Hi, Thanks for your help. The tutorial is very helpful for me. 2015-07-24 19:22 GMT+08:00 Mark Abraham <mark.j.abra...@gmail.com>:
> Hi, > > Check out > > http://manual.gromacs.org/documentation/5.1-rc1/user-guide/mdrun-performance.html > and > > http://manual.gromacs.org/documentation/5.1-rc1/user-guide/mdrun-features.html#running-multi-simulations > . > It's hard to be definitive about the correct thing to do, since it depends > very much on all of your infrastructure. You should observe the performance > when using all the cores (pinned by default) and when using a single > (pinned) core and expect performance to be reasonable consistent as you > change the number of cores. > > Mark > > On Fri, Jul 24, 2015 at 12:18 PM <terrence...@gmail.com> wrote: > > > 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. > > > -- > 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. > -- 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.