[gmx-users] Gromacs benchmarking results
ileontyev at ucdavis.edu
Tue Oct 12 02:06:41 CEST 2010
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?
>> 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,
> 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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