[gmx-users] replica exchange

[X.Periole]

On Thu, 12 Jan 2006 21:41:28 +0100
  David van der Spoel <spoel at xray.bmc.uu.se> wrote:
> 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.
> 
should this increase the speed ??

XAvier
>> 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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