"-nt" is mostly a backward compatibility option and sets the total number of threads (per rank). Instead, you should set both "-ntmpi" (or -np with MPI) and "-ntomp". However, note that unless a single mdrun uses *all* cores/hardware threads on a node, it won't pin the threads to cores. Failing to pin threads will lead to considerable performance degradation; just tried and depending on how (un)lucky the thread placement and migration is, I get 1.5-2x performance degradation with running two mdrun-s on a single dual-socket node without pining threads.
My advise is (yet again) that you should check the http://www.gromacs.org/Documentation/Acceleration_and_parallelization wiki page, in particular the section on how to run simulations. If things are not, clear please ask for clarification - input and constructive criticism should help us improve the wiki. We have been patiently pointing everyone to the wiki, so asking without reading up first is neither productive nor really fair. Cheers, -- Szilárd On Tue, Jun 4, 2013 at 11:22 AM, Chandan Choudhury <iitd...@gmail.com> wrote: > Hi Albert, > > I think using -nt flag (-nt=16) with mdrun would solve your problem. > > Chandan > > > -- > Chandan kumar Choudhury > NCL, Pune > INDIA > > > On Tue, Jun 4, 2013 at 12:56 PM, Albert <mailmd2...@gmail.com> wrote: > >> Dear: >> >> I've got four GPU in one workstation. I am trying to run two GPU job with >> command: >> >> mdrun -s md.tpr -gpu_id 01 >> mdrun -s md.tpr -gpu_id 23 >> >> there are 32 CPU in this workstation. I found that each job trying to use >> the whole CPU, and there are 64 sub job when these two GPU mdrun submitted. >> Moreover, one of the job stopped after short of running, probably because >> of the CPU issue. >> >> I am just wondering, how can we distribute CPU when we run two GPU job in >> a single workstation? >> >> thank you very much >> >> best >> Albert >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >> * Please search the archive at http://www.gromacs.org/** >> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before >> posting! >> * Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to gmx-users-requ...@gromacs.org. >> * Can't post? Read >> http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >> > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
