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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Received on Fri Jun 01 2012 - 13:30:04 PDT
