Re: NAMD 2.7b1 running & performance issues

From: Nicholas M Glykos (
Date: Mon May 25 2009 - 12:43:07 CDT

> I installed NAMD 2.7b1 on a small Bull HPC cluster (four compute nodes, each
> with two quad-core Xeon_at_2.5 GHz CPUs, 8 GB RAM and a management node with two
> quad-core Xeon_at_2.0 GHz CPUs, 8 GB RAM, all running Red Hat Enterprise Linux 5
> and interconnected by a Gigabit Ethernet network) and tested it with the
> ApoA1 benchmark. Using the precompiled Linux-x86_64-TCP binaries,

Just a quick note to say that on similar(ly small) cluster we observed
best performance using the amd64 _UDP_ version of the precompiled NAMD
binaries (but this was for NAMD 2.6). See
for details of the combinations we've tried. Do bear in mind that my
suspicion is that the TCP version's poor scaling was due to me failing to
properly tune the network kernel parameters.


> Marius Micluta
> Institute of Biochemistry of the Romanian Academy

          Dr Nicholas M. Glykos, Department of Molecular Biology
     and Genetics, Democritus University of Thrace, University Campus,
  Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620,
    Ext.77620, Tel (lab) +302551030615,

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