Re: amber-developers: some ideas about multisander

From: David Mathews <>
Date: Sat, 9 Apr 2005 08:00:05 -0700

I have placed some of my recent thoughts about multisander on the


Hi All,

        I looked carefully at the proposal for expanding the role of
and how it would affect nudged elastic band (NEB).

        It is hard to argue with the fact that it would simplify NEB, in
particular the way that igb.f was modified so that the seperate
images/replicates along the path do not interact. Also, using multisander

for NEB would allow NEB to work outside of using the generalized Born

        But the big drawback to making the change is that multisander is
firmly within mpi. In the computing environment I am in, I often run many

more images along a path (~30) than there are processors available for the

calculation. In general, this is likely to be the way that many users
do NEB calculations. In that case, multisander would be a bad
infrastructure because multiple concurrent processes would be run on the
same processor.

        One way to reconcile this might be to have a multisander
that could adapt to run each of the images that is on the same processor
serial. Carlos, do you have any thoughts about whether this is feasible?


David Mathews, MD, PhD
Assistant Professor of Biochemistry & Biophysics
Center for Human Genetics and Molecular Pediatric Disease
Aab Institute of Biomedical Sciences
University of Rochester Medical Center
601 Elmwood Avenue, Box 703
Rochester, New York 14642
Received on Wed Apr 05 2006 - 23:49:59 PDT
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