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

[aeszter at gwdg.de]

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?

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.

A.

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