Re: Launching namd with PBS

From: Brian Bennion (
Date: Wed Sep 24 2003 - 19:15:49 CDT

Maybe you have checked this out already, but PBS sets an environmental
variable that can be accessed and parsed to create a nodelist that namd
can then use. I don't have access to my scripts at the moment but I can
email them to you later if you wish.


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

**Brian Bennion, Ph.D.                                         **
**Computational and Systems Biology Division                   **
**Biology and Biotechnology Research Program                   **
**Lawrence Livermore National Laboratory                       **
**P.O. Box 808, L-448                     **
**7000 East Avenue       phone: (925) 422-5722                 **
**Livermore, CA  94550   fax:   (925) 422-6605                 **

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