_include_keys, anonymous, mode, allow_val_change, resume, force, tensorboard, sync_tensorboard, monitor_gym, save_code, id, settings)
779 if except_exit:
780 os._exit(-1)
--> 781 six.raise_from(Exception("problem"), error_seen)
782 return run
/opt/conda/lib/python3.7/site-packages/six.py in raise_from(value, from_value)
Exception: problem
You may want to try adding report_to="tensorboard" or any other reasonable string array in your TrainingArguments
https://huggingface.co/transformers/main_classes/trainer.html#transformers.TrainingArguments
If you have multiple logger that you want to use report_to="all" (the default value)
try os.environ["WANDB_DISABLED"] = "true" such that wandb is always disabled.
see: https://huggingface.co/transformers/main_classes/trainer.html#transformers.TFTrainer.setup_wandb
I'm trying to run language model finetuning script (run_language_modeling.py) from huggingface examples with my own tokenizer(just added in several tokens, see the comments). I have problem loading the tokenizer. I think the problem is with AutoTokenizer.from_pretrained('local/path/to/directory').
Code:
from transformers import *
tokenizer = AutoTokenizer.from_pretrained('bert-base-uncased')
# special_tokens = ['<HASHTAG>', '<URL>', '<AT_USER>', '<EMOTICON-HAPPY>', '<EMOTICON-SAD>']
# tokenizer.add_tokens(special_tokens)
tokenizer.save_pretrained('../twitter/twittertokenizer/')
tmp = AutoTokenizer.from_pretrained('../twitter/twittertokenizer/')
Error Message:
OSError Traceback (most recent call last)
/z/huggingface_venv/lib/python3.7/site-packages/transformers/configuration_utils.py in get_config_dict(cls, pretrained_model_name_or_path, pretrained_config_archive_map, **kwargs)
248 resume_download=resume_download,
--> 249 local_files_only=local_files_only,
250 )
/z/huggingface_venv/lib/python3.7/site-packages/transformers/file_utils.py in cached_path(url_or_filename, cache_dir, force_download, proxies, resume_download, user_agent, extract_compressed_file, force_extract, local_files_only)
265 # File, but it doesn't exist.
--> 266 raise EnvironmentError("file {} not found".format(url_or_filename))
267 else:
OSError: file ../twitter/twittertokenizer/config.json not found
During handling of the above exception, another exception occurred:
OSError Traceback (most recent call last)
<ipython-input-32-662067cb1297> in <module>
----> 1 tmp = AutoTokenizer.from_pretrained('../twitter/twittertokenizer/')
/z/huggingface_venv/lib/python3.7/site-packages/transformers/tokenization_auto.py in from_pretrained(cls, pretrained_model_name_or_path, *inputs, **kwargs)
190 config = kwargs.pop("config", None)
191 if not isinstance(config, PretrainedConfig):
--> 192 config = AutoConfig.from_pretrained(pretrained_model_name_or_path, **kwargs)
193
194 if "bert-base-japanese" in pretrained_model_name_or_path:
/z/huggingface_venv/lib/python3.7/site-packages/transformers/configuration_auto.py in from_pretrained(cls, pretrained_model_name_or_path, **kwargs)
192 """
193 config_dict, _ = PretrainedConfig.get_config_dict(
--> 194 pretrained_model_name_or_path, pretrained_config_archive_map=ALL_PRETRAINED_CONFIG_ARCHIVE_MAP, **kwargs
195 )
196
/z/huggingface_venv/lib/python3.7/site-packages/transformers/configuration_utils.py in get_config_dict(cls, pretrained_model_name_or_path, pretrained_config_archive_map, **kwargs)
270 )
271 )
--> 272 raise EnvironmentError(msg)
273
274 except json.JSONDecodeError:
OSError: Can't load '../twitter/twittertokenizer/'. Make sure that:
- '../twitter/twittertokenizer/' is a correct model identifier listed on 'https://huggingface.co/models'
- or '../twitter/twittertokenizer/' is the correct path to a directory containing a 'config.json' file
If I change AutoTokenizer to BertTokenizer, the code above can work. Also I can run the script without any problem is I load by shortcut name instead of path. But in the script run_language_modeling.py it uses AutoTokenizer. I'm looking for a way to get it running.
Any idea? Thanks!
The problem is that you are using nothing that would indicate the correct tokenizer to instantiate.
For reference, see the rules defined in the Huggingface docs. Specifically, since you are using BERT:
contains bert: BertTokenizer (Bert model)
Otherwise, you have to specify the exact type yourself, as you mentioned.
AutoTokenizer.from_pretrained fails if the specified path does not contain the model configuration files, which are required solely for the tokenizer class instantiation.
In the context of run_language_modeling.py the usage of AutoTokenizer is buggy (or at least leaky).
There is no point to specify the (optional) tokenizer_name parameter if it's identical to the model name or path. Therefore, to my understanding, it supposes to support exactly the case of a modified tokenizer. I also found this issue very confusing.
The best workaround that I have found is to add config.json to the tokenizer directory with only the "missing" configuration:
{
"model_type": "bert"
}
when loading modified tokenizer or pretrained tokenizer you should load it as follows:
tokenizer = AutoTokenizer.from_pretrained(path_to_json_file_of_tokenizer, config=AutoConfig.from_pretrained('path to thefolderthat contains the config file of the model'))
Imagine that I am manipulating a shapefile in geopandas. I then want to load it using another library (like networkx) but since my file is large I dont want to have to save and reload it. Is there a way I can save it in memory? I imagine it would look something like this:
import geopandas
from io import BytesIO
writeBytes = BytesIO()
### load the demo
world = geopandas.read_file(geopandas.datasets.get_path('naturalearth_lowres'))
### do something trivial to the demo
world['geometry'] = world['geometry'].buffer(0.05)
### save to bytes IO so that I can do something else with it without having to save and read a file
world.to_file(writeBytes)
Running the above yields a TypeError: expected str, bytes or os.PathLike object, not _io.BytesIO
This is the full traceback:
TypeError Traceback (most recent call last)
<ipython-input-1-1ba22f23181a> in <module>
8 world['geometry'] = world['geometry'].buffer(0.05)
9 ### save to bytes IO so that I can do something else with it without having to save and read a file
---> 10 world.to_file(writeBytes)
~/.conda/envs/geopandas/lib/python3.7/site-packages/geopandas/geodataframe.py in to_file(self, filename, driver, schema, **kwargs)
427 """
428 from geopandas.io.file import to_file
--> 429 to_file(self, filename, driver, schema, **kwargs)
430
431 def to_crs(self, crs=None, epsg=None, inplace=False):
~/.conda/envs/geopandas/lib/python3.7/site-packages/geopandas/io/file.py in to_file(df, filename, driver, schema, **kwargs)
125 if schema is None:
126 schema = infer_schema(df)
--> 127 filename = os.path.abspath(os.path.expanduser(filename))
128 with fiona_env():
129 with fiona.open(filename, 'w', driver=driver, crs=df.crs,
~/.conda/envs/geopandas/lib/python3.7/posixpath.py in expanduser(path)
233 """Expand ~ and ~user constructions. If user or $HOME is unknown,
234 do nothing."""
--> 235 path = os.fspath(path)
236 if isinstance(path, bytes):
237 tilde = b'~'
Any assistance is appreciated, Thank You
geopandas.to_file() requires a file path, not a BytesIO object.
Use a temporary file (or folder for shape files)
For example: https://stackoverflow.com/a/70254174/2023941
I am able to save an H2O model, load it again and then show it...
# save the model
model_path_2 = h2o.save_model(model=my_xgboost_2, path="tmp/mymodel", force=True)
print (model_path_2)
>>>/home/dell/Documents/Enigma/tmp/mymodel/XGBoost_model_python_1503367354328_27
# load the model
saved_model_2 = h2o.load_model(model_path_2)
but I cannot use it to predict.
saved_model_2.predict(test)
>>>xgboost prediction progress: | (failed)
---------------------------------------------------------------------------
OSError Traceback (most recent call last)
<ipython-input-100-fa76fd498ee6> in <module>()
----> 1 saved_model_2.predict(test)
/home/dell/anaconda3/lib/python3.6/site-packages/h2o/model/model_base.py in predict(self, test_data)
130 j = H2OJob(h2o.api("POST /4/Predictions/models/%s/frames/%s" % (self.model_id, test_data.frame_id)),
131 self._model_json["algo"] + " prediction")
--> 132 j.poll()
133 return h2o.get_frame(j.dest_key)
134
/home/dell/anaconda3/lib/python3.6/site-packages/h2o/job.py in poll(self, verbose_model_scoring_history)
75 if (isinstance(self.job, dict)) and ("stacktrace" in list(self.job)):
76 raise EnvironmentError("Job with key {} failed with an exception: {}\nstacktrace: "
---> 77 "\n{}".format(self.job_key, self.exception, self.job["stacktrace"]))
78 else:
79 raise EnvironmentError("Job with key %s failed with an exception: %s" % (self.job_key, self.exception))
OSError: Job with key $03017f00000132d4ffffffff$_927b7278904ecf169173d48a23de4c10 failed with an exception: java.lang.NullPointerException
stacktrace:
java.lang.NullPointerException
I can, however, predict on the model without saving it. I am using Python 3.6.1, and H2O 3.14.0.1 on Ubuntu 16.04.
This is a known issue with H2O's XGBoost implementation and should be fixed soon. It does not affect other H2O models.