You should also know that the memory management during openmp mri_em_register execution is not optimal (as found by the HCP group. If you are oversubscribing your processors (ie, have 20 cpus, but run 3 jobs each with 8 cpus), then mri_em_register will slow way down. This appears to be due to some caching issues. I'll change recon-all to allow open mp to be disabled during during mri_em_register, but you should be aware of the problem.

On 5/2/17 3:53 PM, Chris Gorgolewski wrote:

Thank you - this is very useful!

On Tue, May 2, 2017 at 12:05 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote:

Hi Chris

we have found an almost linear speed improvement up to 4, then it
starts to fall off, with not much at all after 8.

cheers
Bruce

On Tue, 2 May 2017, Chris Gorgolewski wrote:

    Hi,
    We are running freesurfer as part of a bigger pipelines with
    other steps
    that can be performed in parallel
    to freesurfer reconstruction. So far we
    have set the openmp flag to the number of all available cores.
    However, our
    experience with ANTs and AFNI which also capitalize on the OpenMP
    parallelization is that there is little benefit of using more
    than 8-10
    cores (even if more are available). Does this also apply
    to FreeSurfer? Does
    anyone have done some benchmarking of this?

    Thanks in advance for your help.

    Best,
    Chris


_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>


The information in this e-mail is intended only for the person to
whom it is
addressed. If you believe this e-mail was sent to you in error and
the e-mail
contains patient information, please contact the Partners
Compliance HelpLine at
http://www.partners.org/complianceline
<http://www.partners.org/complianceline> . If the e-mail was sent
to you in error
but does not contain patient information, please contact the
sender and properly
dispose of the e-mail.

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer