Serial job example

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Revision as of 20:52, 13 October 2011

In this exercise user should obtain prepared simple 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/d/db/Serial.tgz

4. Extract archive :

$ tar xvzf Serial.tgz

5. Enter Serial folder :

$ cd Serial

6. List content of folder:

$ ll

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

$ cat job.pbs

#!/bin/bash
#PBS -q hpsee
#PBS -l nodes=1:ppn=1
#PBS -l walltime=10:00:00
#PBS -e ${PBS_JOBID}.err
#PBS -o ${PBS_JOBID}.out

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

cat job.sh

#!/bin/bash
date
hostname
pwd
sleep 120

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

$ qstat -u ngrkic

ce64.ipb.ac.rs: 
                                                                         Req'd  Req'd   Elap
Job ID               Username Queue    Jobname          SessID NDS   TSK Memory Time  S Time
-------------------- -------- -------- ---------------- ------ ----- --- ------ ----- - -----
1723620.ce64.ipb     ngrkic   hpsee    job.pbs           32715     1  --    --  48000 R   -- 

10. After two minutes your job will be done. List content of <jobID>.ce64.ipb.ac.rs.out file :

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

Tue Oct 11 21:42:58 CEST 2011
n08.ipb.ac.rs
/nfs/ngrkic/serial