[gmx-users] multi threads pinning problem

terrencesun at gmail.com terrencesun at gmail.com
Fri Jul 24 12:17:56 CEST 2015


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.


> On 24 Jul 2015, at 11:53 am, Zhenyu Meng <fdmm1989 at 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
> -- 
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