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 - 09:00:02 PST
