cron test error -- ./modules/transfer_mmar.ipynb

[wyli]

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'

[wyli]

this is still an issue