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
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