Re: NAMD 2.8 job submission script for queenbee

From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Tue Jul 26 2011 - 11:13:57 CDT

It should be the same as Abe, in which case the important bits are (csh):

set RUNDIR = `pwd`
qsub -q ${QUEUE} -V -j oe -N NAMD -l walltime=${TIME},nodes=${NUMNODES}:ppn=8 << ENDINPUT
#!/bin/tcsh
cd $RUNDIR
set BINDIR = /path/to/NAMD_2.8_Linux-x86_64-ibverbs
set MPIEXEC = /path/to/mpiexec_wrapper
set NP = \`awk 'END {print NR}' \$PBS_NODEFILE\`
mvapich2-start-mpd
\$BINDIR/charmrun +p\$NP ++mpiexec ++remote-shell \$MPIEXEC \$BINDIR/namd2 $CONFFILE >& $LOGFILE
mpdallexit
ENDINPUT

Where mpiexec_wrapper looks like this:

#!/bin/csh
exec mpiexec -machinefile $PBS_NODEFILE $*

-Jim

On Mon, 25 Jul 2011, cnu gromacs wrote:

> Hi
>
> Does any body has NAMD 2.8 job submission script for
> queenbee.loni-lsu.teragrid.org<https://www.xsede.org/group/xup/ssh-terminal/-/gsisshterm_WAR_gsisshtermportlet?hostname=queenbee.loni-lsu.teragrid.org>

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