[gmx-developers] Gromacs 4.6 on an inhomogeneous cluster

Szilárd Páll szilard.pall at cbr.su.se
Mon Oct 29 14:54:23 CET 2012

On Mon, Oct 29, 2012 at 2:47 PM, Carsten Kutzner <ckutzne at gwdg.de> 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?

I don't think there is any other way. You should check the difference
between SSE2 and SSE4.1, but at least with the current code (only
Verlet scheme accelerated + plain C Group), SSE4.1 is not that much faster.

> 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?

No, there should not be. if there is one, please file a bug report.


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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