NAMD on WestGrid Systems
Introduction
NAMD is a program for molecular dynamics simulations of large biomolecular systems.
NAMD is currently available to approved WestGrid users on the Bugaboo cluster (bugaboo.westgrid.ca) and the older Matrix cluster (matrix.westgrid.ca) and the special-purpose Tantalus Cray XD1 (tantalus.westgrid.ca). The NAMD license agreement stipulates that "each member of the institution or corporation who has access to or uses Software must agree to and abide by the terms of this license". Therefore, access to the software will be allowed only for those users who have read the license agreeement on the NAMD web site and can agree to the conditions given there. If you would like to use NAMD on WestGrid systems please review the license and send email to support@westgrid.ca with the subject line "NAMD access requested for your_user_name" and indicate that you have read and can abide by the conditions of use.
Users are expected to be generally familiar with NAMD capabilities and input file formats. A user's guide and detailed tutorial notes are available at the NAMD web site (http://www.ks.uiuc.edu/Research/namd/).
Like other jobs on WestGrid systems, NAMD jobs are run by submitting an appropriate script for batch scheduling using the qsub command.
Details of scheduling and job management are explained on the Running Jobs page.
Running NAMD on Bugaboo
We don't have a specific batch job example for running NAMD on Bugboo, but, see the Using Bugaboo section of the Bugaboo QuickStart Guide for some hints about running parallel jobs on Bugaboo. Your batch job could contain lines of the form:
INPUT=input_file
OUTPUT=output_file
mpiexec namd2 $INPUT > $OUTPUT
Running NAMD on Matrix
The following command submits a 72-hour 4-processor parallel job based on the script namd.pbs, for the alanin test case distributed with NAMD.
where namd.pbs is:
#PBS -S /bin/bash
# Script for running NAMD on Matrix
# 2008-12-04 DSP
cd $PBS_O_WORKDIR
echo "Current working directory is `pwd`"
echo "Node file: $PBS_NODEFILE :"
echo "---------------------"
cat $PBS_NODEFILE
echo "---------------------"
NUM_PROCS=`/bin/awk 'END {print NR}' $PBS_NODEFILE`
echo "Running on $NUM_PROCS processors."
INPUT=alanin
OUTPUT=alanin.out
BINDIR=/usr/apps/src/namd/NAMD_2.6_Source/Linux-amd64-MPI
MY_PROG="${BINDIR}/namd2 $INPUT"
echo "Starting run at: `date`"
/usr/apps/bin/PBS_mpirun $MY_PROG > $OUTPUT
echo "Job finished at: `date`"
Modify the INPUT and OUTPUT lines in the script to specify your own input and output files.
The sample script and input files are available on Matrix in the directory /usr/apps/examples/namd.
Running NAMD on Tantalus
Tantalus, a special-purpose Cray XD1 is one of the few WestGrid computing resources on which accounts are not automatically created for all users. To request an account on Tantalus, please write to support@westgrid.ca .
Updated 2010-01-18.
