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ImportError: libGL.so.1: cannot open shared object file: No such file or directory #1692

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KumoLiu opened this issue Apr 16, 2024 · 0 comments · Fixed by #1693
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ImportError: libGL.so.1: cannot open shared object file: No such file or directory #1692

KumoLiu opened this issue Apr 16, 2024 · 0 comments · Fixed by #1693
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KumoLiu commented Apr 16, 2024 

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
@KumoLiu KumoLiu self-assigned this Apr 16, 2024
@KumoLiu KumoLiu added the bug Something isn't working label Apr 16, 2024
KumoLiu added a commit to KumoLiu/tutorials that referenced this issue Apr 16, 2024
@KumoLiu
fix Project-MONAI#1692
ca57d81 
Signed-off-by: YunLiu <[email protected]>
@KumoLiu KumoLiu mentioned this issue Apr 16, 2024
Merged
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Nic-Ma pushed a commit that referenced this issue Apr 22, 2024
@KumoLiu
Fix opencv-python issue in TCIA tutorial (#1693)
b46eccc 
Fixes #1692
workaround for #1694 

### Description

- Install dependency required by tcia_utils manually to avoid installing
opencv-python
- comment view command in the notebook

### Checks
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [ ] Avoid including large-size files in the PR.
- [ ] Clean up long text outputs from code cells in the notebook.
- [ ] For security purposes, please check the contents and remove any
sensitive info such as user names and private key.
- [ ] Ensure (1) hyperlinks and markdown anchors are working (2) use
relative paths for tutorial repo files (3) put figure and graphs in the
`./figure` folder
- [ ] Notebook runs automatically `./runner.sh -t <path to .ipynb file>`

---------

Signed-off-by: YunLiu <[email protected]>
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Fix opencv-python issue in TCIA tutorial KumoLiu/tutorials
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