Thanks all for the replay. We will try to get a better switch. Here is more
details for my test:
1821 protein atoms, 18284 total atoms (protein + water), PMEMD.
For the same MD system, when I submitted 10 jobs (each job use one node/12
cores), all the MD sampling rates are roughly same (about 6.5 ns/day).
However, when I submitted 5 jobs using 2nodes/24 cores, the sampling rates
varied from 6.8 ns/day to 0.5 ns/day. Surprisingly, when all other jobs
were done, the last job was still very slow.
Best
Junmei
On Sat, Jun 2, 2012 at 8:06 AM, case <case.biomaps.rutgers.edu> wrote:
> 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 - 07:30:03 PDT
