AMBER Archive (2009)

Subject: Re: [AMBER] What is the parallel efficiency of amber10

From: David A. Case (
Date: Mon Jun 08 2009 - 07:23:11 CDT

On Mon, Jun 08, 2009, Catein Catherine wrote:
> Could you mind to share your experience with me about the parallel
> efficiency of amber10. It seems to me that we can run AMBER10
> efficiently in 8 processors on the same node.
> However, the jobs may have problem to run on 2 nodes with 8 processors each.

This is a pretty common general observation. Details depend on the types of
processors you have, and on the interconnect between nodes. If you use
gigabit ethernet as an interconnect, you are pretty much limited to running
jobs on one node.

Be sure to try pmemd, if it's feature set meets your needs. It should be
faster than sander under almost all job conditions.


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