[gmx-users] Gromacs 4.5.1 on 48 core magny-cours AMDs

Esztermann, Ansgar Ansgar.Esztermann at mpi-bpc.mpg.de
Thu Oct 21 17:28:33 CEST 2010

>>> Thanks for the information; the OpenMPI recommendation is probably because OpenMPI goes to great lengths trying to avoid process migration. The numactl doesn't prevent migration as far as I can tell: it controls where memory gets allocated if it's NUMA. 
>> My understanding is that processes get pinned to cores with the help of 
>> the --physcpubind switch to numactl, but please correct me if I am wrong.
> The documentation isn't clear on that: you bind a process to a set of cores, but that wouldn't necessarily mean that threads that belong to that process are bound to a specific core. They might be allowed to migrate within the set that you give the process.

I've just checked a short (a few seconds) benchmark run -- I didn't observe any migrations with or without numactl.


Ansgar Esztermann
Max-Planck-Institut für biophysikalische Chemie, Abteilung 105

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