From: David Lee Braun (dlbraun_at_umich.edu)
Date: Wed Nov 03 2010 - 15:27:58 CDT
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I am trying to address a performance issue with NAMD 2.7 compiled from
The problem I am having is that NAMD under-preforms. Top will show ~30
user, 70% sys, and 0 io wait for most jobs. For some it runs at ~100%
user and does .15 days/ns ( 100000 atoms). Jobs that are using large
percentages of system run >15x slower.
It is possible that I did not compile charmm++ and NAMD correctly. Can
someone suggest the proper compilation instructions for the following
OS openSuSE 11.1
Compiler Intel 11.1
MPI OFED Intel openmpi-1.4.1
charmm++ was built with the following command:
env MPICXX=mpicxx ./build charm++ mpi-linux-x86_64 --no-build-shared
NAMD was build with the instructions from the notes.txt file included
with the source.
The cluster nodes are dual quad core nodes with one of the following
Intel(R) Xeon(R) CPU E5440 @ 2.83GHz
Intel(R) Xeon(R) CPU E5520 @ 2.27GHz
All nodes have either 2GB RAM or 3GB RAM per core. Jobs will run on
either the 2.83GHz or the 2.27GHz processors, but not a mixture.
David Lee Braun
Manager of Computational Facilities
for Dr Charles L. Brooks, III Ph. D.
930 N. University Ave
Ann Arbor, MI 48109-1055
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