Scaling of Sander on Linux Clusters (fwd)

From: <>
Date: Mon 26 Aug 2002 14:51:57 -0700 (PDT)

---------- Forwarded message ----------
Date: Mon, 26 Aug 2002 14:09:25 +0200
From: Thomas Steinbrecher <>
Subject: Scaling of Sander on Linux Clusters

Dear AMBER users,

I have a question about the tutorials provided on the AMBER
homepage and about the performance of parallel sander in

While running the first tutorial, the DNA 10mer in a box of
water, on our Linux cluster (Dual Athlon 1600MHz CPU's with
a 100 Mbit network, not used by other users), I saw that
the calculation takes longer if I use more CPUs.

Both the minimization and the molecular dynamics run of the
water molecules with restraints on the DNA are completed
faster on two nodes (4CPUs) tha on 4 nodes (8CPUs).

(Minimization takes 370 sec on 4 CPUs and 530 sec on 8
CPUs, dynamics takes 6000 and 7400 sec respectively. If I
use only one node with 2 CPUs, they times are 413 and 6500
sec respectively)

Has anyone experienced this behaviour and if yes, is it to
be expected? I expected about half the calculation times
with double number of CPUs.

If there is an optimum number of CPUs to assign to a given
problem, is there a way to guess it from the imput data
(from number of atoms/molecules of the system)?

If anybody has tried the tutorials recently, could you
share your experience how long the different calculations
took on different systems?


Received on Mon Aug 26 2002 - 14:51:57 PDT
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