AMBER Archive (2002)

Subject: Re: Scaling of Sander on Linux Clusters (fwd)

From: Peter Gannett (pgannett_at_hsc.wvu.edu)
Date: Mon Aug 26 2002 - 19:56:06 CDT

Dear Thomas:

I am just starting to use a cluster but what few results I have suggest
that 4 CPUs is the best. Runs take longer if I use less or more than
this. I have been told that this is typical but don't know of 'proof'
of this.

Pete Gannett
WV University

>>> <amber_at_heimdal.compchem.ucsf.edu> 08/26/02 05:51PM >>>

---------- Forwarded message ----------
Date: Mon, 26 Aug 2002 14:09:25 +0200
From: Thomas Steinbrecher
<thomas.steinbrecher_at_physchem.uni-freiburg.de>
To: amber_at_heimdal.compchem.ucsf.edu
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
general.

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?

Regards,

Thomas