Re: job submission script on KRAKEN @ NICS

From: harish vashisth (harish.vashisth_at_gmail.com)
Date: Fri Mar 06 2009 - 23:28:30 CST

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>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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