[gmx-developers] gromacs 3.3

[David van der Spoel]

On Mon, 2005-10-10 at 13:50 +0200, 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?

I would guess it is a hardware problem. We use Supermicro boards (2 Dual
Core 270 chips) in 1U cases. These are very stable, we haven't had a
single hardware problem since we started production in august. You could
also check whether there could be kernel issues (we are using 2.6.9 for
production).



> 
> Thanks!
> Rainer
> 
-- 
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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