Desmond is a Molecular Dynamic Package provided by D.E.Shaw Research. This package has its own kind of job scheduler. For running on VSC-1 the following job script can be used:

#$ -N desmond 
#$ -pe mpich 16
#$ -V
#$ -q all.q


#desmond seems to need a shared tmp directory which is
#reachable by all compute nodes
schrodinger_tmp=`pwd`

slots_to_use=$NSLOTS
processors_per_node=8
#generate hosts string for desmond call
my_hosts=`uniq $TMPDIR/machines | tr '\n' ',' `
my_hosts=${my_hosts%?}
echo "using hosts: $my_hosts"

#setup schrodinger.hosts for this specific job. 
export SCHRODINGER_HOSTS=$TMPDIR/schrodinger.hosts
for i in `uniq $TMPDIR/machines`
do
	cat >> $SCHRODINGER_HOSTS << EOF 
name: $i
schrodinger:  $SCHRODINGER_HOSTS
tmpdir: $schrodinger_tmp
processors: $processors_per_node
EOF
done

#
#-WAIT: wait for desmond to be finished. is needed that job script does not terminate some seconds after desmond start
#LOGINTERVAL,INTERVAL: logging (i.e. copying files from /tmp to startdirectory) is only sparsely needed, because /tmp must be reachable by user anyway. 
$SCHRODINGER/desmond -HOST $my_hosts  -WAIT -LOGINTERVAL 3600 -INTERVAL 3600 -exec mdsim -comm mpi -p $slots_to_use -c setup_step3.cfg -in setup_step3.cms
  • doku/desmond.txt
  • Last modified: 2013/02/05 10:26
  • (external edit)