[AMBER] Sander.MPI speed vs cpu x node

From: Changwoo Do <dokira.gmail.com>
Date: Fri, 16 Dec 2011 11:58:23 -0500

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,


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Received on Fri Dec 16 2011 - 09:00:02 PST
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