Advanced Computing Research Centre

NAMD

Description

NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.

Links

• Visit the NAMD home page.

Template job submission script

#!/bin/bash -v
# Tell PBS to use 2 nodes and 4 processes per node ----------------------
#PBS -l nodes=2:ppn=4
#PBS -j oe
#PBS -o namd.test.output


# Set the working directory for the job ---------------------------------
#
# Set this to the full path of your working directory:

export RUNDIR="/exports/gpfs/iszcjw/src/namd/namd-tutorial-files/1-2-sphere"


# Any required run flags/input files etc. -------------------------------

export RUNFLAGS="ubq_ws_eq.conf"



# DO NOT CHANGE ANYTHING BELOW THIS LINE --------------------------------
# -----------------------------------------------------------------------


# Add path to charmrun --------------------------------------------------

export PATH=/usr/local/NAMD-2.6/NAMD_2.6_Linux-amd64:$PATH

# Name of application ---------------------------------------------------

export APPLICATION="/usr/local/NAMD-2.6/NAMD_2.6_Linux-amd64/namd2"


# Change into the working directory -------------------------------------

cd $RUNDIR


# Add module ------------------------------------------------------------

. /etc/profile.d/modules.sh
module add  namd-2.6

# Generate the list of nodes the code will run on -----------------------

cat $PBS_NODEFILE
export nodes=`cat $PBS_NODEFILE`
export nnodes=`cat $PBS_NODEFILE | wc -l`

export confile=inf.$PBS_JOBID.conf

# Formats the hostfile in the format required by charmrun: --------------

#  host hostname
#  host hostname
#  ... etc.

for i in $nodes; do
   echo "host "${i} >>$confile
done

# Execute the code ------------------------------------------------------

charmrun ++nodelist $confile ++remote-shell ssh +p$nnodes $APPLICATION $RUNFLAGS