General Usage of Hydra: Difference between revisions
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(Created page with "<ul> <li>Login <pre> ssh hydra </pre> </li> <li>Example of job.pbs file <pre> ### AUTOMATICALLY GENERATED BATCH FILE # ### name of job #PBS -N [name_] # ### mail for begi...") |
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# ### name of job |
# ### name of job |
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#PBS -N [ |
#PBS -N [name_of_job] |
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# ### mail for begin/end/abort |
# ### mail for begin/end/abort |
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#PBS -m ea |
#PBS -m ea |
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#PBS -M |
#PBS -M [email_address] |
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# ### maximum |
# ### maximum wall time |
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####PBS -l cput=5000:00:00 |
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#PBS -l walltime=30:00:00:00 |
#PBS -l walltime=30:00:00:00 |
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# # ### queue |
# # ### queue |
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###PBS -q |
###PBS -q [queue] |
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# ### indicates that job should not rerun if it fails |
# ### indicates that job should not rerun if it fails |
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#PBS -S /bin/bash |
#PBS -S /bin/bash |
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cd /home/[job_location] |
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cd /home/zonghui/Scratch/Multi_chain/Double_length_DNA_experiment/ppa12.peg5_cr_5_double_ka_4/ppa.cat12.pegcat2.peg5 |
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#mpirun -np 2 /opt/lammps/lmp2013_mpi -in input.dat |
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time /opt/lammps/lmp2013 < input.dat |
time /opt/lammps/lmp2013 < input.dat |
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#/home/wei/Install/lammps/current/src/lmp_suse_linux < input.dat |
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if [ $? -eq 0 ] ; then |
if [ $? -eq 0 ] ; then |
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fi |
fi |
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</pre> |
</pre> |
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<tt>[ |
<tt>[name_of_job]</tt> |
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This is the |
This is the name of the job that will be showed in the queue. |
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<tt>[dd:hh:mm:ss]</tt> |
<tt>[dd:hh:mm:ss]</tt> |
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This is the maximum allowed running time for your job. dd: days; hh: hours; mm: minutes; ss: seconds. |
This is the maximum allowed running time for your job. dd: days; hh: hours; mm: minutes; ss: seconds. |
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<tt>[job_location]</tt> |
<tt>[job_location]</tt> |
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<li>Submit jobs |
<li>Submit jobs |
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<pre> |
<pre> |
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qsub job.pbs |
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</pre> |
</pre> |
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<li>Check job status |
<li>Check job status |
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<pre> |
<pre> |
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qstat |
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showq |
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</pre> |
</pre> |
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show all jobs |
show status of all jobs. |
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<pre> |
<pre> |
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qstat |
qstat -u [username] |
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</pre> |
</pre> |
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where <tt>[username]</tt> is your own user name. This command will show the status of your own jobs. |
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show your own jobs |
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</ul> |
</ul> |
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Revision as of 17:50, 9 June 2014
- Login
ssh hydra
- Example of job.pbs file
### AUTOMATICALLY GENERATED BATCH FILE # ### name of job #PBS -N [name_of_job] # ### mail for begin/end/abort #PBS -m ea #PBS -M [email_address] # ### maximum wall time #PBS -l walltime=30:00:00:00 # ### number of nodes and processors per node #PBS -l nodes=1:ppn=1 # # ### queue ###PBS -q [queue] # ### indicates that job should not rerun if it fails #PBS -r n # ### stdout and stderr merged as stderr #PBS -j eo # ### write stderr to file #PBS -e log.err # ### the shell that interprets the job script #PBS -S /bin/bash cd /home/[job_location] time /opt/lammps/lmp2013 < input.dat if [ $? -eq 0 ] ; then touch COMPLETED fi
[name_of_job] This is the name of the job that will be showed in the queue.
[email_address] This is the email address you used to receive the system notice when job begins, aborted or ended.
[dd:hh:mm:ss] This is the maximum allowed running time for your job. dd: days; hh: hours; mm: minutes; ss: seconds.
[job_location] This is the address of the folder where your input file is located.
- Submit jobs
qsub job.pbs
- Check job status
qstat
show status of all jobs.
qstat -u [username]
where [username] is your own user name. This command will show the status of your own jobs.