[2023-09-08T01:43:38.188Z] Running ./modules/transforms_demo_2d.ipynb
[2023-09-08T01:43:38.188Z] Checking PEP8 compliance...
[2023-09-08T01:43:38.752Z] Running notebook...
[2023-09-08T01:43:46.854Z] MONAI version: 1.2.0+110.gef7debe4
[2023-09-08T01:43:46.854Z] Numpy version: 1.26.0rc1
[2023-09-08T01:43:46.854Z] Pytorch version: 2.1.0a0+29c30b1
[2023-09-08T01:43:46.854Z] MONAI flags: HAS_EXT = False, USE_COMPILED = False, USE_META_DICT = False
[2023-09-08T01:43:46.854Z] MONAI rev id: ef7debe47603f882513b255e449b26659766b64f
[2023-09-08T01:43:46.854Z] MONAI __file__: /home/jenkins/agent/workspace/Monai-notebooks/MONAI/monai/__init__.py
[2023-09-08T01:43:46.854Z]
[2023-09-08T01:43:46.854Z] Optional dependencies:
[2023-09-08T01:43:46.854Z] Pytorch Ignite version: 0.4.11
[2023-09-08T01:43:46.854Z] ITK version: 5.3.0
[2023-09-08T01:43:46.854Z] Nibabel version: 5.1.0
[2023-09-08T01:43:46.854Z] scikit-image version: 0.21.0
[2023-09-08T01:43:46.854Z] scipy version: 1.11.1
[2023-09-08T01:43:46.854Z] Pillow version: 9.2.0
[2023-09-08T01:43:46.854Z] Tensorboard version: 2.9.0
[2023-09-08T01:43:46.854Z] gdown version: 4.7.1
[2023-09-08T01:43:46.854Z] TorchVision version: 0.16.0a0
[2023-09-08T01:43:46.854Z] tqdm version: 4.65.0
[2023-09-08T01:43:46.854Z] lmdb version: 1.4.1
[2023-09-08T01:43:46.854Z] psutil version: 5.9.4
[2023-09-08T01:43:46.854Z] pandas version: 2.1.0
[2023-09-08T01:43:46.854Z] einops version: 0.6.1
[2023-09-08T01:43:46.854Z] transformers version: 4.21.3
[2023-09-08T01:43:46.854Z] mlflow version: 2.6.0
[2023-09-08T01:43:46.854Z] pynrrd version: 1.0.0
[2023-09-08T01:43:46.854Z] clearml version: 1.12.2
[2023-09-08T01:43:46.854Z]
[2023-09-08T01:43:46.854Z] For details about installing the optional dependencies, please visit:
[2023-09-08T01:43:46.854Z] https://docs.monai.io/en/latest/installation.html#installing-the-recommended-dependencies
[2023-09-08T01:43:46.854Z]
[2023-09-08T01:43:48.745Z] papermill --progress-bar -k python3
[2023-09-08T01:43:49.003Z] /usr/local/lib/python3.10/dist-packages/papermill/iorw.py:153: UserWarning: the file is not specified with any extension : -
[2023-09-08T01:43:49.004Z] warnings.warn(
[2023-09-08T01:44:54.678Z]
Executing: 0%| | 0/21 [00:00<?, ?cell/s]
Executing: 5%|▍ | 1/21 [00:01<00:29, 1.48s/cell]
Executing: 19%|█▉ | 4/21 [00:10<00:45, 2.68s/cell]
Executing: 29%|██▊ | 6/21 [00:16<00:42, 2.81s/cell]
Executing: 48%|████▊ | 10/21 [01:03<01:25, 7.77s/cell]
Executing: 48%|████▊ | 10/21 [01:05<01:11, 6.52s/cell]
[2023-09-08T01:44:54.678Z] /usr/local/lib/python3.10/dist-packages/papermill/iorw.py:153: UserWarning: the file is not specified with any extension : -
[2023-09-08T01:44:54.678Z] warnings.warn(
[2023-09-08T01:44:54.678Z] Traceback (most recent call last):
[2023-09-08T01:44:54.678Z] File "/usr/local/bin/papermill", line 8, in <module>
[2023-09-08T01:44:54.678Z] sys.exit(papermill())
[2023-09-08T01:44:54.678Z] File "/usr/local/lib/python3.10/dist-packages/click/core.py", line 1157, in __call__
[2023-09-08T01:44:54.678Z] return self.main(*args, **kwargs)
[2023-09-08T01:44:54.678Z] File "/usr/local/lib/python3.10/dist-packages/click/core.py", line 1078, in main
[2023-09-08T01:44:54.678Z] rv = self.invoke(ctx)
[2023-09-08T01:44:54.678Z] File "/usr/local/lib/python3.10/dist-packages/click/core.py", line 1434, in invoke
[2023-09-08T01:44:54.678Z] return ctx.invoke(self.callback, **ctx.params)
[2023-09-08T01:44:54.678Z] File "/usr/local/lib/python3.10/dist-packages/click/core.py", line 783, in invoke
[2023-09-08T01:44:54.678Z] return __callback(*args, **kwargs)
[2023-09-08T01:44:54.678Z] File "/usr/local/lib/python3.10/dist-packages/click/decorators.py", line 33, in new_func
[2023-09-08T01:44:54.678Z] return f(get_current_context(), *args, **kwargs)
[2023-09-08T01:44:54.678Z] File "/usr/local/lib/python3.10/dist-packages/papermill/cli.py", line 250, in papermill
[2023-09-08T01:44:54.678Z] execute_notebook(
[2023-09-08T01:44:54.678Z] File "/usr/local/lib/python3.10/dist-packages/papermill/execute.py", line 128, in execute_notebook
[2023-09-08T01:44:54.678Z] raise_for_execution_errors(nb, output_path)
[2023-09-08T01:44:54.678Z] File "/usr/local/lib/python3.10/dist-packages/papermill/execute.py", line 232, in raise_for_execution_errors
[2023-09-08T01:44:54.678Z] raise error
[2023-09-08T01:44:54.678Z] papermill.exceptions.PapermillExecutionError:
[2023-09-08T01:44:54.678Z] ---------------------------------------------------------------------------
[2023-09-08T01:44:54.678Z] Exception encountered at "In [4]":
[2023-09-08T01:44:54.678Z] ---------------------------------------------------------------------------
[2023-09-08T01:44:54.678Z] ContentTooShortError Traceback (most recent call last)
[2023-09-08T01:44:54.678Z] Cell In[4], line 10
[2023-09-08T01:44:54.678Z] 8 data_dir = os.path.join(root_dir, "Warwick QU Dataset (Released 2016_07_08)")
[2023-09-08T01:44:54.678Z] 9 if not os.path.exists(data_dir):
[2023-09-08T01:44:54.678Z] ---> 10 download_and_extract(resource, compressed_file, root_dir, md5)
[2023-09-08T01:44:54.678Z]
[2023-09-08T01:44:54.678Z] File /home/jenkins/agent/workspace/Monai-notebooks/MONAI/monai/apps/utils.py:328, in download_and_extract(url, filepath, output_dir, hash_val, hash_type, file_type, has_base, progress)
[2023-09-08T01:44:54.678Z] 326 with tempfile.TemporaryDirectory() as tmp_dir:
[2023-09-08T01:44:54.678Z] 327 filename = filepath or Path(tmp_dir, _basename(url)).resolve()
[2023-09-08T01:44:54.678Z] --> 328 download_url(url=url, filepath=filename, hash_val=hash_val, hash_type=hash_type, progress=progress)
[2023-09-08T01:44:54.678Z] 329 extractall(filepath=filename, output_dir=output_dir, file_type=file_type, has_base=has_base)
[2023-09-08T01:44:54.678Z]
[2023-09-08T01:44:54.678Z] File /home/jenkins/agent/workspace/Monai-notebooks/MONAI/monai/apps/utils.py:219, in download_url(url, filepath, hash_val, hash_type, progress, **gdown_kwargs)
[2023-09-08T01:44:54.678Z] 214 raise RuntimeError(
[2023-09-08T01:44:54.678Z] 215 f"Download of file from {download_url}, received from {url} "
[2023-09-08T01:44:54.678Z] 216 + f" to {filepath} failed due to network issue or denied permission."
[2023-09-08T01:44:54.678Z] 217 )
[2023-09-08T01:44:54.678Z] 218 else:
[2023-09-08T01:44:54.678Z] --> 219 _download_with_progress(url, tmp_name, progress=progress)
[2023-09-08T01:44:54.678Z] 220 if not tmp_name.exists():
[2023-09-08T01:44:54.678Z] 221 raise RuntimeError(
[2023-09-08T01:44:54.678Z] 222 f"Download of file from {url} to {filepath} failed due to network issue or denied permission."
[2023-09-08T01:44:54.678Z] 223 )
[2023-09-08T01:44:54.678Z]
[2023-09-08T01:44:54.678Z] File /home/jenkins/agent/workspace/Monai-notebooks/MONAI/monai/apps/utils.py:119, in _download_with_progress(url, filepath, progress)
[2023-09-08T01:44:54.678Z] 117 except (URLError, HTTPError, ContentTooShortError, OSError) as e:
[2023-09-08T01:44:54.678Z] 118 logger.error(f"Download failed from {url} to {filepath}.")
[2023-09-08T01:44:54.678Z] --> 119 raise e
[2023-09-08T01:44:54.678Z]
[2023-09-08T01:44:54.678Z] File /home/jenkins/agent/workspace/Monai-notebooks/MONAI/monai/apps/utils.py:112, in _download_with_progress(url, filepath, progress)
[2023-09-08T01:44:54.678Z] 109 self.update(b * bsize - self.n) # will also set self.n = b * bsize
[2023-09-08T01:44:54.678Z] 111 with TqdmUpTo(unit="B", unit_scale=True, unit_divisor=1024, miniters=1, desc=_basename(filepath)) as t:
[2023-09-08T01:44:54.678Z] --> 112 urlretrieve(url, filepath, reporthook=t.update_to)
[2023-09-08T01:44:54.678Z] 113 else:
[2023-09-08T01:44:54.678Z] 114 if not has_tqdm and progress:
[2023-09-08T01:44:54.678Z]
[2023-09-08T01:44:54.678Z] File /usr/lib/python3.10/urllib/request.py:280, in urlretrieve(url, filename, reporthook, data)
[2023-09-08T01:44:54.678Z] 277 reporthook(blocknum, bs, size)
[2023-09-08T01:44:54.678Z] 279 if size >= 0 and read < size:
[2023-09-08T01:44:54.678Z] --> 280 raise ContentTooShortError(
[2023-09-08T01:44:54.678Z] 281 "retrieval incomplete: got only %i out of %i bytes"
[2023-09-08T01:44:54.678Z] 282 % (read, size), result)
[2023-09-08T01:44:54.678Z] 284 return result
[2023-09-08T01:44:54.678Z]
[2023-09-08T01:44:54.678Z] ContentTooShortError: <urlopen error retrieval incomplete: got only 117802284 out of 180902609 bytes>
