[gmx-users] Output pinning for mdrun

Mark Abraham mark.j.abraham at gmail.com
Thu Oct 24 16:25:20 CEST 2013


No. mdrun reports the stride with which it moves over the logical cores
reported by the OS, setting the affinity of GROMACS threads to logical
cores, and warnings are written for various wrong-looking cases, but we
haven't taken the time to write a sane report of how GROMACS logical
threads and ranks are actually mapped to CPU cores. Where supported by the
processor, the CPUID information is available and used in
gmx_thread_affinity.c. It's just not much fun to try to report that in a
way that will make sense on all possible hardware that supports CPUID - and
then people will ask why it doesn't map to what their mpirun reports, get
confused by hyper-threading, etc.

What question were you seeking to answer?


On Thu, Oct 24, 2013 at 11:44 AM, Carsten Kutzner <ckutzne at gwdg.de> wrote:

> Hi,
> can one output how mdrun threads are pinned to CPU cores?
> Thanks,
>   Carsten
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