Ethernet is a very narrow bottleneck for that kind of a system. You won't
achieve speed up without improving interconnection between nodes.
2012/6/1 Junmei Wang <junmwang.gmail.com>
> Dear All,
>
> We recently installed a rock cluster (centos) and compiled AMBER12 with
> mpich2. The cluster has 10 compute nodes and each has 12 CPU cores.
> Interestingly, the scaling is reasonable when I used CPU cores no more than
> 12. However, when two or more nodes are involved, the computer time are all
> longer than only using single node. For example, using 12 cores (one node),
> I can sample 6.5 ns/day, and using 24 cores (2 nodes), I can only sample
> 3.5 ns/day. Although we did not use Infiniband (we used a gigabit switch),
> this parallel performance is really a surprise to me.
>
> Any suggestion? I have tried different mpi compilers (openmpi and different
> versions of mpich2), the results are similar.
>
> Thanks.
>
> Junmei
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>
--
Sincerely,
Dmitry Mukha
Institute of Bioorganic Chemistry, NAS, Minsk, Belarus
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Received on Sat Jun 02 2012 - 03:00:03 PDT
