[gmx-users] replica exchange

[David van der Spoel]

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?
No,

this is due to the different density, you will see that at high 
temperature fewer inteeractions are calculated.

> 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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> 
> 
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-- 
David.
________________________________________________________________________
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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