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01:43:42 Running ./modules/resample_benchmark.ipynb
01:43:42 Checking PEP8 compliance...
01:43:42 Running notebook...
01:43:43 MONAI version: 1.0.0+142.gd0db5fd9
01:43:43 Numpy version: 1.22.2
01:43:43 Pytorch version: 1.10.2+cu102
01:43:43 MONAI flags: HAS_EXT = False, USE_COMPILED = False, USE_META_DICT = False
01:43:43 MONAI rev id: d0db5fd9d4da3bc7027d22c52bb9c405c3b9e879
01:43:43 MONAI __file__: /home/jenkins/agent/workspace/Monai-notebooks/MONAI/monai/__init__.py
01:43:43
01:43:43 Optional dependencies:
01:43:43 Pytorch Ignite version: 0.4.10
01:43:43 Nibabel version: 4.0.2
01:43:43 scikit-image version: 0.19.3
01:43:43 Pillow version: 9.0.1
01:43:43 Tensorboard version: 2.10.1
01:43:43 gdown version: 4.5.4
01:43:43 TorchVision version: 0.11.3+cu102
01:43:43 tqdm version: 4.64.1
01:43:43 lmdb version: 1.3.0
01:43:43 psutil version: 5.9.2
01:43:43 pandas version: 1.1.5
01:43:43 einops version: 0.6.0
01:43:43 transformers version: 4.21.3
01:43:43 mlflow version: 2.0.1
01:43:43 pynrrd version: 1.0.0
01:43:43
01:43:43 For details about installing the optional dependencies, please visit:
01:43:43 https://docs.monai.io/en/latest/installation.html#installing-the-recommended-dependencies
01:43:43
01:43:44 /opt/conda/lib/python3.8/site-packages/papermill/iorw.py:153: UserWarning: the file is not specified with any extension : -
01:43:44 warnings.warn(
01:44:07
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Executing: 11%|█ | 3/27 [00:19<02:51, 7.13s/cell]
Executing: 19%|█▊ | 5/27 [00:21<01:27, 3.97s/cell]
Executing: 19%|█▊ | 5/27 [00:22<01:40, 4.56s/cell]
01:44:07 /opt/conda/lib/python3.8/site-packages/papermill/iorw.py:153: UserWarning: the file is not specified with any extension : -
01:44:07 warnings.warn(
01:44:07 Traceback (most recent call last):
01:44:07 File "/opt/conda/bin/papermill", line 8, in <module>
01:44:07 sys.exit(papermill())
01:44:07 File "/opt/conda/lib/python3.8/site-packages/click/core.py", line 1130, in __call__
01:44:07 return self.main(*args, **kwargs)
01:44:07 File "/opt/conda/lib/python3.8/site-packages/click/core.py", line 1055, in main
01:44:07 rv = self.invoke(ctx)
01:44:07 File "/opt/conda/lib/python3.8/site-packages/click/core.py", line 1404, in invoke
01:44:07 return ctx.invoke(self.callback, **ctx.params)
01:44:07 File "/opt/conda/lib/python3.8/site-packages/click/core.py", line 760, in invoke
01:44:07 return __callback(*args, **kwargs)
01:44:07 File "/opt/conda/lib/python3.8/site-packages/click/decorators.py", line 26, in new_func
01:44:07 return f(get_current_context(), *args, **kwargs)
01:44:07 File "/opt/conda/lib/python3.8/site-packages/papermill/cli.py", line 250, in papermill
01:44:07 execute_notebook(
01:44:07 File "/opt/conda/lib/python3.8/site-packages/papermill/execute.py", line 128, in execute_notebook
01:44:07 raise_for_execution_errors(nb, output_path)
01:44:07 File "/opt/conda/lib/python3.8/site-packages/papermill/execute.py", line 232, in raise_for_execution_errors
01:44:07 raise error
01:44:07 papermill.exceptions.PapermillExecutionError:
01:44:07 ---------------------------------------------------------------------------
01:44:07 Exception encountered at "In [2]":
01:44:07 ---------------------------------------------------------------------------
01:44:07 HTTPError Traceback (most recent call last)
01:44:07 Cell In [2], line 14
01:44:07 12 # download and rename
01:44:07 13 for k, v in url_dict.items():
01:44:07 ---> 14 download_url(v, f"{root_dir}/{k}")
01:44:07
01:44:07 File /home/jenkins/agent/workspace/Monai-notebooks/MONAI/monai/apps/utils.py:203, in download_url(url, filepath, hash_val, hash_type, progress, **gdown_kwargs)
01:44:07 201 gdown.download(url, f"{tmp_name}", quiet=not progress, **gdown_kwargs)
01:44:07 202 else:
01:44:07 --> 203 _download_with_progress(url, tmp_name, progress=progress)
01:44:07 204 if not tmp_name.exists():
01:44:07 205 raise RuntimeError(
01:44:07 206 f"Download of file from {url} to {filepath} failed due to network issue or denied permission."
01:44:07 207 )
01:44:07
01:44:07 File /home/jenkins/agent/workspace/Monai-notebooks/MONAI/monai/apps/utils.py:114, in _download_with_progress(url, filepath, progress)
01:44:07 112 except (URLError, HTTPError, ContentTooShortError, OSError) as e:
01:44:07 113 logger.error(f"Download failed from {url} to {filepath}.")
01:44:07 --> 114 raise e
01:44:07
01:44:07 File /home/jenkins/agent/workspace/Monai-notebooks/MONAI/monai/apps/utils.py:107, in _download_with_progress(url, filepath, progress)
01:44:07 104 self.update(b * bsize - self.n) # will also set self.n = b * bsize
01:44:07 106 with TqdmUpTo(unit="B", unit_scale=True, unit_divisor=1024, miniters=1, desc=_basename(filepath)) as t:
01:44:07 --> 107 urlretrieve(url, filepath, reporthook=t.update_to)
01:44:07 108 else:
01:44:07 109 if not has_tqdm and progress:
01:44:07
01:44:07 File /opt/conda/lib/python3.8/urllib/request.py:247, in urlretrieve(url, filename, reporthook, data)
01:44:07 230 """
01:44:07 231 Retrieve a URL into a temporary location on disk.
01:44:07 232
01:44:07 (...)
01:44:07 243 data file as well as the resulting HTTPMessage object.
01:44:07 244 """
01:44:07 245 url_type, path = _splittype(url)
01:44:07 --> 247 with contextlib.closing(urlopen(url, data)) as fp:
01:44:07 248 headers = fp.info()
01:44:07 250 # Just return the local path and the "headers" for file://
01:44:07 251 # URLs. No sense in performing a copy unless requested.
01:44:07
01:44:07 File /opt/conda/lib/python3.8/urllib/request.py:222, in urlopen(url, data, timeout, cafile, capath, cadefault, context)
01:44:07 220 else:
01:44:07 221 opener = _opener
01:44:07 --> 222 return opener.open(url, data, timeout)
01:44:07
01:44:07 File /opt/conda/lib/python3.8/urllib/request.py:531, in OpenerDirector.open(self, fullurl, data, timeout)
01:44:07 529 for processor in self.process_response.get(protocol, []):
01:44:07 530 meth = getattr(processor, meth_name)
01:44:07 --> 531 response = meth(req, response)
01:44:07 533 return response
01:44:07
01:44:07 File /opt/conda/lib/python3.8/urllib/request.py:640, in HTTPErrorProcessor.http_response(self, request, response)
01:44:07 637 # According to RFC 2616, "2xx" code indicates that the client's
01:44:07 638 # request was successfully received, understood, and accepted.
01:44:07 639 if not (200 <= code < 300):
01:44:07 --> 640 response = self.parent.error(
01:44:07 641 'http', request, response, code, msg, hdrs)
01:44:07 643 return response
01:44:07
01:44:07 File /opt/conda/lib/python3.8/urllib/request.py:569, in OpenerDirector.error(self, proto, *args)
01:44:07 567 if http_err:
01:44:07 568 args = (dict, 'default', 'http_error_default') + orig_args
01:44:07 --> 569 return self._call_chain(*args)
01:44:07
01:44:07 File /opt/conda/lib/python3.8/urllib/request.py:502, in OpenerDirector._call_chain(self, chain, kind, meth_name, *args)
01:44:07 500 for handler in handlers:
01:44:07 501 func = getattr(handler, meth_name)
01:44:07 --> 502 result = func(*args)
01:44:07 503 if result is not None:
01:44:07 504 return result
01:44:07
01:44:07 File /opt/conda/lib/python3.8/urllib/request.py:649, in HTTPDefaultErrorHandler.http_error_default(self, req, fp, code, msg, hdrs)
01:44:07 648 def http_error_default(self, req, fp, code, msg, hdrs):
01:44:07 --> 649 raise HTTPError(req.full_url, code, msg, hdrs, fp)
01:44:07
01:44:07 HTTPError: HTTP Error 403: Forbidden
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