[gmx-users] multi threads pinning problem

[Mark Abraham]

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 <terrencesun at 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 <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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