Vivek,
thank you for interesting results. What is the configuration of your
cluster: cpu, #cores per node, connection between nodes? It might be
informative to represent your results by the computational efficiency, i.e.
Performance/(number of cores). It would be indeed interesting to see the
results for the latest version of gromacs.
Suppose we are considering buying a cluster. What is the optimal
configuration for the maximum efficiency per dollar spent? More
particularly, is the cluster of nodes with 2 x 12-core Opteron 2.2Ghz = 24
cores of 2.2Ghz more efficient than cluster of nodes with 2 x 6-core Xeon
2.66Ghz = 12 nodes of 2.66Ghz for the same price?
Thanks,
Igor
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.
Mark
David van der Spoel wrote:
And try it with 4.5! Much better performance.
> 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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