[gmx-developers] gromacs 3.3

[Erik Lindahl]

Hi Rainer,

Gromacs doesn't know anything about dual core. From our perspective,  
it is just four separate MPI processes, and the fact they are running  
on the same node just means the communication is faster.

I would be extremely surprised if LAM-MPI had any dual-core specific  
stuff too.

1. Download the CPU stresstest program from www.gromacs.org and let 4  
copies run overnight.
2. Upgrade the kernel

You can also try running 4 separate simulations in parallel, to  
separate MPI-related problems from hardware context-switching problems.

Cheers,

Erik

On Oct 10, 2005, at 1:50 PM, Rainer Böckmann wrote:

> Dear All:
>
> we faced a problem on dual dual-core opterons (2GHz) using gromacs  
> 3.3_rc2/3:
>
> While the Lys/PME benchmark (few minutes runtime) gives very nice  
> results (6.83 ns/day), runs appear to be quite unstable. E.g. a  
> membrane simulation (PME) on the four cores will stop after one to  
> ten hours, without any error message.  To be more precise, the jobs  
> appear to be still running but do not produce any output after a  
> while (cpu temperature <=65 degrees, memory exchanged).
>
> Details:
> suse 9.3, kernel 2.6.11
> gromacs 3.3_rc2 (gromacs 3.3_rc3)
> fftw 2.1.5 (fftw 3.0.1)
> lam 7.1.1
>
> Is there any solution for this problem?
>
> Thanks!
> Rainer
>
> -- 
> __________________________________________________________
> Dr. Rainer Böckmann
> Theoretical & Computational Membrane Biology
> Center for Bioinformatics Saar
> Universität des Saarlandes
> Gebäude 17.1, EG
> D-66041 Saarbrücken, Germany
> Phone: ++49 +681 302-64169  FAX: ++49 +681 302-64180
> E-Mail: rainer at bioinformatik.uni-saarland.de
> http://www.bioinf.uni-sb.de/RB/
> ___________________________________________________________
>
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-----------------------------------------------------------
Erik Lindahl  <lindahl at sbc.su.se>
Assistant Professor, Stockholm Bioinformatics Center
Stockholm University, SE 106 91 Stockholm
Phone: +46 8 5537 8564     Fax: +46 8 5537 8214