[gmx-users] Networking

David van der Spoel spoel at xray.bmc.uu.se
Tue Jan 8 10:41:15 CET 2002

On Mon, 7 Jan 2002, Justin MacCallum wrote:

>Our hardware vendor has given us three gigabit ethernet (Intel PRO/1000T
>Server) and a switch (Intel NetStructure 470T) for evaluation.  We have
>dual PIII 1Ghz nodes in our cluster.  I tried two test systems.  The first
>one was a 64 lipid DOPC bilayer with ~11000 atoms.  The second was a box
>of water containing 81000 atoms.  Both systems used a 0.9 rlist, 1.4 rdw
>and 0.9 rcoulomb with PME, order=4, fourierspacing=0.12, optimize_fft=yes.
>For both systems I ran two simulations, one on two processors and one on
>four.  For both systems, the two processor version performed slightly
>better than the four processor one.  In both cases, the network load in
>the four processor versions was about 5%.  Based on previous benchmarks on
>fast ethernet nodes, I expect things to scale much better without PME.
Did you use grompp -shuffle -sort
It certainly shouldn't be this bad. For a more exact comparison you may 
want to have a look at the gromacs benchmarks which you can download from 

Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

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