3d_segmentation/spleen_segmentation_3d_lightning.ipynb

[wyli]

[2023-04-27T23:07:47.468Z] Running ./3d_segmentation/spleen_segmentation_3d_lightning.ipynb
[2023-04-27T23:07:47.724Z] Checking PEP8 compliance...
[2023-04-27T23:07:48.650Z] Running notebook...
[2023-04-27T23:07:48.650Z] Before:
[2023-04-27T23:07:48.650Z]     "    max_epochs=600,\n",
[2023-04-27T23:07:48.650Z] After:
[2023-04-27T23:07:48.650Z]     "    max_epochs = 1,\n",
[2023-04-27T23:07:55.181Z] Failed to load image Python extension: '/usr/local/lib/python3.8/dist-packages/torchvision/image.so: undefined symbol: _ZN3c104cuda20CUDACachingAllocator9allocatorE'If you don't plan on using image functionality from `torchvision.io`, you can ignore this warning. Otherwise, there might be something wrong with your environment. Did you have `libjpeg` or `libpng` installed before building `torchvision` from source?
[2023-04-27T23:07:55.181Z] MONAI version: 1.2.0rc5+7.gd23221f0
[2023-04-27T23:07:55.181Z] Numpy version: 1.22.2
[2023-04-27T23:07:55.181Z] Pytorch version: 1.13.1+cu117
[2023-04-27T23:07:55.181Z] MONAI flags: HAS_EXT = False, USE_COMPILED = False, USE_META_DICT = False
[2023-04-27T23:07:55.181Z] MONAI rev id: d23221f06afdf5fa7d8e3fde6552b6cceaf4a0bc
[2023-04-27T23:07:55.181Z] MONAI __file__: /home/jenkins/agent/workspace/Monai-notebooks/MONAI/monai/__init__.py
[2023-04-27T23:07:55.181Z] 
[2023-04-27T23:07:55.181Z] Optional dependencies:
[2023-04-27T23:07:55.181Z] Pytorch Ignite version: 0.4.8
[2023-04-27T23:07:55.181Z] ITK version: 5.3.0
[2023-04-27T23:07:55.181Z] Nibabel version: 5.1.0
[2023-04-27T23:07:55.181Z] scikit-image version: 0.20.0
[2023-04-27T23:07:55.181Z] Pillow version: 9.2.0
[2023-04-27T23:07:55.181Z] Tensorboard version: 2.9.0
[2023-04-27T23:07:55.181Z] gdown version: 4.7.1
[2023-04-27T23:07:55.181Z] TorchVision version: 0.15.0a0
[2023-04-27T23:07:55.181Z] tqdm version: 4.65.0
[2023-04-27T23:07:55.181Z] lmdb version: 1.4.1
[2023-04-27T23:07:55.181Z] psutil version: 5.9.4
[2023-04-27T23:07:55.181Z] pandas version: 1.5.2
[2023-04-27T23:07:55.181Z] einops version: 0.6.1
[2023-04-27T23:07:55.181Z] transformers version: 4.21.3
[2023-04-27T23:07:55.181Z] mlflow version: 2.3.0
[2023-04-27T23:07:55.181Z] pynrrd version: 1.0.0
[2023-04-27T23:07:55.181Z] 
[2023-04-27T23:07:55.181Z] For details about installing the optional dependencies, please visit:
[2023-04-27T23:07:55.181Z]     https://docs.monai.io/en/latest/installation.html#installing-the-recommended-dependencies
[2023-04-27T23:07:55.181Z] 
[2023-04-27T23:07:57.695Z] papermill  --progress-bar -k python3
[2023-04-27T23:07:58.258Z] /usr/local/lib/python3.8/dist-packages/papermill/iorw.py:153: UserWarning: the file is not specified with any extension : -
[2023-04-27T23:07:58.258Z]   warnings.warn(
[2023-04-27T23:08:20.082Z] 
Executing:   0%|          | 0/21 [00:00<?, ?cell/s]
Executing:   5%|▍         | 1/21 [00:01<00:31,  1.57s/cell]
Executing:  19%|█▉        | 4/21 [00:16<01:15,  4.44s/cell]Kernel died while waiting for execute reply.
[2023-04-27T23:08:20.082Z] 
Executing:  29%|██▊       | 6/21 [00:21<00:53,  3.60s/cell]
Executing:  29%|██▊       | 6/21 [00:21<00:54,  3.65s/cell]
[2023-04-27T23:08:20.083Z] Traceback (most recent call last):
[2023-04-27T23:08:20.083Z]   File "/usr/local/lib/python3.8/dist-packages/nbclient/client.py", line 1002, in async_execute_cell
[2023-04-27T23:08:20.083Z]     exec_reply = await self.task_poll_for_reply
[2023-04-27T23:08:20.083Z] asyncio.exceptions.CancelledError
[2023-04-27T23:08:20.083Z] 
[2023-04-27T23:08:20.083Z] During handling of the above exception, another exception occurred:
[2023-04-27T23:08:20.083Z] 
[2023-04-27T23:08:20.083Z] Traceback (most recent call last):
[2023-04-27T23:08:20.083Z]   File "/usr/local/lib/python3.8/dist-packages/papermill/cli.py", line 250, in papermill
[2023-04-27T23:08:20.083Z]     execute_notebook(
[2023-04-27T23:08:20.083Z]   File "/usr/local/lib/python3.8/dist-packages/papermill/execute.py", line 113, in execute_notebook
[2023-04-27T23:08:20.083Z]     nb = papermill_engines.execute_notebook_with_engine(
[2023-04-27T23:08:20.083Z]   File "/usr/local/lib/python3.8/dist-packages/papermill/engines.py", line 49, in execute_notebook_with_engine
[2023-04-27T23:08:20.083Z]     return self.get_engine(engine_name).execute_notebook(nb, kernel_name, **kwargs)
[2023-04-27T23:08:20.083Z]   File "/usr/local/lib/python3.8/dist-packages/papermill/engines.py", line 367, in execute_notebook
[2023-04-27T23:08:20.083Z]     cls.execute_managed_notebook(nb_man, kernel_name, log_output=log_output, **kwargs)
[2023-04-27T23:08:20.083Z]   File "/usr/local/lib/python3.8/dist-packages/papermill/engines.py", line 436, in execute_managed_notebook
[2023-04-27T23:08:20.083Z]     return PapermillNotebookClient(nb_man, **final_kwargs).execute()
[2023-04-27T23:08:20.083Z]   File "/usr/local/lib/python3.8/dist-packages/papermill/clientwrap.py", line 45, in execute
[2023-04-27T23:08:20.083Z]     self.papermill_execute_cells()
[2023-04-27T23:08:20.083Z]   File "/usr/local/lib/python3.8/dist-packages/papermill/clientwrap.py", line 72, in papermill_execute_cells
[2023-04-27T23:08:20.083Z]     self.execute_cell(cell, index)
[2023-04-27T23:08:20.083Z]   File "/usr/local/lib/python3.8/dist-packages/jupyter_core/utils/__init__.py", line 166, in wrapped
[2023-04-27T23:08:20.083Z]     return loop.run_until_complete(inner)
[2023-04-27T23:08:20.083Z]   File "/usr/lib/python3.8/asyncio/base_events.py", line 616, in run_until_complete
[2023-04-27T23:08:20.083Z]     return future.result()
[2023-04-27T23:08:20.083Z]   File "/usr/local/lib/python3.8/dist-packages/nbclient/client.py", line 1006, in async_execute_cell
[2023-04-27T23:08:20.083Z]     raise DeadKernelError("Kernel died")
[2023-04-27T23:08:20.083Z] nbclient.exceptions.DeadKernelError: Kernel died