Linden, Its my understanding that that with hyperthreading enabled, you can run a subject for each processor the computer "thinks" it has. For instance, on CentOS (Im not sure the equivalent command on Ubuntu) if I 'cat /proc/cpuinfo' I see 4 processors listed. In this case I would be able to process 4 subjects using the --openmp 4 flag. Though it is sometimes recommended to process n-1 subjects in order to keep one processor available to the user.
Something to keep in mind is the available RAM. We recommend 4gigs of RAM per subject so in the case of 4 subjects, the machine should have 16gig of RAM available. And if you are going to process 8 subjects than you would want 32gigs. -Zeke On 06/17/2014 06:50 AM, Linden Parkes wrote: > Hi FSers, > > I have an Ubuntu machine (14.04 LTS) with a quad-core i7 4770k/32gb RAM > and recon-all is taking me approximately 6 hours per subject without > using openmp (haven't tried this yet). According to the terminal, it > finishes without errors. > I've read (e.g., > https://surfer.nmr.mgh.harvard.edu/fswiki/FsQuizAnswers) and heard that > recon-all should take 20-24 hours per participant to complete. So, > should I be celebrating my 6 hour run time or should I be very > suspicious of it? > > Also, how does freesurfer go with hyper threaded CPUs? (as is the case > with the 4770k; 4 cores, 8 threads). I've read that you should restrict > parallel processing to one subject per core. Can I take advantage of the > hyper threading and run 8 subjects simultaneously or should I be more > conservative and only run 4? > > Cheers, > Linden > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > _______________________________________________ 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.
