From: Edward Patrick Obrien (edobrien_at_Glue.umd.edu)
Date: Wed Mar 02 2005 - 17:22:02 CST
This has always worked for me:
1. In file called "nodelist", located in working directory:
2. to run
charmrun namd2 ++nodelist nodelist +p4 file.namd >& file.log
3. If running with PBS queing system, I also specify the nodes:
> qsub -l nodes=n1+n2 file.pbs
Note on step 1:
This example runs on 2 nodes using 4 processors (2 cpu's per node).
It is necessary to duplicate the computer name to specify that 2 cpu's
will be used on one node.
If you have 1 cpu per node, but still running parallel, the nodelist
file should instead contain:
and step 2 would be:
charmrun namd2 ++nodelist nodelist +p2 file.namd >& file.log
Hope that helps,
On Wed, 2 Mar 2005, Parag Adhangale wrote:
> This mailing list is of great help. Thanks for all the
> I tried running NAMD using charmrun by setting up a
> node list file and using the ++nodelist option.
> Charmrun however, seems to ignore it and goes to the
> that are up. Is there a way to force charmrun to only
> use nodes specified in the nodelist file ?
> Celebrate Yahoo!'s 10th Birthday!
> Yahoo! Netrospective: 100 Moments of the Web
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