[gmx-users] gromacs benchmark SGI ALTIX ICE with Intel Quad-Core E5472

[David van der Spoel]

intra\sa175950 wrote:
> Hi all
> 
>  
> 
> For a research project, I need to know how gromacs work/scale 
> (especially gmx 4.0.4) in SGI ALTIX ICE 8200 EX  machine cluster with 
> Intel Quad-Core E5472. I want to simulate a molecular system (with 14 
> amino acid peptide +/- 5000 water molecules) in explicit conditions with 
> PME and 32 – 64 CPU. I need only to have a (rough) estimation (in 
> ns/day). Does somebody have an example?  
> 
Based on the DHFR benchmark in the 4.0 paper I estimate 200-300 ns/day 
on 64 cores, provided you have fast network. It could well be more. Best 
way is to test it obviously. Probably 32 cores is more CPU/$ efficient.

>  
> 
> Thanks in advance for your help
> 
>  
> 
> Stef
> 
>  
> 
> 
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-- 
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se