[2022-10-12T12:23:15.086Z] Running ./modules/interpretability/covid_classification.ipynb
[2022-10-12T12:23:15.086Z] Checking PEP8 compliance...
[2022-10-12T12:23:16.014Z] Running notebook...
[2022-10-12T12:23:16.014Z] Before:
[2022-10-12T12:23:16.014Z] "max_epochs = 20\n",
[2022-10-12T12:23:16.014Z] After:
[2022-10-12T12:23:16.014Z] "max_epochs = 1\n",
[2022-10-12T12:23:21.265Z] MONAI version: 1.0.0+37.g9731823d
[2022-10-12T12:23:21.265Z] Numpy version: 1.22.2
[2022-10-12T12:23:21.265Z] Pytorch version: 1.10.2+cu102
[2022-10-12T12:23:21.265Z] MONAI flags: HAS_EXT = False, USE_COMPILED = False, USE_META_DICT = False
[2022-10-12T12:23:21.265Z] MONAI rev id: 9731823da40ae7835afad601d7d2b601534c80d3
[2022-10-12T12:23:21.265Z] MONAI __file__: /home/jenkins/agent/workspace/Monai-notebooks/MONAI/monai/__init__.py
[2022-10-12T12:23:21.265Z]
[2022-10-12T12:23:21.265Z] Optional dependencies:
[2022-10-12T12:23:21.265Z] Pytorch Ignite version: 0.4.10
[2022-10-12T12:23:21.265Z] Nibabel version: 4.0.2
[2022-10-12T12:23:21.265Z] scikit-image version: 0.19.3
[2022-10-12T12:23:21.265Z] Pillow version: 9.0.1
[2022-10-12T12:23:21.265Z] Tensorboard version: 2.10.0
[2022-10-12T12:23:21.265Z] gdown version: 4.5.1
[2022-10-12T12:23:21.265Z] TorchVision version: 0.11.3+cu102
[2022-10-12T12:23:21.265Z] tqdm version: 4.64.1
[2022-10-12T12:23:21.265Z] lmdb version: 1.3.0
[2022-10-12T12:23:21.265Z] psutil version: 5.9.2
[2022-10-12T12:23:21.265Z] pandas version: 1.1.5
[2022-10-12T12:23:21.265Z] einops version: 0.5.0
[2022-10-12T12:23:21.265Z] transformers version: 4.21.3
[2022-10-12T12:23:21.265Z] mlflow version: 1.29.0
[2022-10-12T12:23:21.265Z] pynrrd version: 1.0.0
[2022-10-12T12:23:21.265Z]
[2022-10-12T12:23:21.265Z] For details about installing the optional dependencies, please visit:
[2022-10-12T12:23:21.265Z] https://docs.monai.io/en/latest/installation.html#installing-the-recommended-dependencies
[2022-10-12T12:23:21.265Z]
[2022-10-12T12:23:21.827Z] /opt/conda/lib/python3.8/site-packages/papermill/iorw.py:153: UserWarning: the file is not specified with any extension : -
[2022-10-12T12:23:21.827Z] warnings.warn(
[2022-10-12T12:24:36.387Z]
Executing: 0%| | 0/17 [00:00<?, ?cell/s]
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Executing: 29%|██▉ | 5/17 [01:00<02:49, 14.10s/cell]
Executing: 41%|████ | 7/17 [01:07<01:37, 9.72s/cell]
Executing: 53%|█████▎ | 9/17 [01:08<00:51, 6.39s/cell]
Executing: 59%|█████▉ | 10/17 [01:11<00:39, 5.71s/cell]
Executing: 65%|██████▍ | 11/17 [01:12<00:27, 4.62s/cell]
Executing: 65%|██████▍ | 11/17 [01:14<00:40, 6.75s/cell]
[2022-10-12T12:24:36.387Z] /opt/conda/lib/python3.8/site-packages/papermill/iorw.py:153: UserWarning: the file is not specified with any extension : -
[2022-10-12T12:24:36.387Z] warnings.warn(
[2022-10-12T12:24:36.387Z] Traceback (most recent call last):
[2022-10-12T12:24:36.387Z] File "/opt/conda/bin/papermill", line 8, in <module>
[2022-10-12T12:24:36.387Z] sys.exit(papermill())
[2022-10-12T12:24:36.387Z] File "/opt/conda/lib/python3.8/site-packages/click/core.py", line 1130, in __call__
[2022-10-12T12:24:36.387Z] return self.main(*args, **kwargs)
[2022-10-12T12:24:36.387Z] File "/opt/conda/lib/python3.8/site-packages/click/core.py", line 1055, in main
[2022-10-12T12:24:36.387Z] rv = self.invoke(ctx)
[2022-10-12T12:24:36.387Z] File "/opt/conda/lib/python3.8/site-packages/click/core.py", line 1404, in invoke
[2022-10-12T12:24:36.387Z] return ctx.invoke(self.callback, **ctx.params)
[2022-10-12T12:24:36.388Z] File "/opt/conda/lib/python3.8/site-packages/click/core.py", line 760, in invoke
[2022-10-12T12:24:36.388Z] return __callback(*args, **kwargs)
[2022-10-12T12:24:36.388Z] File "/opt/conda/lib/python3.8/site-packages/click/decorators.py", line 26, in new_func
[2022-10-12T12:24:36.388Z] return f(get_current_context(), *args, **kwargs)
[2022-10-12T12:24:36.388Z] File "/opt/conda/lib/python3.8/site-packages/papermill/cli.py", line 250, in papermill
[2022-10-12T12:24:36.388Z] execute_notebook(
[2022-10-12T12:24:36.388Z] File "/opt/conda/lib/python3.8/site-packages/papermill/execute.py", line 128, in execute_notebook
[2022-10-12T12:24:36.388Z] raise_for_execution_errors(nb, output_path)
[2022-10-12T12:24:36.388Z] File "/opt/conda/lib/python3.8/site-packages/papermill/execute.py", line 232, in raise_for_execution_errors
[2022-10-12T12:24:36.388Z] raise error
[2022-10-12T12:24:36.388Z] papermill.exceptions.PapermillExecutionError:
[2022-10-12T12:24:36.388Z] ---------------------------------------------------------------------------
[2022-10-12T12:24:36.388Z] Exception encountered at "In [9]":
[2022-10-12T12:24:36.388Z] ---------------------------------------------------------------------------
[2022-10-12T12:24:36.388Z] ImportError Traceback (most recent call last)
[2022-10-12T12:24:36.388Z] Cell In [9], line 2
[2022-10-12T12:24:36.388Z] 1 max_epochs = 1
[2022-10-12T12:24:36.388Z] ----> 2 tr = trange(max_epochs, desc="Epoch")
[2022-10-12T12:24:36.388Z] 3 for epoch in tr:
[2022-10-12T12:24:36.388Z] 4 loss, acc = 0, 0
[2022-10-12T12:24:36.388Z]
[2022-10-12T12:24:36.388Z] File /opt/conda/lib/python3.8/site-packages/tqdm/notebook.py:324, in tnrange(*args, **kwargs)
[2022-10-12T12:24:36.388Z] 319 def tnrange(*args, **kwargs):
[2022-10-12T12:24:36.388Z] 320 """
[2022-10-12T12:24:36.388Z] 321 A shortcut for `tqdm.notebook.tqdm(xrange(*args), **kwargs)`.
[2022-10-12T12:24:36.388Z] 322 On Python3+, `range` is used instead of `xrange`.
[2022-10-12T12:24:36.388Z] 323 """
[2022-10-12T12:24:36.388Z] --> 324 return tqdm_notebook(_range(*args), **kwargs)
[2022-10-12T12:24:36.388Z]
[2022-10-12T12:24:36.388Z] File /opt/conda/lib/python3.8/site-packages/tqdm/notebook.py:243, in tqdm_notebook.__init__(self, *args, **kwargs)
[2022-10-12T12:24:36.388Z] 241 unit_scale = 1 if self.unit_scale is True else self.unit_scale or 1
[2022-10-12T12:24:36.388Z] 242 total = self.total * unit_scale if self.total else self.total
[2022-10-12T12:24:36.388Z] --> 243 self.container = self.status_printer(self.fp, total, self.desc, self.ncols)
[2022-10-12T12:24:36.388Z] 244 self.container.pbar = proxy(self)
[2022-10-12T12:24:36.388Z] 245 self.displayed = False
[2022-10-12T12:24:36.388Z]
[2022-10-12T12:24:36.388Z] File /opt/conda/lib/python3.8/site-packages/tqdm/notebook.py:118, in tqdm_notebook.status_printer(_, total, desc, ncols)
[2022-10-12T12:24:36.388Z] 109 # Fallback to text bar if there's no total
[2022-10-12T12:24:36.388Z] 110 # DEPRECATED: replaced with an 'info' style bar
[2022-10-12T12:24:36.388Z] 111 # if not total:
[2022-10-12T12:24:36.388Z] (...)
[2022-10-12T12:24:36.388Z] 115
[2022-10-12T12:24:36.388Z] 116 # Prepare IPython progress bar
[2022-10-12T12:24:36.388Z] 117 if IProgress is None: # #187 #451 #558 #872
[2022-10-12T12:24:36.388Z] --> 118 raise ImportError(WARN_NOIPYW)
[2022-10-12T12:24:36.388Z] 119 if total:
[2022-10-12T12:24:36.388Z] 120 pbar = IProgress(min=0, max=total)
[2022-10-12T12:24:36.388Z]
[2022-10-12T12:24:36.388Z] ImportError: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html
