Hi, The -pin is used to prevent the OS switching threads across physical cores, which may result in performance loss. If you want to pin your threads to cores, use -pin on. -pinoffset can help you set to which cores your threads are pinned, which is stated in mdrun -h.
Regards Terry > On 24 Jul 2015, at 11:53 am, Zhenyu Meng <fdmm1...@gmail.com> wrote: > > Dear all, > When I'm running gromacs with mdrun, I always receive such message: > > 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). > > The server I use has 128 cores, and usually I use mdrun with flag -nt 32 or > -nt 64 to specify the threads, I also notice there's large performance lost > in each run. > I wonder what's the difference between '-pin on' and '-pinoffset'. I > usually run multi jobs on the server so will '-pin on' or '-pinoffset' > affect the other jobs? If I use '-pinoffset' what value I should > set(suppose I have already use 32 cores for other jobs)? > > -- > Sincerely, > Mr. Meng Zhenyu > Division of Chemistry and Biological Chemistry > School of Physical and Mathematical Sciences > Nanyang Technological University > -- > 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.