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Sierra User Guide: Running Jobs

Sierra uses the TORQUE Resource Manager (also known by its historical name Portable Batch System (PBS)) with the Moab Workload Manager to define and manage job queues. TORQUE allows the user to submit one or more jobs for execution, using parameters specified in a job script. Users have options for runing in batch mode are:
Queue Name Limits Comments
normal/short max wallclock = 24 hours Used for short to normal length jobs.
long max wallclock = 168 hours Used for longer-running jobs.

Batch Jobs

Example Script:

[user@sierra]$ cat script
# the queue to be used.
#PBS -q normal
# number of nodes and number of processors per node requested
#PBS -l nodes=8:ppn=8
# requested Wall-clock time.
#PBS -l walltime=HH:MM:SS
# name of the standard out file to be "output-file".
#PBS -o job_output
# name of the job
cd $PBS_O_WORKDIR #change to the working directory
mpirun -np 256 -hostfile $PBS_NODEFILE <executable>

Submit the job via:

[user@sierra]$ qsub <batch_script>

Monitoring Batch Queues

Users can monitor batch queues using the qstat and showq commands. Common qstat options are as follows:

Command Description
qstat -a Display the status of batch jobs
qdel <pbs_jobid> Delete (cancel) a queued job
qstat -r Show all running jobs on system
qstat -f <pbs_jobid> Show detailed information of the specified job
qstat -q Show all queues on system
qstat -Q Show queues limits for all queues
qstat -B Show quick information of the server
pbsnodes -a Show node status

View the qstat manpage for more options.

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