Hi Diana,
Can you send the recon-all.cmd file? Have you tried running without parallel
processing enabled?
Best,
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of DIANA ORTEGA CRUZ
<100315...@alumnos.uc3m.es>
Date: Friday, May 21, 2021 at 11:00 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Recon-all running on a loop
External Email - Use Caution
Dear FreeSurfer team,
My name is Diana Ortega, I am a Neuroscience PhD student at Universidad
Politécnica of Madrid. I run a job to compute recon-all in parallel for 30
subjects remotely on a supercomputer at my research institution. This job
finished due to timeout, and all subjects but one finished without errors.
However, one of the subjects was not finished and it appears as if it was stuck
on a loop. Its recon-all.log is constantly adding new lines (the file is 20GB
in size), and from recon-all-status.log it appears to be stuck in the "Fix
Topology" step. Have you ever encountered a similar situation? Would you know
why this could have occurred?
Here are the details:
FreeSurfer version: 7.1.1-centos8_x86_64
Operative System: CentOS8
Hardware: Supercomputer - 68 nodes of Lenovo ThinkSystem
SD530<https://secure-web.cisco.com/1Bch1AH1AvTKzQqcdunZ0FIqTIHtdhvL6XMYZuyZxpRjtV9TB6kEZn1nh48ZtbJGIw41ngjalVrelQDieE52ynIv7RkZ7f4BZtvzTIxvrOmGmA3JirLjPRIeUkGZzhBEi_NAarb-drp-U-IpLwb1OwHc9qiofX0w5uSIqj3r6yvgPVMj00Wrwio5IAMXe7yXue7tddIlb73tamNyfvbBKIuqQ_TSHGyNsCNyd4NSVZUxvMlbsarqYSxR1oVHqb0XP2bkT1mGLxlsjaijzsxSTjw/https%3A%2F%2Fwww.lenovo.com%2Fes%2Fes%2Fdata-center%2Fservers%2Fhigh-density%2FThinkSystem-SD530%2Fp%2F77XX7DSSD53>
Line run for that subject:
recon-all -subjid NoUMA0233 -i filepath.nii -all -qcache -parallel -openmp 16
When opening recon-all.log, it keeps adding the following lines:
Remesher::removeTria( 240873 )
Remesher::removeTria( 240876 )
NEXTIDX : 88755
Remesher::removeCollapsedTrias( 88755 , 120326 )
v_to_t[vidx] :
Trias are identical : ... removing ...
When opening the error.log of the complete job, there are several lines of this
error:
rm: No match.
Any advice will be of great help! Thanks a big lot!
Best,
Diana Ortega Cruz.
PhD Student
Laboratory for Clinical Neuroscience
Centro de Tecnología Biomédica - Universidad Politécnica de Madrid
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