job submission script on KRAKEN @ NICS

From: harish vashisth (harish.vashisth_at_gmail.com)
Date: Fri Mar 06 2009 - 22:22:50 CST

Hi, I am not sure if it is the right place to ask---but, is there someone
who is running NAMD2.6 on kraken successfully? I would like to know the
location of NAMDv2.6 on KRAKEN and also any job submission scripts someone
can share. I looked into kraken's website and they say using "module load
namd" command but I see nothing explicit about where is the location of
built 'namd2' binary or how to use in detail this module stuff......I have
tried using following job submission scripts as pasted below where the job
goes into the queue but dies immediately saying--can not locate 'mpirun' or
command not found....

I would appreciate any help.

-------------------------------------------------------------------------------------------------------------------------------------
#!/bin/bash

#PBS -l nodes=2:ppn=8

#PBS -l walltime=24:00:00

# name of this job
#PBS -N kraken

# the queue to submit my job to
#PBS -q medium

# Account to charge
#PBS -A TG-MCB070073N

cd /nics/d/home/hl332/pmf_t/smd_sec0

/sw/xt5/namd/2.6/cnl2.1_pgi7.2.5_debug/bin/charmrun +p16
/sw/xt5/namd/2.6/cnl2.1_pgi7.2.5_debug/bin/namd2 smd.conf > v.log

--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

#!/bin/tcsh

if ( $# != 3 ) then
  echo "This script requires three arguments:"
  echo " NAMD input file"
  echo " NAMD log file"
  echo " number of nodes"
  exit -1
endif

set CONFFILE = $1
set LOGFILE = $2
set NUMNODES = $3

if ( ! -f $CONFFILE) then
  echo "NAMD input file $CONFFILE does not exist!"
  exit -1
endif

if ( -f $LOGFILE) then
  echo "NAMD input file $LOGFILE already exists!"
  exit -1
endif

set RUNDIR = `pwd`

echo "Submitting NAMD run to batch queue..."
echo ""

# Run in a batch queue
#cat << ENDINPUT
qsub -q medium -V -j oe -N runbatch -l
walltime=24:00:00,nodes=${NUMNODES}:ppn=8 << ENDINP
UT
#!/bin/tcsh

cd $RUNDIR

echo \$PBS_NODEFILE
cat \$PBS_NODEFILE
set NP = \`awk 'END {print NR}' \$PBS_NODEFILE\`
echo \$NP
#PBS -A TG-MCB070073N
mpirun -machinefile \$PBS_NODEFILE -np \$NP
/sw/xt5/namd/2.6/cnl2.1_pgi7.2.5_debug/bin/nam
d2 $CONFFILE >& $LOGFILE

setenv MPICH_PTL_SEND_CREDITS -1
setenv MPICH_MAX_SHORT_MSG_SIZE 8000
setenv MPICH_PTL_UNEX_EVENTS 80000
setenv MPICH_UNEX_BUFFER_SIZE 100M

ENDINPUT

echo ""
echo "NAMD is submitted to the queue, to check on your job use this
command:"
echo ""
echo " qstat -u $USER"
echo ""
echo "Your job is running if there is an R (running) in the S (state)
column."
echo "Once the job has started you may monitor progress with this command:"
echo ""
echo " tail -f $LOGFILE"
echo ""
echo "You will need to press Control-C to exit the tail command."
echo ""
-------------------------------------------------------------------------------------------------

Regards,
-Harish

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