On Fri, Jun 01, 2012, Junmei Wang wrote:
>
> 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.
As noted, this is expected. Be sure you are using pmemd and not sander, if
possible.
....dac
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Received on Sat Jun 02 2012 - 06:30:03 PDT
