On Fri, Oct 18, 2019 at 4:36 PM <aesz...@gwdg.de> wrote: > On Thu, Oct 17, 2019 at 10:34:39AM +0000, Kutzner, Carsten wrote: > > > > is it intended that the thread-MPI version of mdrun 2018 does pin to its > core > > if started with -nt 1 -pin auto? >
No, I don't think that's intended. > > I think I have a (partial) idea about what's happening. > get_thread_affinity_layout() performs various checks to determin if > pinning is possible, and for -pin auto, it looks at the number of > mdrun threads vs hardware threads. However, the number of mdrun > threads ultimately comes from gmx_omp_nthreads_get(). > Of course, if OMP_NUM_THREADS is unset, OpenMP will default to the > whole machine, and the above check will always succeed. And sure > enough, setting OMP_NUM_THREADS to 1 will turn off pinning in our test > case. > The source of total number of hardware threads should not be OpenMP but a system call or hwloc -- which should (and was IIRC a while ago at least) checked agianst the gmx_omp_nthreads_get() value. If however the behavior you describe is actually reproducible, please do file a bug report. -- Szilárd > > A. > > -- > Ansgar Esztermann > Sysadmin Dep. Theoretical and Computational Biophysics > http://www.mpibpc.mpg.de/grubmueller/esztermann > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.