[gmx-users] Gromacs benchmarking results

[Igor Leontyev]

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