I find it helps to install something like gridengine which interfaces with fsl_sub. You can then queue up the jobs and they will all run automatically. You can choose how many to run at a time. I believe you don’t need to specify an openmp flag unless you want fewer than all of the cores.
Peace, Matt. From: Vanessa K <[email protected]<mailto:[email protected]>> Date: Wednesday, April 26, 2017 at 4:39 AM To: Matt Glasser <[email protected]<mailto:[email protected]>> Cc: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] Using multiple cores while running Structural Pipelines 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]<mailto:[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]<mailto:[email protected]>> on behalf of Vanessa K <[email protected]<mailto:[email protected]>> Date: Tuesday, April 25, 2017 at 7:36 AM To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[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]<mailto:[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. ________________________________ 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
