The number of windows you use to launch the processing is irrelevant. But if you only have 8 cores on your machine, and only want to use 7 of them, you can’t run 50 subjects at once.
In this case, where you have a bunch of subjects to process, I would run 7 subjects at a time, while limiting each to just 1 core, by setting whatever variable in the pipeline that is used to limit/control the number of threads used for multi-thread capable binaries. cheers, -MH -- Michael Harms, Ph.D. ----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Vanessa K <vanessakr1...@gmail.com<mailto:vanessakr1...@gmail.com>> Date: Thursday, April 27, 2017 at 4:30 AM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: [HCP-Users] Fwd: Using multiple cores while running Structural Pipelines Alright, thanks! And just for clarification for dummies: if not installing something like grid_engine, will running all 50 subjects in one Terminal window or 10 subjects in each of five different windows be more efficient? Or doesn't it make any difference? And I estimate around 20 days for 50 subjects (for the structural pipelines), is it a normal processing time? Thanks again! 2017-04-26 16:20 GMT+02:00 Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>>: 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 <vanessakr1...@gmail.com<mailto:vanessakr1...@gmail.com>> Date: Wednesday, April 26, 2017 at 4:39 AM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>> Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> 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 <glass...@wustl.edu<mailto:glass...@wustl.edu>>: 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: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Vanessa K <vanessakr1...@gmail.com<mailto:vanessakr1...@gmail.com>> Date: Tuesday, April 25, 2017 at 7:36 AM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> 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 HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> 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. 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