search

MICA-MNI / micapipe

micapipe from the Multimodal imaging and connectome analysis lab (http://mica-mni.github.io) at the Montreal Neurological Institute. Read The Docs documentation below
http://micapipe.readthedocs.io
GNU General Public License v3.0
80 stars 27 forks source link

Error Encountered During dwifslpreproc Execution #115

Open swwalsh opened 3 months ago

swwalsh commented 3 months ago

Description: I encountered an error while running dwifslpreproc in the micapipe processing pipeline. Here's a detailed description of the issue along with my troubleshooting steps.

Error Message: Upon executing the command:

dwifslpreproc /tmp/29559_micapipe_proc-dwi_<SUBJ_ID>/dwi_dns_even.mif /...<redacted>.../sub-<SUBJ_ID>/ses-<SES>/dwi/sub-<SUBJ_ID>_ses-<SES_ID>_space-dwi_desc-preproc_dwi.mif -rpe_none -pe_dir j- -readout_time 0.0959 -eddy_options " --data_is_shelled --slm=linear --repol" -nthreads 6 -nocleanup -scratch /tmp/29559_micapipe_proc-dwi_<SUBJ_ID> -force

The error message was:

dwifslpreproc: [ERROR] eddy* --imain=eddy_in.nii --mask=eddy_mask.nii --acqp=eddy_config.txt --index=eddy_indices.txt --bvecs=bvecs --bvals=bvals --data_is_shelled --slm=linear --repol --out=dwi_post_eddy --verbose (app.py:197)
dwifslpreproc: [ERROR] Information from failed command:
dwifslpreproc:
               ============
               eddy_cuda9.1
               ============

               ===========
               eddy_openmp
               ===========
               Reading images
               Performing volume-to-volume registration
               ...
               eddy_cuda9.1: error while loading shared libraries: libcudart.so.9.1: cannot open shared object file: No such file or directory

Troubleshooting Steps:

  1. Investigating Log Output:

    • The log indicated an issue with loading libcudart.so.9.1 shared library.

  2. Examining Container Contents:

    • I explored the container using Singularity: 
      singularity shell micapipe.sif
cd /opt/
find . | grep libcudart # No libcudart.so.9.1 found

Environment Details:

Conclusion: It appears that the required libcudart.so.9.1 shared library is missing in the container environment. This absence leads to the failure of the eddy_cuda9.1 command within dwifslpreproc. I'm looking for guidance on how to resolve this issue or obtain the necessary library to ensure successful execution of the pipeline.