Work with another dataset: Training: NameError: name 'index' is not defined
I am going to spam issues to have ourselves a memory of common log errors and solutions for future documentation.
files:
cattle_000_training_config.yml
cattle_000_preprocessed_params.csv
Setup:
data_root: /home/pjobic/Work/DNADNA/master/cattle
Format: data_root/scenario_XXX/cattle_NNN_NN.npz
dataset_path_on_titanic: titanic:/home/tau/thsanche/data/cattle/scenario_{0_to_99}
working directory: /home/pjobic/Work/DNADNA/master
Issue
I am trying to work with dnadna
with another dataset:
Here are the steps I did:
Command: dnadna simulation init cattle
=> Then, modified cattle/cattle_simulation_config.yml (find in attached file)
Command: dnadna init --simulation-config=cattle/cattle_simulation_config.yml
=> Then, modified cattle/cattle_training_config.yml (find in attached file)
Command: dnadna --debug preprocess cattle/cattle_training_config.yml
Command: dnadna --debug train cattle/run_000/cattle_000_training_config.yml
Log Error: `NameError: name 'index' is not defined`
dnadna --debug train cattle/run_000/cattle_000_training_config.yml
20/05/2020 11:11:37; INFO; 100 samples in the validation set and 9900 in the training set
20/05/2020 11:11:37; INFO; Start training
20/05/2020 11:11:37; INFO; Starting Epoch #0
epoch 0/1: 0%| | 0/9900 [00:00<?, ?batch/s]
an unexpected error occurred: Caught NameError in DataLoader worker process 0. | 0/9900 [00:00<?, ?batch/s]
Original Traceback (most recent call last):
File "/home/pjobic/anaconda3/envs/dnadna/lib/python3.7/site-packages/torch/utils/data/_utils/worker.py", line 178, in _worker_loop
data = fetcher.fetch(index)
File "/home/pjobic/anaconda3/envs/dnadna/lib/python3.7/site-packages/torch/utils/data/_utils/fetch.py", line 44, in fetch
data = [self.dataset[idx] for idx in possibly_batched_index]
File "/home/pjobic/anaconda3/envs/dnadna/lib/python3.7/site-packages/torch/utils/data/_utils/fetch.py", line 44, in <listcomp>
data = [self.dataset[idx] for idx in possibly_batched_index]
File "/home/pjobic/Work/DNADNA/master/dnadna/datasets.py", line 845, in __getitem__
self._validate_sample(index, sample)
File "/home/pjobic/Work/DNADNA/master/dnadna/datasets.py", line 964, in _validate_sample
scenario_idx, replicate_idx = self._get_index(index)
NameError: name 'index' is not defined
; run again with --debug to view the full traceback
an unexpected error occurred: Caught NameError in DataLoader worker process 0.
Original Traceback (most recent call last):
File "/home/pjobic/anaconda3/envs/dnadna/lib/python3.7/site-packages/torch/utils/data/_utils/worker.py", line 178, in _worker_loop
data = fetcher.fetch(index)
File "/home/pjobic/anaconda3/envs/dnadna/lib/python3.7/site-packages/torch/utils/data/_utils/fetch.py", line 44, in fetch
data = [self.dataset[idx] for idx in possibly_batched_index]
File "/home/pjobic/anaconda3/envs/dnadna/lib/python3.7/site-packages/torch/utils/data/_utils/fetch.py", line 44, in <listcomp>
data = [self.dataset[idx] for idx in possibly_batched_index]
File "/home/pjobic/Work/DNADNA/master/dnadna/datasets.py", line 845, in __getitem__
self._validate_sample(index, sample)
File "/home/pjobic/Work/DNADNA/master/dnadna/datasets.py", line 964, in _validate_sample
scenario_idx, replicate_idx = self._get_index(index)
NameError: name 'index' is not defined
; run again with --debug to view the full traceback
Traceback (most recent call last):
File "/home/pjobic/anaconda3/envs/dnadna/bin/dnadna", line 11, in <module>
load_entry_point('dnadna', 'console_scripts', 'dnadna')()
File "/home/pjobic/Work/DNADNA/master/dnadna/utils/__init__.py", line 820, in main
raise exc
File "/home/pjobic/Work/DNADNA/master/dnadna/utils/__init__.py", line 812, in main
ret2 = cls.run_subcommand(args)
File "/home/pjobic/Work/DNADNA/master/dnadna/utils/__init__.py", line 781, in run_subcommand
return command_cls.main(command[1:], namespace=args)
File "/home/pjobic/Work/DNADNA/master/dnadna/utils/__init__.py", line 820, in main
raise exc
File "/home/pjobic/Work/DNADNA/master/dnadna/utils/__init__.py", line 804, in main
ret = cls.run(args)
File "/home/pjobic/Work/DNADNA/master/dnadna/training.py", line 663, in run
model_trainer.run_training()
File "/home/pjobic/Work/DNADNA/master/dnadna/training.py", line 400, in run_training
best_loss = self.train()
File "/home/pjobic/Work/DNADNA/master/dnadna/training.py", line 386, in train
return best_loss
File "/home/pjobic/Work/DNADNA/master/dnadna/utils/__init__.py", line 403, in __exit__
raise exc_value
File "/home/pjobic/Work/DNADNA/master/dnadna/training.py", line 376, in train
best_loss = self._train_outer_loop(bar)
File "/home/pjobic/Work/DNADNA/master/dnadna/training.py", line 431, in _train_outer_loop
for batch, data in enumerate(self.training_loader):
File "/home/pjobic/anaconda3/envs/dnadna/lib/python3.7/site-packages/torch/utils/data/dataloader.py", line 819, in __next__
return self._process_data(data)
File "/home/pjobic/anaconda3/envs/dnadna/lib/python3.7/site-packages/torch/utils/data/dataloader.py", line 846, in _process_data
data.reraise()
File "/home/pjobic/anaconda3/envs/dnadna/lib/python3.7/site-packages/torch/_utils.py", line 369, in reraise
raise self.exc_type(msg)
NameError: Caught NameError in DataLoader worker process 0.
Original Traceback (most recent call last):
File "/home/pjobic/anaconda3/envs/dnadna/lib/python3.7/site-packages/torch/utils/data/_utils/worker.py", line 178, in _worker_loop
data = fetcher.fetch(index)
File "/home/pjobic/anaconda3/envs/dnadna/lib/python3.7/site-packages/torch/utils/data/_utils/fetch.py", line 44, in fetch
data = [self.dataset[idx] for idx in possibly_batched_index]
File "/home/pjobic/anaconda3/envs/dnadna/lib/python3.7/site-packages/torch/utils/data/_utils/fetch.py", line 44, in <listcomp>
data = [self.dataset[idx] for idx in possibly_batched_index]
File "/home/pjobic/Work/DNADNA/master/dnadna/datasets.py", line 845, in __getitem__
self._validate_sample(index, sample)
File "/home/pjobic/Work/DNADNA/master/dnadna/datasets.py", line 964, in _validate_sample
scenario_idx, replicate_idx = self._get_index(index)
NameError: name 'index' is not defined