[gmx-users] Gromacs benchmarking results

[David van der Spoel]

On 2010-10-11 12.20, Mark Abraham wrote:
> g_tune_pme in 4.5.2 is your friend here. Otherwise, stay at 48 or below,
> probably.

And try it with 4.5! Much better performance.
>
> Mark
>
> ----- Original Message -----
> From: vivek sharma <viveksharma.iitb at gmail.com>
> Date: Monday, October 11, 2010 21:10
> Subject: [gmx-users] Gromacs benchmarking results
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>
>  > Hi all,
>  > I have some gromacs benchmarking results to share.
>  > I have tried the lysozyme example distributed in the benchmarking
>  > suite "gmxbench-3.0.tar.gz". I have used the case provided in d.lzm/
>  > with pme.mdp parameter file.
>  >
>  > Following is the performance (in ns/day) I got with gromacs-
>  > 4.0.5 on
>  > my cluster with different number of processors. I have tried different
>  > npme for each run and reporting here the best one.
>  >
>  > #processors
>  > #npme Performance ( ns/day)
>  >
>  > 1 2.898
>  >
>  > 24 8 44.698
>  >
>  > 48 16 75.262
>  >
>  > 72 24 86.835
>  >
>  > 84 20 102.249
>  >
>  > 96 16 97.079
>  > 120 40 97.738
>  > 144 64 93.204
>  > 156 76 89.534
>  >
>  > I am looking for some more benchmarks on the same example set, to
>  > compare these results. Please, share if somebody has tried it.
>  >
>  > Expecting some helpful comments and suggestions to improve the
>  > performance further.
>  >
>  > Thanks,
>  > Vivek Sharma
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-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se