Application specific job example (NAMD)

From MediaWiki

Revision as of 09:55, 12 October 2011 by Ngrkic (Talk | contribs)
(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to: navigation, search

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 ui.ipb.ac.rs:

$ ssh ngrkic@ui.ipb.ac.rs

2. Navigate to your folder in nfs filesystem.

$ cd /nfs/ngrkic

3. Download tgz archive with example files.

wget http://wiki.ipb.ac.rs/images/3/3c/Namd.tgz

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
#!/bin/bash
#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

cd $PBS_O_WORKDIR
chmod +x script.sh
./script.sh
$ cat script.sh
#!/bin/sh -x

PROC_NUM=32

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
                                    
                                    
#         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 :

<jobID>.ce64.ipb.ac.rs

9. Monitor your job :

qstat <jobID>.ce64.ipb.ac.rs

10.When job is done list content of <jobID>.ce64.ipb.ac.rs.out file :

cat <jobID>.ce64.ipb.ac.rs.out
Personal tools