ImportError: libGL.so.1: cannot open shared object file: No such file or directory
KumoLiu opened this issue · 0 comments
KumoLiu commented
4:34:51 Running ./model_zoo/TCIA_PROSTATEx_Prostate_MRI_Anatomy_Model.ipynb
14:34:51 Checking PEP8 compliance...
14:34:52 Running notebook...
14:35:04 MONAI version: 1.3.1rc3
14:35:04 Numpy version: 1.24.4
14:35:04 Pytorch version: 2.3.0a0+40ec155e58.nv24.03
14:35:04 MONAI flags: HAS_EXT = False, USE_COMPILED = False, USE_META_DICT = False
14:35:04 MONAI rev id: bff4b1559a147f570fc881717eadc7b3e8a98b96
14:35:04 MONAI __file__: /home/jenkins/agent/workspace/Monai-notebooks/MONAI/monai/__init__.py
14:35:04
14:35:04 Optional dependencies:
14:35:04 Pytorch Ignite version: 0.4.11
14:35:04 ITK version: 5.3.0
14:35:04 Nibabel version: 5.2.1
14:35:04 scikit-image version: 0.22.0
14:35:04 scipy version: 1.12.0
14:35:04 Pillow version: 10.2.0
14:35:04 Tensorboard version: 2.16.2
14:35:04 gdown version: 4.7.3
14:35:04 TorchVision version: 0.18.0a0
14:35:04 tqdm version: 4.66.2
14:35:04 lmdb version: 1.4.1
14:35:04 psutil version: 5.9.4
14:35:04 pandas version: 1.5.3
14:35:04 einops version: 0.7.0
14:35:04 transformers version: 4.39.3
14:35:04 mlflow version: 2.11.3
14:35:04 pynrrd version: 1.0.0
14:35:04 clearml version: 1.15.1
14:35:04
14:35:04 For details about installing the optional dependencies, please visit:
14:35:04 https://docs.monai.io/en/latest/installation.html#installing-the-recommended-dependencies
14:35:04
14:35:05 papermill --progress-bar --log-output -k python3
14:35:05 /usr/local/lib/python3.10/dist-packages/papermill/iorw.py:153: UserWarning: the file is not specified with any extension : -
14:35:05 warnings.warn(
14:36:14
Executing: 0%| | 0/32 [00:00<?, ?cell/s]
Executing: 3%|▎ | 1/32 [00:01<00:33, 1.07s/cell]
Executing: 22%|██▏ | 7/32 [01:01<03:50, 9.20s/cell]
Executing: 28%|██▊ | 9/32 [01:05<02:39, 6.95s/cell]
Executing: 28%|██▊ | 9/32 [01:06<02:49, 7.36s/cell]
14:36:14 /usr/local/lib/python3.10/dist-packages/papermill/iorw.py:153: UserWarning: the file is not specified with any extension : -
14:36:14 warnings.warn(
14:36:14 Traceback (most recent call last):
14:36:14 File "/usr/local/bin/papermill", line 8, in <module>
14:36:14 sys.exit(papermill())
14:36:14 File "/usr/local/lib/python3.10/dist-packages/click/core.py", line 1157, in __call__
14:36:14 return self.main(*args, **kwargs)
14:36:14 File "/usr/local/lib/python3.10/dist-packages/click/core.py", line 1078, in main
14:36:14 rv = self.invoke(ctx)
14:36:14 File "/usr/local/lib/python3.10/dist-packages/click/core.py", line 1434, in invoke
14:36:14 return ctx.invoke(self.callback, **ctx.params)
14:36:14 File "/usr/local/lib/python3.10/dist-packages/click/core.py", line 783, in invoke
14:36:14 return __callback(*args, **kwargs)
14:36:14 File "/usr/local/lib/python3.10/dist-packages/click/decorators.py", line 33, in new_func
14:36:14 return f(get_current_context(), *args, **kwargs)
14:36:14 File "/usr/local/lib/python3.10/dist-packages/papermill/cli.py", line 254, in papermill
14:36:14 execute_notebook(
14:36:14 File "/usr/local/lib/python3.10/dist-packages/papermill/execute.py", line 134, in execute_notebook
14:36:14 raise_for_execution_errors(nb, output_path)
14:36:14 File "/usr/local/lib/python3.10/dist-packages/papermill/execute.py", line 241, in raise_for_execution_errors
14:36:14 raise error
14:36:14 papermill.exceptions.PapermillExecutionError:
14:36:14 ---------------------------------------------------------------------------
14:36:14 Exception encountered at "In [2]":
14:36:14 ---------------------------------------------------------------------------
14:36:14 ImportError Traceback (most recent call last)
14:36:14 Cell In[2], line 15
14:36:14 12 import pydicom_seg
14:36:14 14 # for downloading data from TCIA
14:36:14 ---> 15 from tcia_utils import nbia
14:36:14 17 # This is the most common import command for itkWidgets.
14:36:14 18 # The view() function opens an interactive viewer for 2D and 3D
14:36:14 19 # data in a variety of formats.
14:36:14 20 from itkwidgets import view
14:36:14
14:36:14 File /usr/local/lib/python3.10/dist-packages/tcia_utils/__init__.py:1
14:36:14 ----> 1 from . import nbia
14:36:14 2 from . import datacite
14:36:14 3 from . import pathdb
14:36:14
14:36:14 File /usr/local/lib/python3.10/dist-packages/tcia_utils/nbia.py:17
14:36:14 15 import pydicom
14:36:14 16 import pydicom_seg
14:36:14 ---> 17 import rt_utils
14:36:14 18 import numpy as np
14:36:14 19 from ipywidgets import interact
14:36:14
14:36:14 File /usr/local/lib/python3.10/dist-packages/rt_utils/__init__.py:1
14:36:14 ----> 1 from .rtstruct import RTStruct
14:36:14 2 from .rtstruct_builder import RTStructBuilder
14:36:14
14:36:14 File /usr/local/lib/python3.10/dist-packages/rt_utils/rtstruct.py:7
14:36:14 4 from pydicom.dataset import FileDataset
14:36:14 6 from rt_utils.utils import ROIData
14:36:14 ----> 7 from . import ds_helper, image_helper
14:36:14 10 class RTStruct:
14:36:14 11 """
14:36:14 12 Wrapper class to facilitate appending and extracting ROI's within an RTStruct
14:36:14 13 """
14:36:14
14:36:14 File /usr/local/lib/python3.10/dist-packages/rt_utils/ds_helper.py:2
14:36:14 1 import datetime
14:36:14 ----> 2 from rt_utils.image_helper import get_contours_coords
14:36:14 3 from rt_utils.utils import ROIData, SOPClassUID
14:36:14 4 import numpy as np
14:36:14
14:36:14 File /usr/local/lib/python3.10/dist-packages/rt_utils/image_helper.py:5
14:36:14 2 from typing import List
14:36:14 3 from enum import IntEnum
14:36:14 ----> 5 import cv2 as cv
14:36:14 6 import numpy as np
14:36:14 7 from pydicom import dcmread
14:36:14
14:36:14 File /usr/local/lib/python3.10/dist-packages/cv2/__init__.py:181
14:36:14 176 if DEBUG: print("Extra Python code for", submodule, "is loaded")
14:36:14 178 if DEBUG: print('OpenCV loader: DONE')
14:36:14 --> 181 bootstrap()
14:36:14
14:36:14 File /usr/local/lib/python3.10/dist-packages/cv2/__init__.py:153, in bootstrap()
14:36:14 149 if DEBUG: print("Relink everything from native cv2 module to cv2 package")
14:36:14 151 py_module = sys.modules.pop("cv2")
14:36:14 --> 153 native_module = importlib.import_module("cv2")
14:36:14 155 sys.modules["cv2"] = py_module
14:36:14 156 setattr(py_module, "_native", native_module)
14:36:14
14:36:14 File /usr/lib/python3.10/importlib/__init__.py:126, in import_module(name, package)
14:36:14 124 break
14:36:14 125 level += 1
14:36:14 --> 126 return _bootstrap._gcd_import(name[level:], package, level)
14:36:14
14:36:14 ImportError: libGL.so.1: cannot open shared object file: No such file or directory