Summary of what happened:
I am running fmriprep v24.1.1 to process some BOLD fMRI data on hpc and after some processing steps, it seems to get stuck. I don’t see any particular error so am unsure how to go about this. I am specifying --ntasks=1 --cpus-per-task=8 in my slurm file. I’ve specified --mem 64G and 128G but encounter the same problem in both cases.
Version:
24.1.1
Command Used
PASTE CODE HERE
Environment (Docker, Singularity / Apptainer, custom installation):
Singularity
Relevant log outputs (up to 20 lines):
The last 5 lines of the code are:2025-05-05 10:03:13,871 [ INFO] [Node] Outdated cache found for "fmriprep_24_1_wf.sub_003_wf.bold_ses_1_task_LOCALISER5_wf.bold_confounds_wf.tcc_metadata_fmt".
2025-05-05 10:03:13,885 [ INFO] [Node] Executing "tcc_metadata_fmt" <niworkflows.interfaces.utility.TSV2JSON>
2025-05-05 10:03:14,167 [ INFO] [Node] Finished "tcc_metadata_fmt", elapsed time 0.282167s.
2025-05-05 10:03:14,932 [ INFO] [Node] Finished "dvars", elapsed time 37.012805s.
2025-05-05 10:03:16,825 [ INFO] [Node] Finished "dvars", elapsed time 36.881818s.
2025-05-05 10:03:37,825 [ INFO] [Node] Finished "dvars", elapsed time 45.900756s.
I also tried running it with more verbosity and the log shows:
2025-05-07 14:23:21,017 [ DEBUG] Cannot allocate job 1812 (0.20GB, 1 threads).
2025-05-07 14:23:21,017 [ DEBUG] Cannot allocate job 1813 (0.20GB, 1 threads).
2025-05-07 14:23:21,028 [ INFO] [Node] Executing "_autorecon_surfs0" <smriprep.interfaces.freesurfer.ReconAll>
2025-05-07 14:23:21,059 [ INFO] resume recon-all : recon-all -autorecon-hemi lh -noparcstats -noparcstats2 -noparcstats3 -nohyporelabel -nobalabels -lh-only -openmp 8 -subjid sub-003 -sd /scratch/users/gajawell/fmriprep/sourcedata/freesurfer -notessellate -nosmooth1 -noinflate1 -noqsphere
2025-05-07 14:23:21,060 [ INFO] resume recon-all : recon-all -autorecon-hemi lh -noparcstats -noparcstats2 -noparcstats3 -nohyporelabel -nobalabels -lh-only -openmp 8 -subjid sub-003 -sd /scratch/users/gajawell/fmriprep/sourcedata/freesurfer -notessellate -nosmooth1 -noinflate1 -noqsphere
2025-05-07 14:23:22,857 [ DEBUG] Progress: 1816 jobs, 430/1/15 (done/running/ready), 1/1385 (pending_tasks/waiting).
2025-05-07 14:23:22,858 [ DEBUG] Tasks currently running: 1. Pending: 1.
2025-05-07 14:23:22,860 [ INFO] [MultiProc] Running 1 tasks, and 15 jobs ready. Free memory (GB): 221.14/226.14, Free processors: 0/1.
Currently running:
* _autorecon_surfs0
2025-05-07 14:23:22,860 [ DEBUG] No resources available
2025-05-07 14:23:24,859 [ DEBUG] No resources available
The last 2 lines continue until the time limit is reached.
Thank you!