performance differences on 2.4 vs. 2.6 Linux kernels

From: Matt Harrington (
Date: Thu Apr 07 2005 - 19:10:54 CDT

I upgraded a Linux cluster and now only see NAMD utilizing about 46% of
each node. The details are:

1 head node, 16 slave nodes
Asus PR-DL533 motherboards
dual Xeon 3.0GHz processors
2GB RAM per node
gigabit ethernet on a PCI-X bus

NAMD = NAMD_2.5_Linux-i686-TCP precompiled binary
old OS = Rocks 3.3.0, Linux kernel v2.4.21, built on RHEL 3
new OS = Rocks 4.0.0 beta, Linux kernel 2.6.9-5.0.3.ELsmp, built on
RHEL 4 (CentOS 4)

the same input files and the same version of NAMD are being used before
and after the upgrade. both processors are used on any given slave
node, but only at about 50% each. the total load average hovers around
1.0. jobs are launched like this:

charmrun namd2 +p32 minimization.inp > logmin

we had significantly better performance with the older operating
system. any clues about how to troubleshoot this would be appreciated.


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