[gmx-developers] Gromacs 4.6 on an inhomogeneous cluster

Carsten Kutzner ckutzne at gwdg.de
Mon Oct 29 14:47:38 CET 2012

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,

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

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