Hybrid job example
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- | In this exercise user should obtain prepared | + | 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: | 1. Login on ui.ipb.ac.rs: | ||
Line 11: | Line 11: | ||
3. Download tgz archive with example files. | 3. Download tgz archive with example files. | ||
- | wget http://wiki.ipb.ac.rs/images/ | + | wget http://wiki.ipb.ac.rs/images/b/bb/Hybrid.tgz |
4. Extract archive : | 4. Extract archive : | ||
- | $ tar xvzf | + | $ tar xvzf Hybrid.tgz |
5. Enter Mpich folder | 5. Enter Mpich folder | ||
- | $ cd | + | $ cd Hybrid |
6. List content of folder: | 6. List content of folder: | ||
Line 25: | Line 25: | ||
$ ll | $ ll | ||
- | 7. List content of job.pbs and | + | 7. List content of job.pbs and files: |
$ cat job.pbs | $ cat job.pbs | ||
Line 31: | Line 31: | ||
#!/bin/bash | #!/bin/bash | ||
#PBS -q hpsee | #PBS -q hpsee | ||
- | #PBS -l nodes= | + | #PBS -l nodes=4:ppn=8 |
#PBS -l walltime=10:00:00 | #PBS -l walltime=10:00:00 | ||
#PBS -e ${PBS_JOBID}.err | #PBS -e ${PBS_JOBID}.err | ||
#PBS -o ${PBS_JOBID}.out | #PBS -o ${PBS_JOBID}.out | ||
+ | export OMP_NUM_THREADS=8 | ||
cd $PBS_O_WORKDIR | cd $PBS_O_WORKDIR | ||
chmod +x job | chmod +x job | ||
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- | / | + | ${MPI_OPENMPI_MPIEXEC} -np 4 -npernode 1 ./job |
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8. Submit job : | 8. Submit job : | ||
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cat <jobID>.ce64.ipb.ac.rs.out | cat <jobID>.ce64.ipb.ac.rs.out | ||
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Latest revision as of 07:15, 13 October 2011
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