AMBER: Improving pmemd parallel scaling

From: Alessandro Nascimento <>
Date: Thu, 28 Jun 2007 13:07:15 -0300

Hi amber users,

I'm running amber9 (lam-mpi) on 6 Intel Xeon 3.4 processors in Gigabit network.
Looking the processors usage with linux "top" over the machines when
running pmemd in a equilibrium simulation (~58K atoms, periodic box) I
see that most of the times one processor is fully used, another one
with ~50% usage and the resting are idle.
sande.MPI has given me better results, although previous e-mail in
this list argue that pmemd should scale better.

My question is: which simulation parameters can be adjusted in order
to achieve a better scaling? How can I improve it? Could there be any
(hardware?) reason for the poor scaling in pmemd?

Thanks in advance,

[ ]s
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Received on Sun Jul 01 2007 - 06:07:22 PDT
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