[gmx-users] replica exchange
David van der Spoel
spoel at xray.bmc.uu.se
Thu Jan 12 21:41:28 CET 2006
Andrea C. Vaiana wrote:
> 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?
this is due to the different density, you will see that at high
temperature fewer inteeractions are calculated.
> 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 their
>>>> 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 mpich,
>>>> 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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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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