[torqueusers] MPI and NAMD?

Brock Palen brockp at umich.edu
Mon Jun 18 10:12:53 MDT 2007

NAMD uses the 'charmrun'  command,  but if you built with mpi  
'charmrun'  just calls your underlying MPI launcher (mpirun, mpiexec,  

So you will find you can use the namd2 executable the same way you  
use any MPI application
We use the TM interface hooked with OpenMPI So for us a basic script is:

#PBS -N jobname
#PBS -M email at sanofi-aventis.com
#PBS -m abe
#PBS -V  #this is for our environtment
#PBS -l nodes=2:ppn=2,walltime=48:00:00

#change to input directory
cd ~/mynamdinput/

#run namd2  (this assumes namd2 is in my $PATH)
mpirun -np 4 namd2 <configfile>

#end scripts

You can use charmrun  but i hate it personally,  most mpirun's  are  
all the same and it just confuses our users who have access to:  
charmm, Amber, NAMD2 gormacs DLPOLY etc.
But again thats my personal opinion (KISS,  Keep it simple stupid)

Brock Palen
Center for Advanced Computing
brockp at umich.edu

On Jun 18, 2007, at 12:09 PM, Dan Roberts wrote:

> Hello All
> Anyone have any generic examples of how to run NAMD using MPI and
> Torque/MAUI.
> I have examples of NAMD and SGE but not quite sure how to engineer  
> them
> to work within MAUI/TORQUE..
> THanks!
> Dan
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