[gmx-users] replica exchange
Andrea C. Vaiana
vaiana at lanl.gov
Thu Jan 12 21:12:26 CET 2006
We're using mpich-1.2.4 and it does'nt hang with anything from 2 to
48 replicas. What I do see is a ~20% difference in performance
between the 2 and 48 replicas, can anyone explain this? Would it just
be sufficient to switch to LAM to get optimal performance?
Andrea C. Vaiana
Post Doctoral Research Associate
Theoretical Biology and Biophysics
Mail stop K710, T-10
Los Alamos, NM 87545
Los Alamos National Laboratory
On Jan 12, 2006, at 9:15 AM, Carsten Kutzner wrote:
> On Fri, 13 Jan 2006, Mark Abraham wrote:
>> Marc F. Lensink wrote:
>>> i do not understand why this is. replica's only need to talk to
>>> neighbours, and only then every so many simulation steps. for that,
>>> communication by phone should be enough!
>> Of course!
>>> i'm talking about 16-20 replica's ie cpu's (8-10 nodes). using
>>> not lam.
>> MPICH is not supported/recommended. LAM is. Please read the
>> documentation on the gromacs webpage.
> If you definitely need mpich, you might want to try mpich-2.
> mpich-1.x Gromacs hangs when using more than 4 CPUs on Ethernet,
> don't know why.
> Schoene Gruesse,
> Dr. Carsten Kutzner
> Max Planck Institute for Biophysical Chemistry
> Theoretical and Computational Biophysics Department
> Am Fassberg 11
> 37077 Goettingen, Germany
> Tel. +49-551-2012313, Fax: +49-551-2012302
> eMail ckutzne at gwdg.de
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