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.
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