Re: job submission script on KRAKEN @ NICS

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Tue Mar 10 2009 - 11:22:21 CDT

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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