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Thank you for your reply!
Best regards, Peter
On Wed, Nov 8, 2023 at 2:41 PM Huang, Yujing YHUANG43@mgh.harvard.edu wrote:
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-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@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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