AMBER Archive (2002)

Subject: parallel sander on T3E

From: Peter Gannett (pgannett_at_hsc.wvu.edu)
Date: Sat May 25 2002 - 09:46:37 CDT

Amber users:

We ran two MD simulations on two solvated DNAs, a duplex and a triplex. Both runs were 1 ns and 16 nodes (64 CPU) were used. Both runs took about twice as long as we had expected based on a single cpu run. I am guessing that there must be some point at which additional CPUs don't get you any speed up. If true, than how can you make a rough estimate of the optimal number of CPUs to use for a given job. If I'm wrong in my guess, then what in our setup might be the problem. Thanks.

Pete Gannett