NAMD speed on MPICH2 Ubuntu 64 bit Cluster

From: Robert McCarrick (
Date: Tue Apr 05 2011 - 13:51:55 CDT

Hi Everyone,
I'm new to the cluster computer world. I've built a four-computer
cluster, each with a 6-core AMD Phenom processor running Ubuntu Server
10.10 64 bit. I've tried both the TCP optimized version on NAMD and
compiling from scratch with the mpi-Linux-X86_64 build of Charm. In all
cases, I'm getting about a 4-fold reduction in calculation times when I
run the job utilizing all four computers (i.e. going from +p6 to +p24
causes a big slowdown). This seems odd and I was wondering if anyone
had any suggestions as to where I might have gone wrong.

Robert M. McCarrick, Ph.D.
EPR Instrumentation Specialist
Department of Chemistry and Biochemistry
Miami University
701 E. High Street
101 Hughes Laboratories
Oxford, OH 45056
513.529.0507 CW Room
513.529.6829 Pulse Room
513.529.5715 fax

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