[gmx-users] Gromacs on Gigabit Ethernet Dual Opteron Cluster

[David]

On Wed, 2003-10-01 at 18:53, Ghermes Chilov wrote:
> Dear gmx-users,
> 
> I've got preliminary results of Gromacs's performance on Dual Opteron
> cluster (Gigabit Ethernet, LAM-MPI 7.0). The scalability is good (>80%)
> with up to 3 nodes used, but than it drops (44% for 8 nodes) and this
> decrease seems to correlate with CPU load (which also drops from
> 100-95% for 1 node to 60% for 8 nodes).
> 
> Should I play with LAM compilation options or go fishing somewhere
> else? Probably parameters --with-tcp-short and --with-shm-short for
> Gigabit Ethernet may be increased? (with respect to 500 kb for Fast
> Ethernet).
which system do you use?

I'd suggest starting with the DPPC benchmark. Don't forget to use
-shuffle for grompp
> 
> Ghermes Chilov
> Moscow State University
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. 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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