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05_spleen_segmentation_lightning #1550

Closed wyli closed 1 year ago

wyli commented 1 year ago 
[2023-10-19T00:18:16.476Z] Running ./bundle/05_spleen_segmentation_lightning.ipynb
[2023-10-19T00:18:16.476Z] Checking PEP8 compliance...
[2023-10-19T00:18:16.731Z] Running notebook...
[2023-10-19T00:18:16.731Z] Before:
[2023-10-19T00:18:16.731Z]     "We can now train as normal to replicate the original code. For demonstration purpose, we set `max_epochs=1`."
[2023-10-19T00:18:16.731Z]       "`Trainer.fit` stopped: `max_epochs=1` reached.\n"
[2023-10-19T00:18:16.731Z] After:
[2023-10-19T00:18:16.731Z]     "We can now train as normal to replicate the original code. For demonstration purpose, we set `max_epochs = 1`."
[2023-10-19T00:18:16.731Z]       "`Trainer.fit` stopped: `max_epochs = 1` reached.\n"
[2023-10-19T00:18:24.813Z] MONAI version: 1.3.0+4.g9f1168f4
[2023-10-19T00:18:24.813Z] Numpy version: 1.26.1
[2023-10-19T00:18:24.813Z] Pytorch version: 2.1.0a0+29c30b1
[2023-10-19T00:18:24.813Z] MONAI flags: HAS_EXT = False, USE_COMPILED = False, USE_META_DICT = False
[2023-10-19T00:18:24.814Z] MONAI rev id: 9f1168f43c4cb22cf4ef4ce72caeffd7209fa772
[2023-10-19T00:18:24.814Z] MONAI __file__: /home/jenkins/agent/workspace/Monai-notebooks/MONAI/monai/__init__.py
[2023-10-19T00:18:24.814Z] 
[2023-10-19T00:18:24.814Z] Optional dependencies:
[2023-10-19T00:18:24.814Z] Pytorch Ignite version: 0.4.11
[2023-10-19T00:18:24.814Z] ITK version: 5.3.0
[2023-10-19T00:18:24.814Z] Nibabel version: 5.1.0
[2023-10-19T00:18:24.814Z] scikit-image version: 0.22.0
[2023-10-19T00:18:24.814Z] scipy version: 1.11.1
[2023-10-19T00:18:24.814Z] Pillow version: 9.2.0
[2023-10-19T00:18:24.814Z] Tensorboard version: 2.9.0
[2023-10-19T00:18:24.814Z] gdown version: 4.7.1
[2023-10-19T00:18:24.814Z] TorchVision version: 0.16.0a0
[2023-10-19T00:18:24.814Z] tqdm version: 4.65.0
[2023-10-19T00:18:24.814Z] lmdb version: 1.4.1
[2023-10-19T00:18:24.814Z] psutil version: 5.9.4
[2023-10-19T00:18:24.814Z] pandas version: 2.1.1
[2023-10-19T00:18:24.814Z] einops version: 0.6.1
[2023-10-19T00:18:24.814Z] transformers version: 4.21.3
[2023-10-19T00:18:24.814Z] mlflow version: 2.7.1
[2023-10-19T00:18:24.814Z] pynrrd version: 1.0.0
[2023-10-19T00:18:24.814Z] clearml version: 1.13.2rc0
[2023-10-19T00:18:24.814Z] 
[2023-10-19T00:18:24.814Z] For details about installing the optional dependencies, please visit:
[2023-10-19T00:18:24.814Z]     https://docs.monai.io/en/latest/installation.html#installing-the-recommended-dependencies
[2023-10-19T00:18:24.814Z] 
[2023-10-19T00:18:26.181Z] papermill  --progress-bar -k python3
[2023-10-19T00:18:26.742Z] /usr/local/lib/python3.10/dist-packages/papermill/iorw.py:153: UserWarning: the file is not specified with any extension : -
[2023-10-19T00:18:26.742Z]   warnings.warn(
[2023-10-19T00:19:06.769Z] 
Executing:   0%|          | 0/28 [00:00<?, ?cell/s]
Executing:   4%|▎         | 1/28 [00:01<00:34,  1.26s/cell]
Executing:  11%|█         | 3/28 [00:15<02:15,  5.43s/cell]
Executing:  18%|█▊        | 5/28 [00:21<01:38,  4.30s/cell]
Executing:  29%|██▊       | 8/28 [00:29<01:08,  3.43s/cell]
Executing:  71%|███████▏  | 20/28 [00:38<00:11,  1.43s/cell]
Executing:  71%|███████▏  | 20/28 [00:40<00:16,  2.01s/cell]
[2023-10-19T00:19:06.769Z] /usr/local/lib/python3.10/dist-packages/papermill/iorw.py:153: UserWarning: the file is not specified with any extension : -
[2023-10-19T00:19:06.769Z]   warnings.warn(
[2023-10-19T00:19:06.769Z] Traceback (most recent call last):
[2023-10-19T00:19:06.769Z]   File "/usr/local/bin/papermill", line 8, in <module>
[2023-10-19T00:19:06.769Z]     sys.exit(papermill())
[2023-10-19T00:19:06.769Z]   File "/usr/local/lib/python3.10/dist-packages/click/core.py", line 1157, in __call__
[2023-10-19T00:19:06.769Z]     return self.main(*args, **kwargs)
[2023-10-19T00:19:06.769Z]   File "/usr/local/lib/python3.10/dist-packages/click/core.py", line 1078, in main
[2023-10-19T00:19:06.769Z]     rv = self.invoke(ctx)
[2023-10-19T00:19:06.769Z]   File "/usr/local/lib/python3.10/dist-packages/click/core.py", line 1434, in invoke
[2023-10-19T00:19:06.769Z]     return ctx.invoke(self.callback, **ctx.params)
[2023-10-19T00:19:06.769Z]   File "/usr/local/lib/python3.10/dist-packages/click/core.py", line 783, in invoke
[2023-10-19T00:19:06.769Z]     return __callback(*args, **kwargs)
[2023-10-19T00:19:06.769Z]   File "/usr/local/lib/python3.10/dist-packages/click/decorators.py", line 33, in new_func
[2023-10-19T00:19:06.769Z]     return f(get_current_context(), *args, **kwargs)
[2023-10-19T00:19:06.769Z]   File "/usr/local/lib/python3.10/dist-packages/papermill/cli.py", line 250, in papermill
[2023-10-19T00:19:06.769Z]     execute_notebook(
[2023-10-19T00:19:06.769Z]   File "/usr/local/lib/python3.10/dist-packages/papermill/execute.py", line 128, in execute_notebook
[2023-10-19T00:19:06.769Z]     raise_for_execution_errors(nb, output_path)
[2023-10-19T00:19:06.769Z]   File "/usr/local/lib/python3.10/dist-packages/papermill/execute.py", line 232, in raise_for_execution_errors
[2023-10-19T00:19:06.769Z]     raise error
[2023-10-19T00:19:06.769Z] papermill.exceptions.PapermillExecutionError: 
[2023-10-19T00:19:06.769Z] ---------------------------------------------------------------------------
[2023-10-19T00:19:06.769Z] Exception encountered at "In [9]":
[2023-10-19T00:19:06.769Z] ---------------------------------------------------------------------------
[2023-10-19T00:19:06.769Z] CalledProcessError                        Traceback (most recent call last)
[2023-10-19T00:19:06.769Z] Cell In[9], line 1
[2023-10-19T00:19:06.769Z] ----> 1 get_ipython().run_cell_magic('bash', '', '\nBUNDLE="./SpleenSegLightning"\nDATA_DIR="./Task09_Spleen"\nexport PYTHONPATH="$BUNDLE"\n\n# run the bundle with epochs set to 1 for speed during testing, change this to get a better result\npython -m monai.bundle run train \\\n    --bundle_dir "$BUNDLE" \\\n    --data_dir "$DATA_DIR" \\\n    --meta_file "$BUNDLE/configs/metadata.json" \\\n    --config_file "[\'$BUNDLE/configs/common.yaml\',\'$BUNDLE/configs/train.yaml\']" \\\n    --max_epochs 1\n')
[2023-10-19T00:19:06.769Z] 
[2023-10-19T00:19:06.769Z] File /usr/local/lib/python3.10/dist-packages/IPython/core/interactiveshell.py:2478, in InteractiveShell.run_cell_magic(self, magic_name, line, cell)
[2023-10-19T00:19:06.769Z]    2476 with self.builtin_trap:
[2023-10-19T00:19:06.769Z]    2477     args = (magic_arg_s, cell)
[2023-10-19T00:19:06.769Z] -> 2478     result = fn(*args, **kwargs)
[2023-10-19T00:19:06.769Z]    2480 # The code below prevents the output from being displayed
[2023-10-19T00:19:06.769Z]    2481 # when using magics with decodator @output_can_be_silenced
[2023-10-19T00:19:06.770Z]    2482 # when the last Python token in the expression is a ';'.
[2023-10-19T00:19:06.770Z]    2483 if getattr(fn, magic.MAGIC_OUTPUT_CAN_BE_SILENCED, False):
[2023-10-19T00:19:06.770Z] 
[2023-10-19T00:19:06.770Z] File /usr/local/lib/python3.10/dist-packages/IPython/core/magics/script.py:154, in ScriptMagics._make_script_magic.<locals>.named_script_magic(line, cell)
[2023-10-19T00:19:06.770Z]     152 else:
[2023-10-19T00:19:06.770Z]     153     line = script
[2023-10-19T00:19:06.770Z] --> 154 return self.shebang(line, cell)
[2023-10-19T00:19:06.770Z] 
[2023-10-19T00:19:06.770Z] File /usr/local/lib/python3.10/dist-packages/IPython/core/magics/script.py:314, in ScriptMagics.shebang(self, line, cell)
[2023-10-19T00:19:06.770Z]     309 if args.raise_error and p.returncode != 0:
[2023-10-19T00:19:06.770Z]     310     # If we get here and p.returncode is still None, we must have
[2023-10-19T00:19:06.770Z]     311     # killed it but not yet seen its return code. We don't wait for it,
[2023-10-19T00:19:06.770Z]     312     # in case it's stuck in uninterruptible sleep. -9 = SIGKILL
[2023-10-19T00:19:06.770Z]     313     rc = p.returncode or -9
[2023-10-19T00:19:06.770Z] --> 314     raise CalledProcessError(rc, cell)
[2023-10-19T00:19:06.770Z] 
[2023-10-19T00:19:06.770Z] CalledProcessError: Command 'b'\nBUNDLE="./SpleenSegLightning"\nDATA_DIR="./Task09_Spleen"\nexport PYTHONPATH="$BUNDLE"\n\n# run the bundle with epochs set to 1 for speed during testing, change this to get a better result\npython -m monai.bundle run train \\\n    --bundle_dir "$BUNDLE" \\\n    --data_dir "$DATA_DIR" \\\n    --meta_file "$BUNDLE/configs/metadata.json" \\\n    --config_file "[\'$BUNDLE/configs/common.yaml\',\'$BUNDLE/configs/train.yaml\']" \\\n    --max_epochs 1\n'' returned non-zero exit status 1.
wyli commented 1 year ago

hi @OeslleLucena @ericspod any idea about this issue?

OeslleLucena commented 1 year ago

The dataset has to be downloaded beforehand and put into that directory. Maybe I need to improve the notebook there. Will submit a PR with the updated version by tomorrow.