[gmx-developers] gromacs 3.3

Rainer Böckmann rainer at bioinformatik.uni-saarland.de
Mon Oct 10 13:50:23 CEST 2005

Dear All:

 we faced a problem on dual dual-core opterons (2GHz) using gromacs 

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).

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?


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

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