Utilizing Amber6 on Linux Cluster

From: Scott E. Boesch <sboesch_at_chemdept.chem.ou.edu>
Date: Wed 22 Aug 2001 09:24:42 -0500

Amber uses,

I have several questions regarding the use of amber6 on a linux cluster.

First, some general comments/questions.
The choice of the type of networking technology is probably an important
consideration. Since
there are several different types (fast ethernet, Myrinet, SCI, etc), I
was curious which
technology was being utilized and also if anyone has done a study comparing
these different setups.
Another important consideration is the version of MPI. (MPICH, LAM-MPI,
etc) I know there are several freely available versions of MPI and also
some commercially available. I wanted to see what was the
most common.
There's a very interesting technical report about cluster computing for
chemistry talking about various issues from price to performance. The
report is
DHPC Tenchnical Report DHPC-073 "Commodity Cluster Computing for Computational
Chemistry" by KA Hawick, DA Grove, PD Coddington, and MA Buntime" 21 Jan 2000

Now I have some more specific questions about amber6.
Since Gibbs will not run under MPI, I wanted to know if there are plans to
do so,
either officially or unofficially.

The primary networking technology that I'm using is SCI. It comes with its
own version of MPI.
I was unable to compile amber6 using this version of MPI and this must be
used in order to
utilize the SCI. I wanted to know if anyone was able to successfully
compile amber6 using
SCI. We bought the hardware/software for SCI from Scali (www.scali.com).

Since I was unable to get amber6 working using SCI, I decided to try fast
I installed MPICH. I've been told that one must use MPICH-1.2.1, because
of some problem
with a previous version. However, MPICH-1.2.1 would not install on my
system, but
MPICH-1.2.0 would install.
I then successfully compiled amber6.
When running sander if I set ntc=3, the job bombs and I get the message
for this parallel version only works for ntc < 3
Is this legitimate?

Thanks for information anyone can provide.



Scott E. Boesch Voice: 405-325-3502
Department of Chemistry Fax: 405-325-6111
University of Oklahoma

Received on Wed Aug 22 2001 - 07:24:42 PDT
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