[gmx-users] problems with GROMACS 4.6.2

Szilárd Páll szilard.pall at cbr.su.se
Tue Jun 4 20:48:24 CEST 2013

Just a few minor details:

- You can set the affinities yourself through the job scheduler which
should give nearly identical results compared to the mdrun internal
affinity if you simply assign cores to mdrun threads in a sequential
order (or with an #physical cores stride if you want to use

- At low parallelization and without OpenMP (i.e. -ntomp 1) you may
not notice much regression even though threads won't be pinned.


On Tue, Jun 4, 2013 at 7:05 PM, Mark Abraham <mark.j.abraham at gmail.com> wrote:
> Hi GROMACS users,
> It's come to our attention that some changes we made in 4.6.2 to the way we
> detect low-level hardware attributes sometimes affects mdrun performance.
> Specifically:
> * using real MPI will likely lead to lower performance than 4.6.1, if
> GROMACS managing the setting of thread affinities would have been a good
> thing
> * on Mac OS, mdrun might hang completely
> If the simulation runs, then it's correct :-)
> We've identified fixes and will release 4.6.3 in the next few days. In the
> meantime, we suggest not bothering to install 4.6.2.
> Apologies,
> Mark
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