Re: NAMD with pbs script

From: Branko (bdrakuli_at_chem.bg.ac.rs)
Date: Sun Aug 25 2013 - 10:20:28 CDT

Manzoor,

In clusters with pbs you usually should put number of nodes and number
of processors that you need, input and output file names and the line
that execute script (for example script.sh) all in pbs file. In script
you should put path to the exe files (charmrun and namd2) as well as to
your file which give all 'instructions' for namd run. In this way you
could execute program with 'qsub <file_name>.pbs' , In your scrip it is
uncertain are charmrun and namd2 are in the same directory. Best
solution is to ask your system administrator, for example see below

Branko

PBS:

#!/bin/bash
#PBS -q <your_q>
#PBS -l nodes=1:ppn=1
#PBS -l walltime=100:00:00
#PBS -e ${PBS_JOBID}.err
#PBS -o ${PBS_JOBID}.out

cd $PBS_O_WORKDIR
chmod +x job.sh
./job.sh

job.sh:

#!/bin/sh -x

PROC_NUM=number_of_procesor_same_as_in_PBS

echo
"***********************************************************************"
echo "Running on: $HOSTNAME"
echo
"***********************************************************************"

if [ "x$PBS_NODEFILE" != "x" ] ; then
   echo "PBS Nodefile: $PBS_NODEFILE"
     HOST_NODEFILE=$PBS_NODEFILE
     fi

     if [ "x$HOST_NODEFILE" = "x" ]; then
       echo "No hosts file defined. Exiting..."
         exit
         fi

         echo "Creating host file..."

         export NODES=`cat $PBS_NODEFILE`
         export NODELIST=nodelist
         echo group main > $NODELIST
                         for node in $NODES ; do
                                         echo host $node ++shell ssh >>
$NODELIST
                                                 done

                                     echo "Nodelist file:"
                                     cat $NODELIST

/path_to_charmrun/charmrun ++remote-shell ssh ++nodelist $NODELIST
+p$PROC_NUM /path_to_namd2/namd2
/path_to_your_namd_instructive_file/<file_name>.namd

On 8/25/2013 4:36 PM, k.manzoorolajdad wrote:
> Dear NAMD user:
> I use cluster with rock cluster 6 and pbs torque
> and see this address
> http://www.ks.uiuc.edu/Research/namd/wiki/index.cgi?NamdOnPBS
> but cant handel
> i write the script below:
> #!/bin/csh
> #PBS -N NAMD
> #PBS -k oe
> #PBS -m be
> #PBS -M kazem.manzoor_at_gmail.com <mailto:kazem.manzoor_at_gmail.com>
>
> #set path=(/home/homes53/nbhard2/C2/wrong/namd2 $path .)
> cd $PBS_O_WORKDIR
>
> ./make-namd-nodelist
> ./charmrun ./namd2 +p$np ++nodelist ~/namd.$PBS_JOBID MinEqu.conf >&
> test.log
>
> and create ./make-namd-nodelist :
>
> #!/bin/sh
>
> nodelist=~/namd.$PBS_JOBID
> lists=`cat "$PBS_NODEFILE" | sort`
>
> echo group main > $nodelist
> for i in $lists
> do
> echo host $i >> $nodelist
> done
>
>
> and submit with:
> qsub -v np=40 -l nodes=5 namd.pbs
>
> what's my wrong?
> thanks
> manzoor

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