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

Sander Pronk pronk at cbr.su.se
Thu Oct 21 17:07:28 CEST 2010

On 21 Oct 2010, at 16:50 , Carsten Kutzner wrote:

> On Oct 21, 2010, at 4:44 PM, Sander Pronk wrote:
>> 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.

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