[gmx-users] No scale up beyond 4 processors for 240000 atom system

Christian Burisch burisch at bph.rub.de
Tue Oct 9 14:59:33 CEST 2007

Berk Hess schrieb:

Hi all,

> So this is 4 cores sharing one ethernet connection?

perhaps the two Gigabit NICs were bundled somehow. But I guess this 
doesn't work out-of-the-box&plug'n'play. And latency and not bandwidth 
may be limiting in this case.

> With such a setup you will never get good scaling.
> You need something like an Infiniband network.

Or check:

Carsten Kutzner, David van der Spoel, Martin Fechner, Erik Lindahl, Udo 
W. Schmitt, Bert L. de Groot and Helmut Grubmuller: Speeding up parallel 
GROMACS on high-latency networks J. Comp. Chem 28 pp. 2075-2084 (2007)

Haven't tried it yet but sounds good!



Dr. Christian Burisch
Lehrstuhl für Biophysik
PG Theoretische Biophysik
Ruhr-Universität Bochum
D-44780 Bochum
Raum ND04/67
Fon: +49 234 32 28363
Fax: +49 234 32 14626

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