Re: Launching namd with PBS

From: Juan Alfredo Freites (
Date: Wed Sep 24 2003 - 20:03:09 CDT

PBS stores the node list in $PBS_NODEFILE. What you need to do is
add to your PBS submission script a command to edit $PBS_NODEFILE and
create the nodelist file

your_script $PBSNODEFILE > nodelist

here is how I do it

awk 'BEGIN{print "group main"} {print " host",$1}' $PBS_NODEFILE >

On Wed, 24 Sep 2003, Scott Stagg wrote:

> Hi all,
> I have been using namd successfully on my local Linux cluster for
> several months, but now we are looking to implement a batch queue
> system. We are trying to use PBS but I am having problems with the
> nodelist file. Basically charmrun overrides PBS in choosing the nodes
> namd runs on. The point a batch queue though is so users don't have to
> choose the nodes on which they run. Has anyone run into this problem?
> Any suggestions on what I should do?
> Thanks,
> Scott Stagg

J. Alfredo Freites
Department of Physics
University of California, Irvine
Irvine, CA 92697-4575
(949) 824-9921

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