FileNotFoundError in profiling_camelyon_pipeline.ipynb
KumoLiu opened this issue · 1 comments
KumoLiu commented
08:26:03 Running ./pathology/tumor_detection/ignite/profiling_camelyon_pipeline.ipynb
08:26:03 Checking PEP8 compliance...
08:26:03 Running notebook...
08:26:11 MONAI version: 1.3.0+87.ge9e27385
08:26:11 Numpy version: 1.22.2
08:26:11 Pytorch version: 2.1.0a0+29c30b1
08:26:11 MONAI flags: HAS_EXT = False, USE_COMPILED = False, USE_META_DICT = False
08:26:11 MONAI rev id: e9e273858b6904659b0cd581d357662dc5c782f6
08:26:11 MONAI __file__: /home/jenkins/agent/workspace/Monai-notebooks/MONAI/monai/__init__.py
08:26:11
08:26:11 Optional dependencies:
08:26:11 Pytorch Ignite version: 0.4.11
08:26:11 ITK version: 5.3.0
08:26:11 Nibabel version: 5.2.1
08:26:11 scikit-image version: 0.22.0
08:26:11 scipy version: 1.11.1
08:26:11 Pillow version: 9.2.0
08:26:11 Tensorboard version: 2.16.2
08:26:11 gdown version: 4.7.3
08:26:11 TorchVision version: 0.16.0a0
08:26:11 tqdm version: 4.65.0
08:26:11 lmdb version: 1.4.1
08:26:11 psutil version: 5.9.4
08:26:11 pandas version: 1.5.2
08:26:11 einops version: 0.6.1
08:26:11 transformers version: 4.38.2
08:26:11 mlflow version: 2.11.1
08:26:11 pynrrd version: 1.0.0
08:26:11 clearml version: 1.14.5rc0
08:26:11
08:26:11 For details about installing the optional dependencies, please visit:
08:26:11 https://docs.monai.io/en/latest/installation.html#installing-the-recommended-dependencies
08:26:11
08:26:13 papermill --progress-bar -k python3
08:26:13 /usr/local/lib/python3.10/dist-packages/papermill/iorw.py:153: UserWarning: the file is not specified with any extension : -
08:26:13 warnings.warn(
08:27:04
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Executing: 89%|████████▉ | 17/19 [00:50<00:05, 2.96s/cell]
08:27:04 /usr/local/lib/python3.10/dist-packages/papermill/iorw.py:153: UserWarning: the file is not specified with any extension : -
08:27:04 warnings.warn(
08:27:04 Traceback (most recent call last):
08:27:04 File "/usr/local/bin/papermill", line 8, in <module>
08:27:04 sys.exit(papermill())
08:27:04 File "/usr/local/lib/python3.10/dist-packages/click/core.py", line 1157, in __call__
08:27:04 return self.main(*args, **kwargs)
08:27:04 File "/usr/local/lib/python3.10/dist-packages/click/core.py", line 1078, in main
08:27:04 rv = self.invoke(ctx)
08:27:04 File "/usr/local/lib/python3.10/dist-packages/click/core.py", line 1434, in invoke
08:27:04 return ctx.invoke(self.callback, **ctx.params)
08:27:04 File "/usr/local/lib/python3.10/dist-packages/click/core.py", line 783, in invoke
08:27:04 return __callback(*args, **kwargs)
08:27:04 File "/usr/local/lib/python3.10/dist-packages/click/decorators.py", line 33, in new_func
08:27:04 return f(get_current_context(), *args, **kwargs)
08:27:04 File "/usr/local/lib/python3.10/dist-packages/papermill/cli.py", line 254, in papermill
08:27:04 execute_notebook(
08:27:04 File "/usr/local/lib/python3.10/dist-packages/papermill/execute.py", line 134, in execute_notebook
08:27:04 raise_for_execution_errors(nb, output_path)
08:27:04 File "/usr/local/lib/python3.10/dist-packages/papermill/execute.py", line 241, in raise_for_execution_errors
08:27:04 raise error
08:27:04 papermill.exceptions.PapermillExecutionError:
08:27:04 ---------------------------------------------------------------------------
08:27:04 Exception encountered at "In [7]":
08:27:04 ---------------------------------------------------------------------------
08:27:04 FileNotFoundError Traceback (most recent call last)
08:27:04 Cell In[7], line 2
08:27:04 1 # Load NVTX Push/Pop Range Summary
08:27:04 ----> 2 summary = pd.read_csv("profile_report_nvtxppsum.csv")
08:27:04 3 # display(summary)
08:27:04 4
08:27:04 5 # Set the Range (which is the name of each range) as the index
08:27:04 6 summary.set_index("Range", inplace=True)
08:27:04
08:27:04 File /usr/local/lib/python3.10/dist-packages/pandas/util/_decorators.py:211, in deprecate_kwarg.<locals>._deprecate_kwarg.<locals>.wrapper(*args, **kwargs)
08:27:04 209 else:
08:27:04 210 kwargs[new_arg_name] = new_arg_value
08:27:04 --> 211 return func(*args, **kwargs)
08:27:04
08:27:04 File /usr/local/lib/python3.10/dist-packages/pandas/util/_decorators.py:331, in deprecate_nonkeyword_arguments.<locals>.decorate.<locals>.wrapper(*args, **kwargs)
08:27:04 325 if len(args) > num_allow_args:
08:27:04 326 warnings.warn(
08:27:04 327 msg.format(arguments=_format_argument_list(allow_args)),
08:27:04 328 FutureWarning,
08:27:04 329 stacklevel=find_stack_level(),
08:27:04 330 )
08:27:04 --> 331 return func(*args, **kwargs)
08:27:04
08:27:04 File /usr/local/lib/python3.10/dist-packages/pandas/io/parsers/readers.py:950, in read_csv(filepath_or_buffer, sep, delimiter, header, names, index_col, usecols, squeeze, prefix, mangle_dupe_cols, dtype, engine, converters, true_values, false_values, skipinitialspace, skiprows, skipfooter, nrows, na_values, keep_default_na, na_filter, verbose, skip_blank_lines, parse_dates, infer_datetime_format, keep_date_col, date_parser, dayfirst, cache_dates, iterator, chunksize, compression, thousands, decimal, lineterminator, quotechar, quoting, doublequote, escapechar, comment, encoding, encoding_errors, dialect, error_bad_lines, warn_bad_lines, on_bad_lines, delim_whitespace, low_memory, memory_map, float_precision, storage_options)
08:27:04 935 kwds_defaults = _refine_defaults_read(
08:27:04 936 dialect,
08:27:04 937 delimiter,
08:27:04 (...)
08:27:04 946 defaults={"delimiter": ","},
08:27:04 947 )
08:27:04 948 kwds.update(kwds_defaults)
08:27:04 --> 950 return _read(filepath_or_buffer, kwds)
08:27:04
08:27:04 File /usr/local/lib/python3.10/dist-packages/pandas/io/parsers/readers.py:605, in _read(filepath_or_buffer, kwds)
08:27:04 602 _validate_names(kwds.get("names", None))
08:27:04 604 # Create the parser.
08:27:04 --> 605 parser = TextFileReader(filepath_or_buffer, **kwds)
08:27:04 607 if chunksize or iterator:
08:27:04 608 return parser
08:27:04
08:27:04 File /usr/local/lib/python3.10/dist-packages/pandas/io/parsers/readers.py:1442, in TextFileReader.__init__(self, f, engine, **kwds)
08:27:04 1439 self.options["has_index_names"] = kwds["has_index_names"]
08:27:04 1441 self.handles: IOHandles | None = None
08:27:04 -> 1442 self._engine = self._make_engine(f, self.engine)
08:27:04
08:27:04 File /usr/local/lib/python3.10/dist-packages/pandas/io/parsers/readers.py:1735, in TextFileReader._make_engine(self, f, engine)
08:27:04 1733 if "b" not in mode:
08:27:04 1734 mode += "b"
08:27:04 -> 1735 self.handles = get_handle(
08:27:04 1736 f,
08:27:04 1737 mode,
08:27:04 1738 encoding=self.options.get("encoding", None),
08:27:04 1739 compression=self.options.get("compression", None),
08:27:04 1740 memory_map=self.options.get("memory_map", False),
08:27:04 1741 is_text=is_text,
08:27:04 1742 errors=self.options.get("encoding_errors", "strict"),
08:27:04 1743 storage_options=self.options.get("storage_options", None),
08:27:04 1744 )
08:27:04 1745 assert self.handles is not None
08:27:04 1746 f = self.handles.handle
08:27:04
08:27:04 File /usr/local/lib/python3.10/dist-packages/pandas/io/common.py:856, in get_handle(path_or_buf, mode, encoding, compression, memory_map, is_text, errors, storage_options)
08:27:04 851 elif isinstance(handle, str):
08:27:04 852 # Check whether the filename is to be opened in binary mode.
08:27:04 853 # Binary mode does not support 'encoding' and 'newline'.
08:27:04 854 if ioargs.encoding and "b" not in ioargs.mode:
08:27:04 855 # Encoding
08:27:04 --> 856 handle = open(
08:27:04 857 handle,
08:27:04 858 ioargs.mode,
08:27:04 859 encoding=ioargs.encoding,
08:27:04 860 errors=errors,
08:27:04 861 newline="",
08:27:04 862 )
08:27:04 863 else:
08:27:04 864 # Binary mode
08:27:04 865 handle = open(handle, ioargs.mode)
08:27:04
08:27:04 FileNotFoundError: [Errno 2] No such file or directory: 'profile_report_nvtxppsum.csv'
KumoLiu commented
Fixed by updated the base image.