NAMD/CHARM source installation option

From: Jyh-Shyong Ho (
Date: Sat Dec 17 2005 - 23:36:55 CST


Recently we got a AMD Opteron cluster and I like to install NAMD on it,
however, due to the special environement configuration of the cluster,
I like to ask your opinions on how to proceed the installation.

In order to have better performance of the cluster, all computing
nodes have their rsh/ssh turn off, users can only logon one of the two
front nodes and submit their jobs through TORQUE, parallel jobs using
mpiexec (both lam and mpich) under TORQUE environment do not need
rsh/ssh to to communication among the computing nodes assigned by TORQUE.
All computing nodes have two dual-core Opteron 275 CPUs.

Under this environment, what would be the choice/combination of the
options for installing CHARM++ and NAMD?

We have Intel 9.0, GCC 4.0.0 and Pathscale compilers available on the
system, both mpich and lammpi are also installed. Should I try
net-linux-amd64-icc/gcc, or mpi-linux-amd64-icc/gcc? I have done
some trials, but have not been successful.

Any suggestion is appreciated.

Jyh-Shyong Ho, Ph.D.
Research Scientist
National Center for High Performance Computing
Hsinchu, Taiwan, ROC

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