Running namd on Rice Teracluster

From: Amarda Shehu (
Date: Sun Apr 11 2004 - 19:15:41 CDT

Dear all,

I have installed namd on the Rice Teracluster, which is a 1 TeraFLOP Linux
cluster based on IntelR ItaniumR 2 Processors. The jobs in the teracluster
are run through a PBS script. In the teracluster, parallel jobs are run by
using mpiexec and specifying the number of processes needed.

I am running into problems trying to run namd in parallel on the
teracluster nodes.

Does namd run in parallel by trying to do rsh to the
nodes of the specified nodelist? As this is basically trying to log in to
the nodes of the cluster, it fails because rsh to the nodes is not
allowed. Is this the only way to run namd in parallel?

I thought I would check with you before contacting my system's administrators.

Thank you,
Amarda Shehu.

Amarda Shehu
Graduate Student,
Computer Science, Rice University.

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