Linden, The fastest runtime that I have seen is just under 3.5 hours using a new and very fast system such as yours, using the -openmp 8 flag.
Processing four participants in separate tcsh sessions is the recommended way of 'parallel' processing. There are flags in recon-all to allow splitting the pipeline into two when the hemisphere processing starts, but thats more hassle than its worth, given that people usually have multiple subjects, so 'spending' a cpu on each subject is better than speeding-up any one subject. I'd recommend staggering the start times of your subjects a bit, by say 20 minutes. Nick On Wed, 2014-06-18 at 09:55 +1000, Linden Parkes wrote: > Hi Peter, Bruce, and Zeke, > > Thank you all for the various input. > > According to the tutorial Peter posted, the handful of subjects I've > done look good. > I ran another subject with -openmp 4 flag and it shaved the processing > down to <4 hours, so that is a very nice saving! > > The System Monitor app in Ubuntu indeed lists 8 CPUs so the hyper > threading makes Ubuntu "think" it has 8 cores. Given the 32gb of ram I > have, I'll try -openmp 8 flag and see how it goes. > > > Does anyone have some tips on how to setup parallel processing? Is it > better to set up, say, 4 participants all with the -openmp 2 flag in 4 > separate tcsh sessions in order to saturate the 8 cores and 32gb ram? > Or is there a more sophisticated way of doing it that I should > consider? > > > Cheers, > Linden > > > > On 18 June 2014 07:27, Z K <zkauf...@nmr.mgh.harvard.edu> wrote: > 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. > > > > _______________________________________________ > 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
