[gmx-users] replica exchange

[Andrea C. Vaiana]

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

--
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.
>>
>> Mark
>
>
> 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,
>
>    Carsten
>
>
> ---------------------------------------------------
> 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
> http://www.gwdg.de/~ckutzne
>
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