[gmx-users] Re: efficient use of pme with gromacs

[Carsten Kutzner]

Hi Léo,

please keep Gromacs-related issues on the Gromacs-users mailing
list. This will give others with similar problems the possibility to profit from 
already answered questions by searching this list. Also, please choose
a descriptive subject (I have done that for you). Thank you!

The message you see

> DD  step 543999  vol min/aver 0.331  load imb.: force 76.6%  pme mesh/force 0.909

is just meant for your information, meaning that the PME mesh processors
finish their calculation earlier than the short-range Coulomb force processors. 
To balance that optimally, please use the g_tune_pme tool that is provided 
since version 4.5.  If you need this tool for 4.0, look here:

http://www.mpibpc.mpg.de/home/grubmueller/projects/MethodAdvancements/Gromacs/

The DD info message is however no reason for mdrun to stop. So there must be another
problem here. Can you find an error message in any of the output files?

Best,
  Carsten


On Sep 21, 2010, at 8:01 PM, Léo Degrève wrote:

> 
> Prof. Kutzner,
> I found papers and other materials that you have published on the efficient use of pme with the gromacs software.
> I have a problem that maybe you can help me, if you wish, to solve since I didn’t found what to do.
> Using gromacs on 96 processors the program stops systematically after warnings like:
> 
> DD  step 543999  vol min/aver 0.331  load imb.: force 76.6%  pme mesh/force 0.909
> 
> Defining –npme according to grompp, the result is the same. Is there a solution?
> Thank you for your attention.
> Léo Degrève
> 
> Grupo de Simulação Molecular
> Departamento de Química  - FFCLRP
> Universidade de São Paulo
> Av. Bandeirantes, 3900
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>  e-mail: leo at obelix.ffclrp.usp.br
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--
Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne