hi andrew, i haven't done many systematic comparisons but there are a few practical considerations to take into account. in recon-all, i believe a few steps are affected by the openmp option and that creates resource underutilization. processors run idle when those steps are not being run.
in my ad hoc analysis i have found i can process a single subject in about 5 hours using openmp 8, but that holds up 8 processors for that subject. the same subject can be processed in about 12 hours one 1 processor. say i have 16 processors, i can process 16 subjects in say 12 hours using 1 processor per recon. however, using 8 per recon would take about 40 hours, 2 subjects every 5 hours. so on our cluster, we tend to process with openmp 1 or 2 depending on the average load on the cluster. this is also dependent on your hardware, amount of memory, cluster scheduler, etc.,. if i really need speed on an individual case i go with -openmp 8. cheers, satra On Wed, Aug 20, 2014 at 11:04 AM, O'Shea,Andrew <aos...@ufl.edu> wrote: > Hello all, > Traditionally I have only processed FS data using a single core per > person, but processing many people at once. Now we have caught up with the > backlog of scans, we have a continuos trickle of scans coming in 1 by 1. I > was wondering if anyone has tested how the speed-up of open-mp varies with > number of cores used simultaneously. For example how much faster is using > 100 cores versus 10? I am trying to find a sweet spot of resource usage and > speed. Thanks! > -Andrew > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > 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 . 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. > >
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