Overlaoded processors when running NAMD on NCSA Altix

From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Sat May 19 2007 - 20:06:08 CDT

Dear all,

I am running NAMD on the NCSA SGI Altix supercomputer (Cobalt). In some
runs NAMD prints in the log file the following warning message:

n processors are overloaded due to high background load.

"n" is usually a number between 1 and 8. I have noticed that when this
happens I lose 20-30% of performance compared to the runs where this
warning is not printed. Because this happens randomly I have increased the
requested time from the queue to almost its maximum to avoid that my jobs
get killed because of exceeded walltime.

I reported this problem to the administrators of Cobalt but they replied
that they have never seen this kind of message and they don't know what
the cause might be. For this reason I decided to write to the NAMD list
in case somebody else has seen the same warning.

What does this warning exactly mean? How can I figure out what is causing
a high background load? How can I help NCSA administrators locate and
resolve the problem?

This is kind of annoying because in this way I'm wasting some of the
awarded time on the supercomputer. Thus I would like to solve this
problem.

Many thanks,

          Gianluca

-----------------------------------------------------
Dr. Gianluca Interlandi gianluca_at_u.washington.edu
                    +1 (206) 685 4435
                    +1 (206) 714 4303
                    http://biocroma.unizh.ch/gianluca/

Postdoc at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
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