Re: job submission script on KRAKEN @ NICS

From: harish vashisth (harish.vashisth_at_gmail.com)
Date: Tue Mar 10 2009 - 12:10:03 CDT

Hi Peter,
 I could not locate any directory in XT5 using this path:
/nics/d/home/jphillip/NAMD_scripts/runbatch/

Can you provide the exact path to runbatch script.

Thanks and Regards,
-Harish

On Tue, Mar 10, 2009 at 12:22 PM, Peter Freddolino <petefred_at_ks.uiuc.edu>wrote:

> Hi Harish,
> there's now a run script in ~jphillip/NAMD_scripts/runbatch.
>
> Best,
> Peter
>
> harish vashisth wrote:
> > Hi Peter,
> > Thanks a lot for this prompt reply. Yes, i have an account only on XT5.
> > I don't see any XT4 machine even on TeraGrid user portal resources link.
> >
> > Please let me know where i can look for on XT5 machine if there is any
> > successful build and job submission script.
> >
> >
> > On Sat, Mar 7, 2009 at 12:12 AM, Peter Freddolino <petefred_at_ks.uiuc.edu
> > <mailto:petefred_at_ks.uiuc.edu>> wrote:
> >
> > Hi Harish,
> > Jim is currently working on building for the XT5. If you're talking
> > about the XT4, try /nics/b/home/jphillip/NAMD_scripts/runbatch
> >
> > Peter
> >
> >
> > harish vashisth wrote:
> >
> > 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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