Application specific job example (NAMD)

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In this exercise user should obtain prepared specific application job, extract archive, list content of files, submit job on PARADOX cluster, monitor his progress with information from queue and when job is done list resaults file.

1. Login on

$ ssh

2. Navigate to your folder in nfs filesystem.

$ cd /nfs/ngrkic

3. Download tgz archive with example files.


4. Extract archive :

$ tar xvzf Namd.tgz

5. Enter Namd folder

$ cd Namd

6. List content of folder:

$ ll

7. List content of job.pbs and job.c files:

$ cat job.pbs
#PBS -q hpsee
#PBS -l nodes=4:ppn=8
#PBS -l walltime=10:00:00
#PBS -e ${PBS_JOBID}.err
#PBS -o ${PBS_JOBID}.out

chmod +x
$ cat
#!/bin/sh -x


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

if [ "x$PBS_NODEFILE" != "x" ] ; then 
  echo "PBS Nodefile: $PBS_NODEFILE" 
    if [ "x$HOST_NODEFILE" = "x" ]; then
      echo "No hosts file defined.  Exiting..."
        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
                                    echo "Nodelist file:"
                                    cat $NODELIST
#         tar zxvf bench28.tgz
         echo "Executing Namd..."
/opt/exp_soft/aegis/namd-2.7b2/charmrun ++remote-shell ssh ++nodelist $NODELIST  +p$PROC_NUM /opt/exp_soft/aegis/namd-2.7b2/namd2 /nfs/ngrkic/namd/bencmark/apoa1.namd

8. Submit job :

qsub job.pbs

qsub will print output :


9. Monitor your job :

qstat <jobID>

10.When job is done list content of <jobID> file :

cat <jobID>
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