Application specific job example (NAMD)
From MediaWiki
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