I'm not part of the development team, but the first thing I'd ask is, are
all of those cores equivalent? I realize you've structured things such
that the total number of cores is equal, but is it the case that the CPUs
with the higher core count are simply not clocked as high as those with
fewer cores?
Perhaps another issue could be bandwidth between cores, which would perhaps
be smaller on the higher core-count CPUs, but that isn't really something I
can speak to.
~Aron
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
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Dec 16 2011 - 09:30:03 PST
