btw, it will almost certainly be more efficient to run each subject with
1 thread and run them all at the same time rather than running a few of
them with 4 or 8. If you can run them all with multiple threads, then
that might be more efficient (depends on your scheduler, for slurm it
would be).
On 5/3/2022 3:57 PM, Wighton, Paul wrote:
There's a small percentage of subjects that need more than the 8Gb of
memory (for mris_fix_topology if my memory is correct).
You could increase the memory allocation for all subjects, or you
could run your entire dataset with 8Gb per subject, then re-run the
ones that failed with increased memory.
-Paul
------------------------------------------------------------------------
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Horn, Mitchell
Jacob <mjh...@mgh.harvard.edu>
*Sent:* Tuesday, May 3, 2022 2:26 PM
*To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [Freesurfer] Scalable recon workflow
Hi Paul,
Thanks for your speedy response! In that case, I assume 1GB/core is
the memory allocation? Is it helpful to increase that?
Best,
Mitch
------------------------------------------------------------------------
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Paul Wighton
<p...@corticometrics.com>
*Sent:* Tuesday, May 3, 2022 1:34 PM
*To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [Freesurfer] Scalable recon workflow
External Email - Use Caution
Hi Mitch,
In our experience, -openmp 8 gives faster recons than -openmp 4, but
the gains after -openmp 8 diminish quickly and aren't worth it.
-Paul
On Tue, May 3, 2022 at 12:51 PM Horn, Mitchell Jacob
<mjh...@mgh.harvard.edu> wrote:
Hi Experts,
If I have 100s of subjects to recon and have access to an HPC with
both GPU and CPU options what is the recommended flags to maximize
speed performance? Is … -parallel -openmp 4 … still the best
approach? And if so, is 2GB memory/core best (keeping it 8GB
memory/subject) or is there some better arrangement?
Best,
Mitch
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