At a glance, this looks normal to me. The less cpu/node used, the more
cpu's are free to handle bookeeping/communication. See the benchmarks at
http://ambermd.org/amber10.bench1.html I believe this shows the same thing
your talking about.
Regards,
Andrew
On Fri, Dec 16, 2011 at 11:58 AM, Changwoo Do <dokira.gmail.com> wrote:
> Dear Amber teams,
>
> I have been using Amber 10 for polymer system MD simulations. One
> thing I found recently is that the calculation speed has strange
> dependency to the number of CPUs in one nodes.
>
> For the same MD simulation I tested
>
> 1) 8 nodes x 4 cpu/node
> 2) 4 nodes x 8 cpu/node
>
> Case #1 was faster by about 30 %. Huge difference.
>
> Another test run was
> 1) 3 nodes x 8 cpu/node
> 2) 4 nodes x 6 cpu/node
> 3) 6 nodes x 4 cpu/node
>
> #3 was fastest. Next one was #2 and #1 was the slowest.
>
> Can anyone suggest what this result indicates? Does this suggest that
> the openMPI I'm using is not optimized? and not very efficient ? Or is
> this normal?
>
> Thank you,
>
> Changwoo
>
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Received on Fri Dec 16 2011 - 09:30:04 PST
