[gmx-users] Question about default auto setting of mdrun -pin

[Szilárd Páll]

On Fri, Oct 18, 2019 at 4:36 PM <aeszter at gwdg.de> wrote:

> On Thu, Oct 17, 2019 at 10:34:39AM +0000, Kutzner, Carsten wrote:
> >
> > is it intended that the thread-MPI version of mdrun 2018 does pin to its
> core
> > if started with -nt 1 -pin auto?
>

No, I don't think that's intended.


>
> I think I have a (partial) idea about what's happening.
> get_thread_affinity_layout() performs various checks to determin if
> pinning is possible, and for -pin auto, it looks at the number of
> mdrun threads vs hardware threads. However, the number of mdrun
> threads ultimately comes from gmx_omp_nthreads_get().
> Of course, if OMP_NUM_THREADS is unset, OpenMP will default to the
> whole machine, and the above check will always succeed. And sure
> enough, setting OMP_NUM_THREADS to 1 will turn off pinning in our test
> case.
>

The source of total number of hardware threads should not be OpenMP but a
system call or hwloc -- which should (and was IIRC a while ago at least)
checked agianst the  gmx_omp_nthreads_get() value.

If however the behavior you describe is actually reproducible, please do
file a bug report.

--
Szilárd


>
> A.
>
> --
> Ansgar Esztermann
> Sysadmin Dep. Theoretical and Computational Biophysics
> http://www.mpibpc.mpg.de/grubmueller/esztermann
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