AMBER Archive (2008)

Subject: AMBER: Amber 10 timing

From: Ed Pate (pate_at_math.wsu.edu)
Date: Fri Jun 20 2008 - 12:08:37 CDT

Dear Amber community:

We have recently installed Amber 10 as an upgrade from Amber 8. As a test
case for timings, we ran a pmemd simulation of a protein in a box of TIP3P
waters. The entire simulation was approximately 100,000 atoms. I have
been unable to find any timing benchmarks for Amber 10. We find about a
10% speedup with Amber 10 over Amber 8. Is this what we should expect?

The system nodes are dual processor, dual core Opteron 2220s, infiniband
interconnects, Suse 10.0. Amber 10 and Amber 8 were compiled with
Portland Group compilers. The pmemd job was run on 16 nodes.

Thanks for the help.

Ed Pate

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