qsub on a linux cluster

From: Per Jr. Greisen (greisen_at_binf.ku.dk)
Date: Fri Jul 14 2006 - 02:12:54 CDT

Hey,

I am trying to run namd on a linux cluster and have looked at the namdwiki
but cannot get the script working correctly; i Have made the file
specifying which nodes to use - anybody has experience for running on
linux clusters?

Thanks

#!/bin/csh -f

# Name of the job
#$ - N NAMD_test
# Execute from the current directory
#$ -cwd

# Error logs
#$ -e ./
#$ -o ./

set NODES = 'cat $HOST_FILE'
set NODELIST = $TMPDIR/namd2.nodelist
echo group main >! $NODELIST

foreach node ( $nodes )
        echo host $node >> $NODELIST
end

@ NUMPROCS = 1* $#NODES

#$ -e namd-job.errout
charmrun namd2 +p$NUMPROCS ++nodelist $NODELIST minimization.conf > data.log 

-- 
Best Regards
Per Jr. Greisen

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