Hybrid job example
From MediaWiki
In this exercise user should obtain prepared hybrid 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/b/bb/Hybrid.tgz
4. Extract archive :
$ tar xvzf Hybrid.tgz
5. Enter Mpich folder
$ cd Hybrid
6. List content of folder:
$ ll
7. List content of job.pbs and 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
export OMP_NUM_THREADS=8
cd $PBS_O_WORKDIR
chmod +x job
${MPI_OPENMPI_MPIEXEC} -np 4 -npernode 1 ./job
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
n06.ipb.ac.rs n06.ipb.ac.rs n08.ipb.ac.rs n08.ipb.ac.rs n13.ipb.ac.rs n13.ipb.ac.rs Node: 2 Node integral: 0.523599 Node: 1 Node integral: 0.523599 Node: 3 Node integral: 0.523599 Node: 4 Node integral: 0.523599 Node: 5 Node integral: 0.523599 Compiled on Oct 12 2011 at 11:34:11 Number of nodes: 6 Number of intervals: 300000000 Node: 0 Node integral: 0.523599 PI exact : 3.1415926535897931 PI estimate: 3.1415926535899650 PI diff : 0.0000000000001719 Wall clock: 1.894531
