CREST fmriprep: FITK subjects take 5+ days to run #10
Description
Script/Job File
#!/bin/bash
#$ -pe smp 16
#$ -q UI
#$ -m bea
#$ -M [email protected]
#$ -o /Shared/vosslabhpc/Projects/CREST/code/fmriprep/out/
#$ -e /Shared/vosslabhpc/Projects/CREST/code/fmriprep/err/
OMP_NUM_THREADS=10
singularity run -H ${HOME}/singularity_home -B /Shared/vosslabhpc:/mnt \
/Shared/vosslabhpc/UniversalSoftware/SingularityContainers/fmriprep-1.2.1.simg \
/mnt/Projects/CREST/ /mnt/Projects/CREST/derivatives \
participant --participant_label FITK314 \
-w /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep \
--write-graph --mem_mb 35000 --omp-nthreads 10 --nthreads 16 --use-aroma \
--output-space template \
--template MNI152NLin2009cAsym \
--fs-license-file /mnt/UniversalSoftware/freesurfer_license.txt
Email Message
Job 5768491 (sub-FITK314.job) Complete
User = ariveradompenciel
Queue = [email protected]
Host = argon-lc-g11-15.hpc
**Start Time = 03/16/2020 14:31:41
End Time = 03/21/2020 05:45:32**
User Time = 08:06:37
System Time = 00:01:50
Wallclock Time = 111:13:51
CPU = 194:13:52
Max vmem = 20.288G
Exit Status = 0
Output File
The following is an excerpt from output indicating how long it took to run this sub (this example shows it took a day to complete the left hemisphere alone):
200317-07:49:44,322 nipype.interface INFO:
resume recon-all : recon-all -autorecon-hemi lh -noparcstats -nocortparc2 -noparcstats2 -nocortparc3 -noparcstats3 -nopctsurfcon -nohyporelabel -noaparc2aseg -noapas2aseg -nosegstats -nowmparc -nobalabels -openmp 10 -subjid sub-FITK314 -sd /mnt/Projects/CREST/derivatives/freesurfer
200318-09:14:32,797 nipype.workflow INFO:
[Node] Finished "_autorecon_surfs0".
Error (stderr file)
N/A
Potential Solution
Increase ram, memory and/or threads assigned to job.