The message is perfectly normal. When you do not use all available cores/hardware threads (seen as "CPUs" by the OS), to avoid potential clashes, mdrun does not pin threads (i.e. it lets the OS migrate threads). On NUMA systems (most multi-CPU machines), this will cause performance degradation as without pinning the OS can move tightly coupled threads belonging to the same process/MPI rank to different NUMA regions (e.g. cores on different CPU sockets).
With four physical cores the machines in question are most probably single-processor and for these pinning will not improve performance by much (if at all). Cheers, -- Szilárd On Fri, Jul 26, 2013 at 12:09 AM, Tim Moore <tcmoo...@gmail.com> wrote: > I am running GROMACS 4.6.2 on a GPU cluster in our reasearch group. I am > trying to bench mark some systems, and I am getting this message: > > NOTE: The number of threads is not equal to the number of (logical) cores > and the -pin option is set to auto: will not pin thread to cores. > This can lead to significant performance degradation. > Consider using -pin on (and -pinoffset in case you run multiple jobs). > > Each node has 2 GTX 580s and 4 physical cores. So when I submit a job I set > -nt 2. But since we have a queuing system, there is no way to know which > cores will be available to set -pinoffset. Does anyone have a solution, or > should I even be worrying about that at all? > > Thanks, > Tim-- > 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
