Thanks for your quick answer! Just to make sure: it means I shouldn't specify -openmp 5 in the recon-all line and that the multi-threading happens automatically? So given that I have around 50 subjects who I need to run this on, would the best way to accelerate the performance be to just open several terminal windows (e.g. 5) and run ten subjects in each? Or would it make no difference from running all 50 in one window? I considered looking into GNU parallel, but not sure it would make sense. What would your advice for such a number of subjects be?
Thanks so much for your help. V 2017-04-25 16:55 GMT+02:00 Glasser, Matthew <[email protected]>: > PreFreeSurfer uses mostly single threaded tools. Some of FreeSurfer is > multi-threaded (and importantly one binary has some issues with > oversubscribed cores leading to much longer execution times). > PostFreeSurfer is largely multi-threaded. In all cases, the pipelines use > multiple threads by default if they can. > > Peace, > > Matt. > > From: <[email protected]> on behalf of Vanessa K < > [email protected]> > Date: Tuesday, April 25, 2017 at 7:36 AM > To: "[email protected]" <[email protected]> > Subject: [HCP-Users] Using multiple cores while running Structural > Pipelines > > Dear users, > > it might be a silly question but I hope you can help. I have a computer > with 8 cores and I would like to use 7 of them while running pipelines that > take a lot of time (such as FreeSurfer). Is there any way to specify the > core number when running the script? Or are there any tricks to speed up > the processing time? > > Thanks a lot! > > V > > _______________________________________________ > HCP-Users mailing list > [email protected] > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > ------------------------------ > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If you > are not the intended recipient, be advised that any unauthorized use, > disclosure, copying or the taking of any action in reliance on the contents > of this information is strictly prohibited. If you have received this email > in error, please immediately notify the sender via telephone or return mail. > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
