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

[Esztermann, Ansgar]

>>> 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.


A.

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