[gmx-users] Running GROMACS on mini GPU cluster

Szilárd Páll szilard.pall at cbr.su.se
Mon Jul 29 20:20:43 CEST 2013

The message is perfectly normal. When you do not use all available
cores/hardware threads (seen as "CPUs" by the OS), to avoid potential
clashes, mdrun does not pin threads (i.e. it lets the OS migrate
threads). On NUMA systems (most multi-CPU machines), this will cause
performance degradation as without pinning the OS can move tightly
coupled threads belonging to the same process/MPI rank to different
NUMA regions (e.g. cores on different CPU sockets).

With four physical cores the machines in question are most probably
single-processor and for these pinning will not improve performance by
much (if at all).


On Fri, Jul 26, 2013 at 12:09 AM, Tim Moore <tcmoore3 at gmail.com> wrote:
> I am running GROMACS 4.6.2 on a GPU cluster in our reasearch group. I am trying to bench mark some systems, and I am getting this message:
> NOTE: The number of threads is not equal to the number of (logical) cores
>       and the -pin option is set to auto: will not pin thread to cores.
>       This can lead to significant performance degradation.
>       Consider using -pin on (and -pinoffset in case you run multiple jobs).
> Each node has 2 GTX 580s and 4 physical cores. So when I submit a job I set -nt 2. But since we have a queuing system, there is no way to know which cores will be available to set -pinoffset. Does anyone have a solution, or should I even be worrying about that at all?
> Thanks,
> Tim--
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