Michael: Created page with "Scripts and commands for torque / maui (pbs) ==== Torque/Maui Commands ==== qsub submit_script.sh # submit Job qmgr print server # show the se..."

2013-05-13T10:04:05Z

Created page with "Scripts and commands for torque / maui (pbs) ==== Torque/Maui Commands ==== <syntaxhighlight> qsub submit_script.sh # submit Job qmgr print server # show the se..."

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Scripts and commands for torque / maui (pbs)

==== Torque/Maui Commands ====
<syntaxhighlight>
qsub submit_script.sh # submit Job

qmgr print server # show the server configuration/settings
qmgr print node compute-0-0 # show the compute nodes configuration/settings

qstat # list information about queues and jobs
qstat -q # list all queues on system
qstat -Q # list queue limits for all queues
qstat -a # list all jobs on system
qstat -au userid # list all jobs owned by user userid (returns jobid)
qstat -s # list all jobs with status comments
qstat -r # list all running jobs
qstat -f jobid # list all information known about specified job
qstat -Qf queue # list all information known about specified queue
qstat -B # list summary information about the PBS server
qstat -n # list nodes allocated to jobs
qstat -ans -u {username} # this will show the nodes, jobid's of a given {username}

qdel jobid # delete job jobid
qdel -p job (as root) # purge job from system, last resort
qalter jobid # modify the attributes of the job or jobs specified by jobid

pbsnodes -a # show nodes online and some node characteristics
pbsnodes -l # list which nodes are currently offline
pbsnodes -o compute-1-7 # set compute-1-7 to offline (no job will schedule to this node)
pbsnodes -c compute-1-7 # clear compute-1-7 offline node status

showq # shows the current queue status (decide by MAUI)
showq -u {username} # show the queue of jobs that belong to {username}
checkjobs -v {jobid} # show the status of job {jobid}
showbf # shows the total available cpus on the cluster
showbf -f {FEATURE} # shows the total available cpus with feature set {FEATURE} on the cluster.
showstart {jobid} # estimate when the job {jobid} will start/complete
checkjob {jobid} # information on the job that is running or being queued.
showstate # Check if any nodes are down... queue daemon not running
showstats # Stats about queue

</syntaxhighlight>

==== Submit Script Flags ====
<pre>
#PBS -I # submit an interactive job
#PBS -q queue_name # submit to a specific queue
#PBS -l nodes=6 # request 6 nodes
#PBS -l nodes=compute-0-0 # request only node compute-0-0
#PBS -l nodes=4:ppn=2 # request 4 nodes with 2 processes per node
#PBS -j oe # combine both stdout and stderr
#PBS -o output_filename
</pre>

==== Simple PBS Job Submit Script ====
<pre>
#!/bin/bash

# Import BASH variables
#PBS -S /bin/bash
#PBS -V

# Combine error/output and set outputfile
#PBS -j oe
#PBS -o qsub_hpl_output.log

# Request job to run on 46 nodes with 8 processes per node
#PBS -l nodes=46:ppn=8

# Change to the working directory
cd ${PBS_O_WORKDIR}

##########################################
# #
# Output some useful job information. #
# #
##########################################

NPROCS=`wc -l < $PBS_NODEFILE`
echo ------------------------------------------------------
echo ' This job is allocated on '${NPROCS}' cpu(s)'
echo 'Job is running on node(s): '
cat $PBS_NODEFILE
echo ------------------------------------------------------
echo PBS: qsub is running on $PBS_O_HOST
echo PBS: originating queue is $PBS_O_QUEUE
echo PBS: executing queue is $PBS_QUEUE
echo PBS: working directory is $PBS_O_WORKDIR
echo PBS: execution mode is $PBS_ENVIRONMENT
echo PBS: job identifier is $PBS_JOBID
echo PBS: job name is $PBS_JOBNAME
echo PBS: node file is $PBS_NODEFILE
echo PBS: current home directory is $PBS_O_HOME
echo PBS: PATH = $PBS_O_PATH
echo ------------------------------------------------------

# Launch the Job
date
/opt/openmpi/bin/mpirun -np $NPROCS -machinefile $PBS_NODEFILE ./xhpl
date

</pre>

* Use <tt>showstats</tt> to get details on user jobs.
<syntaxhighlight>

[root@fotcluster2 ~]# showstats -u | sort -n -k 3

|------ Active ------|--------------------------------- Completed -----------------------------------|
asmith 0 0 0.00 1 2.27 153600.0 2.53 322.2 2.40 ----- 0.00 0.00 0.00 4771.67 0.20
klangfeld 0 0 0.00 15 34.09 5567999.4 91.77 13068.4 97.45 ----- 0.00 0.00 0.00 21888.98 0.22
maustin 0 0 0.00 28 63.64 345666.6 5.70 20.5 0.15 ----- 0.08 0.00 0.00 5487.95 7.43
statistics initialized Thu Jan 1 01:00:00
user Jobs Procs ProcHours Jobs % PHReq % PHDed % FSTgt AvgXF MaxXF AvgQH Effic WCAcc

</syntaxhighlight>

Rocks: PBS - Revision history

Michael: Created page with "Scripts and commands for torque / maui (pbs) ==== Torque/Maui Commands ==== qsub submit_script.sh # submit Job qmgr print server # show the se..."