Hi Peter,
I would suggest not to use ‘-parallel’. It is handled by recon-all to run
multiple commands in parallel. It can run into collisions if they are not
synchronized.
These recon-all options ‘-threads <>’, ‘-openmp <>’, ‘-nthreads <>’ tell
individual program to split the tasks and run them in parallel. They are the
same flags.
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of P Pieperhoff
Sent: Wednesday, November 8, 2023 5:28 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] parallel processing of long-run fails
External Email - Use Caution
Dear FreeSurfer developers,
when I execute a long-run with parallel processing by calling
recon-all -sd <directory> -threads 64 -openmp 64 -parallel -long <imageid>
<template_id> -all
it fails in step "autorecon3" at the surface registration.
But when I start it again without the option "-parallel", it finishs without
errors.
I'm using FreeSurfer version 7.4.1 with Linux CentOS.
I have attached the log file to this mail.
Best regards,
Peter
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