Trouble with preprocess

[dianawallin]

I have installed WSL2 on a PC Running Windows 10 Pro. I installed Singularity version 3.8.7. However when I run the preprocessing script I am getting the error:

OMP: Error #179: Function Can't open SHM2 failed:
OMP: System error #20: Not a directory
Fatal Python error: Aborted

Current thread 0x00007eff102d0740 (most recent call first):
File "/home/rabies/miniforge/lib/python3.9/site-packages/numpy/linalg/linalg.py", line 1660 in svd
File "<array_function internals>", line 5 in svd
File "/home/rabies/miniforge/lib/python3.9/site-packages/nibabel/orientations.py", line 65 in io_orientation
File "/home/rabies/miniforge/lib/python3.9/site-packages/nibabel/orientations.py", line 381 in aff2axcodes
File "/home/rabies/RABIES/rabies/preprocess_pkg/utils.py", line 167 in convert_to_RAS
File "/home/rabies/RABIES/rabies/run_main.py", line 179 in preprocess
File "/home/rabies/RABIES/rabies/run_main.py", line 44 in execute_workflow
File "/home/rabies/RABIES/scripts/rabies", line 3 in
File "/home/rabies/miniforge/bin/rabies", line 7 in
Aborted

Any ideas on how to solve this? Thanks so much.

[gdevenyi]

This is not a rabies issue, but rather a WSL/Conda/Scipy issue
microsoft/WSL#785

[Gab-D-G]

Hi, I have encountered this same error recently with an old version of singularity, so the singularity version could also have to do with the problem. I got this error when trying to run with singularity version 2.6.1-master.b44d76c, but it worked well for me using versions 3.10.0-jammy and 3.8.7-1.el7. You seem however to be using version 3.8.7, which is likely similar to what I have.