Re: How to run namd on NCSA Tungsten

From: Hyonseok Hwang (
Date: Wed Oct 19 2005 - 16:56:30 CDT

Hi, Snoze

Below is a sample job script file I have to run the NAMD on the
tungsten a year ago. It is an example for a parallel job. I used it a
year ago, so there could be some change by now. I ran NAMD in the
scratch directory and so I copied some files into the scratch directory.
If you are not using the scratch directory, you don't have to copy. I'm
afraid that there could be more you should know to run NAMD.

I hope that will be a little help.


#set 'setenv MPI_COMM TCP' and don't use '-poll' option in cmpirun.

set OWD = u/ac/test/research/namd
set SCR = /scratch/users/test/research/namd
set NPROCS = 8

#BSUB -J s8ap1
#BSUB -n 8

#BSUB -P mqc # Project name
#BSUB -q normal #default queue name
#BSUB -W 24:00

cd $SCR # change to scratch directory
cp $OWD/8mer.namd.cfg $SCR/8mer.namd.cfg # copy config file to scr dir
cp $OWD/8mer.namd.job $SCR/8mer.namd.job # copy job file to scr dir

cmpirun -lsf -np $NPROCS /usr/apps/chemistry/NAMD/namd2
$OWD/8mer.namd.cfg > 8mer.namd.log

PS) The last two lines should be one line

snoze pa wrote:
> Hi,
> I am trying to run a pre-compiled version of namd on ncsa tunguston
> cluster.
> But I don't know the node list. How to check the number of nodes in ncsa
> tunguston. Is there any batch running script for tunguston, if anyone
> has this
> list please send me.
> thanks in advance
> snoze

Hyonseok Hwang
Postdoctoral Fellow
Department of Chemistry
Northwestern University
2145 Sheridan Rd.
Evanston, IL 60208-3113 USA

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