NAMD running only at 40-50% CPU capacity

From: LEWYN LI (
Date: Fri Sep 02 2005 - 11:00:35 CDT

Dear fellow NAMD users,

         I am running a constant-force pulling NAMD simulation on a 14-node
Beowulf cluster. The NAMD version is 2.5 for Linux-i686-Scyld, and I am
using the Scyld Beowulf 27BZ-8 2001 version.

         I noticed that the speed of the simulation is slowing down. For
example, at step = 0, the NAMD log file says there are 30.6536 hours
remaining. At step = 300000, it says that there are 44.9144 hours

         I checked the CPU usage, and found that only about 40-50% of the
CPU (both master and slave nodes) is dedicated to my NAMD simulation. All
the nodes are up, but each node is apparently using only half of its CPU
on my simulation.

         I can find no other process on the cluster that would require 50%
of the CPUs. I have re-niced my NAMD process to 0 or -20, but it didn't
increase the %CPU for my simulation.

         Any help or comment would be greatly appreciated! Thank you very

                                                         LEWYN LI

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