[gmx-developers] Gromacs 4.6 on an inhomogeneous cluster

Berk Hess hess at kth.se
Mon Oct 29 14:51:53 CET 2012


Compiling in GPU functionality has no effect on performance.
We have never timed the effect of compiling in MPI and OpenMP,
but I would expect it to be very small, probably less than 1%.
But it would be good to try that once on a small system.
Note that pure OpenMP can be much faster than MPI.

The difference in performance between SSE2 and SSE4.1 is minor,
less than 5% (AVX is a lot faster though).
So I think you can use a single installation.



On 10/29/12 14:47 , Carsten Kutzner wrote:
> Dear developers,
> we run Gromacs on an inhomogeneous cluster with different node groups -
> old and new ones, where each group requires an individual acceleration
> setting, e.g. SSE2 vs. SSE4.1. If I set GMX_ACCELERATION to SSE2 then I
> won't get the optimal performance on some of the nodes, whereas with SSE4.1
> the code won't run on all nodes. One way around seems to build different
> mdruns, and to select the optimal one after the node has been assigned by the
> queue. Is there a more elegant way like including alternate code paths,
> where the optimal path is selected at run time?
> 2nd question: From a performance point of view, does it hurt to have support
> for GPU, MPI, and threads compiled in - even if it is not used in many cases?
> Or would it be better to have also separate executables for that?
> Thanks for your thoughts,
>    Carsten
> --
> Dr. Carsten Kutzner
> Max Planck Institute for Biophysical Chemistry
> Theoretical and Computational Biophysics
> Am Fassberg 11, 37077 Goettingen, Germany
> Tel. +49-551-2012313, Fax: +49-551-2012302
> http://www.mpibpc.mpg.de/grubmueller/kutzner

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