cron test error -- ./modules/transfer_mmar.ipynb #352
Description
Describe the bug
logs from https://github.com/Project-MONAI/MONAI/runs/3604008777?check_suite_focus=true
real 0m14.757s
user 0m18.861s
sys 0m12.270s
Running ./modules/transfer_mmar.ipynb
Checking PEP8 compliance...
Running notebook...
Before:
"max_epochs = 50\n",
After:
"max_epochs = 1\n",
Before:
"val_interval = 2\n",
After:
"val_interval = 1\n",
Executing: 0%| | 0/30 [00:00<?, ?cell/s]
Executing: 3%|▎ | 1/30 [00:00<00:23, 1.24cell/s]
Executing: 10%|█ | 3/30 [00:04<00:39, 1.47s/cell]
Executing: 13%|█▎ | 4/30 [00:04<00:28, 1.08s/cell]
Executing: 20%|██ | 6/30 [00:06<00:24, 1.03s/cell]
Executing: 37%|███▋ | 11/30 [01:38<03:51, 12.20s/cell]
Executing: 57%|█████▋ | 17/30 [03:49<03:44, 17.24s/cell]
Executing: 70%|███████ | 21/30 [03:55<01:47, 11.96s/cell]
Executing: 87%|████████▋ | 26/30 [03:57<00:30, 7.65s/cell]
Executing: 87%|████████▋ | 26/30 [03:59<00:36, 9.20s/cell]
Traceback (most recent call last):
File "/opt/conda/bin/papermill", line 8, in <module>
sys.exit(papermill())
File "/opt/conda/lib/python3.8/site-packages/click/core.py", line 829, in __call__
return self.main(*args, **kwargs)
File "/opt/conda/lib/python3.8/site-packages/click/core.py", line 782, in main
rv = self.invoke(ctx)
File "/opt/conda/lib/python3.8/site-packages/click/core.py", line 1066, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/opt/conda/lib/python3.8/site-packages/click/core.py", line 610, in invoke
return callback(*args, **kwargs)
File "/opt/conda/lib/python3.8/site-packages/click/decorators.py", line 21, in new_func
return f(get_current_context(), *args, **kwargs)
File "/opt/conda/lib/python3.8/site-packages/papermill/cli.py", line 250, in papermill
execute_notebook(
File "/opt/conda/lib/python3.8/site-packages/papermill/execute.py", line 122, in execute_notebook
raise_for_execution_errors(nb, output_path)
File "/opt/conda/lib/python3.8/site-packages/papermill/execute.py", line 234, in raise_for_execution_errors
raise error
papermill.exceptions.PapermillExecutionError:
---------------------------------------------------------------------------
Exception encountered at "In [14]":
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
/tmp/ipykernel_76540/512289039.py in <module>
16 step = 0
17 set_determinism(seed=42)
---> 18 for batch_data in train_loader:
19 step += 1
20 inputs, labels = (
/opt/conda/lib/python3.8/site-packages/torch/utils/data/dataloader.py in __next__(self)
519 if self._sampler_iter is None:
520 self._reset()
--> 521 data = self._next_data()
522 self._num_yielded += 1
523 if self._dataset_kind == _DatasetKind.Iterable and \
/opt/conda/lib/python3.8/site-packages/torch/utils/data/dataloader.py in _next_data(self)
1201 else:
1202 del self._task_info[idx]
-> 1203 return self._process_data(data)
1204
1205 def _try_put_index(self):
/opt/conda/lib/python3.8/site-packages/torch/utils/data/dataloader.py in _process_data(self, data)
1227 self._try_put_index()
1228 if isinstance(data, ExceptionWrapper):
-> 1229 data.reraise()
1230 return data
1231
/opt/conda/lib/python3.8/site-packages/torch/_utils.py in reraise(self)
429 # instantiate since we don't know how to
430 raise RuntimeError(msg) from None
--> 431 raise exception
432
433
AttributeError: Caught AttributeError in DataLoader worker process 0.
Original Traceback (most recent call last):
File "/opt/conda/lib/python3.8/site-packages/torch/utils/data/_utils/worker.py", line 287, in _worker_loop
data = fetcher.fetch(index)
File "/opt/conda/lib/python3.8/site-packages/torch/utils/data/_utils/fetch.py", line 52, in fetch
return self.collate_fn(data)
File "/opt/conda/lib/python3.8/site-packages/monai/data/utils.py", line 275, in list_data_collate
return default_collate(data)
File "/opt/conda/lib/python3.8/site-packages/torch/utils/data/_utils/collate.py", line 74, in default_collate
return {key: default_collate([d[key] for d in batch]) for key in elem}
File "/opt/conda/lib/python3.8/site-packages/torch/utils/data/_utils/collate.py", line 74, in <dictcomp>
return {key: default_collate([d[key] for d in batch]) for key in elem}
File "/opt/conda/lib/python3.8/site-packages/torch/utils/data/_utils/collate.py", line 84, in default_collate
return [default_collate(samples) for samples in transposed]
File "/opt/conda/lib/python3.8/site-packages/torch/utils/data/_utils/collate.py", line 84, in <listcomp>
return [default_collate(samples) for samples in transposed]
File "/opt/conda/lib/python3.8/site-packages/torch/utils/data/_utils/collate.py", line 74, in default_collate
return {key: default_collate([d[key] for d in batch]) for key in elem}
File "/opt/conda/lib/python3.8/site-packages/torch/utils/data/_utils/collate.py", line 74, in <dictcomp>
return {key: default_collate([d[key] for d in batch]) for key in elem}
File "/opt/conda/lib/python3.8/site-packages/torch/utils/data/_utils/collate.py", line 74, in default_collate
return {key: default_collate([d[key] for d in batch]) for key in elem}
File "/opt/conda/lib/python3.8/site-packages/torch/utils/data/_utils/collate.py", line 74, in <dictcomp>
return {key: default_collate([d[key] for d in batch]) for key in elem}
File "/opt/conda/lib/python3.8/site-packages/torch/utils/data/_utils/collate.py", line 53, in default_collate
numel = sum(x.numel() for x in batch)
File "/opt/conda/lib/python3.8/site-packages/torch/utils/data/_utils/collate.py", line 53, in <genexpr>
numel = sum(x.numel() for x in batch)
AttributeError: 'numpy.ndarray' object has no attribute 'numel'