[gmx-developers] Gromacs 4.6 on an inhomogeneous cluster

[Carsten Kutzner]

Great, thanks!

Carsten


On Oct 29, 2012, at 2:54 PM, Szilárd Páll <szilard.pall at cbr.su.se> wrote:

> 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.
>  
> Cheers,
> --
> Szilárd
> 
> 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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--
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