Summary of what happened:
Hi all,
I am using Tedana to process multiecho functional data on an LPC batch computing cluster that was recently upgraded from CentOS7 to RHEL9. Since this upgrade, Tedana has not been automatically exiting from the batch submit job at the end of the workflow. We also activate a Tedana conda environment within the submission, so I’m not totally sure where to look for the issue that is causing the job to hang or how to fix it without dismantling the conda environment.
The workflow has been consistently finishing successfully, so any errors or bugs that are causing the hangup are thankfully not causing the actual pipeline to fail, but something seems to be overriding the kill signal and holding onto a computing node for much longer than it needs to.
Any advice about how to solve this issue is welcome!
Command used (and if a helper script was used, a link to the helper script or the command generated):
tedana -d "$Subdir"/func/rest/"$DataDirs"/Rest_E*_acpc.nii.gz -e $(cat "$Subdir"/func/rest/"$DataDirs"/TE.txt) --out-dir "$Subdir"/func/rest/"$DataDirs"/Tedana/ \
--tedpca "$MEPCA" --fittype curvefit --mask "$Subdir"/func/rest/"$DataDirs"/brain_mask.nii.gz --maxit "$MaxIterations" --maxrestart "$MaxRestarts" --seed 42 --verbose
Version:
tedana v23.0.2
Environment (Docker, Singularity / Apptainer, custom installation):
Conda environment (miniconda/3-25) on RHEL9 batch computing cluster
Relevant log outputs (up to 20 lines):
INFO ica_reclassify:ica_reclassify_workflow:568 Workflow completed
cp: cannot stat '/project/oathes_analysis2/R61//J007/func/rest//session_1/run_1//Tedana+ManualComponentClassification/desc-optcom_bold.nii.gz': No such file or directory
/home/dickson4/.MathWorks/ServiceHost/-mw_shared_installs/v2025.2.2.1/mci/bin/glnxa64/InstallMathWorksServiceHost: error while loading shared libraries: libgtk-x11-2.0.so.0: cannot open shared object file: No such file or directory
/home/dickson4/.MathWorks/ServiceHost/-mw_shared_installs/v2025.2.2.1/mci/bin/glnxa64/InstallMathWorksServiceHost: error while loading shared libraries: libgtk-x11-2.0.so.0: cannot open shared object file: No such file or directory
/home/dickson4/.MathWorks/ServiceHost/-mw_shared_installs/v2025.2.2.1/mci/bin/glnxa64/InstallMathWorksServiceHost: error while loading shared libraries: libgtk-x11-2.0.so.0: cannot open shared object file: No such file or directory
[Repeats]