ImportError when using dolfinx in PythonCall #729

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1. touste

   added

   bugSomething isn't workingSomething isn't working

   on Dec 1, 2025
2. touste commented on Dec 2, 2025

   

   touste

   on Dec 2, 2025

   Author

   More actions

   The issue somehow disappeared when I started from a clean environment, I'm not able to reproduce it anymore...
3. touste

   closed this as completedon Dec 2, 2025
4. aibiliGaferreira commented on Feb 24, 2026

   

   aibiliGaferreira

   on Feb 24, 2026

   More actions

   I'm having a similar issue, but only when using Ubuntu WSL. It works fine on Windows, but when I try running the same script on WSL I get the error:

   julia> pyimport("fundus_image_toolbox")
   ERROR: Python: OSError: libmkl_gnu_thread.so.2: cannot open shared object file: No such file or directory
   Python stacktrace:
    [1] __init__
      @ ctypes /mnt/d/projects/FOCAL/.CondaPkg/.pixi/envs/default/lib/python3.12/ctypes/__init__.py:379
    [2] _load_global_deps
      @ /mnt/d/projects/FOCAL/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/torch/__init__.py:366
    [3] _preload_cuda_deps
      @ /mnt/d/projects/FOCAL/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/torch/__init__.py:344
    [4] _load_global_deps
      @ /mnt/d/projects/FOCAL/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/torch/__init__.py:388
    [5] <module>
      @ /mnt/d/projects/FOCAL/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/torch/__init__.py:430
    [6] <module>
      @ /mnt/d/projects/FOCAL/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/fundus_image_toolbox/circle_crop/eyeq_preprocess.py:2
    [7] <module>
      @ /mnt/d/projects/FOCAL/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/fundus_image_toolbox/circle_crop/__init__.py:1
    [8] <module>
      @ /mnt/d/projects/FOCAL/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/fundus_image_toolbox/__init__.py:1
   Stacktrace:
    [1] pythrow()
      @ PythonCall.Core ~/.julia/packages/PythonCall/83z4q/src/Core/err.jl:77
    [2] errcheck
      @ ~/.julia/packages/PythonCall/83z4q/src/Core/err.jl:10 [inlined]
    [3] pyimport(m::String)
      @ PythonCall.Core ~/.julia/packages/PythonCall/83z4q/src/Core/builtins.jl:1458
    [4] top-level scope
      @ REPL[7]:1
   

   This is what my CondaPkg.toml looks like:

   [deps]
   pytorch = ""
   numpy = ""
   stringzilla = ""
   
   [pip.deps]
   fundus_image_toolbox = ""
   
   

   I've tried adding the mkl packages to CondaPkg.toml, as well as fixing a python version (3.12), but none of those attempts solved the issue. However, if I run

   julia> using CondaPkg
   pkg> conda run python
   >>> import fundus_image_toolbox as fit
   Module missing, downloading it from https://github.com/berenslab/MIDL24-segmentation_quality_control...
   Adjusting imports...
   Done.
   Module missing, downloading it from https://github.com/dsc/bunch...
   >>> fit.__file__
   '/mnt/d/projects/FOCAL/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/fundus_image_toolbox/__init__.py'
   >>> 
   

   it works. I've also looked at .CondaPkg, at the file libmkl_gnu_thread.so.2 is there, so I'm not sure what the issue could be (.CondaPkg/.pixi/envs/default/lib/libmkl_intel_thread.so.2)