Batch Jobs

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Any kind of calculation on the compute nodes of bwUniCluster requires the user to define calculations as a sequence of commands or single command together with required run time, number of CPU cores and main memory and submit all, i.e., the batch job, to a resource and workload managing software. All bwHPC cluster, including bwUniCluster, have installed the workload managing software MOAB. Therefore any job submission by the user is to be executed by commands of the MOAB software. MOAB queues and runs user jobs based on fair sharing policies.

MOAB commands Brief explanation
msub submits an job and queues it in an input queue
checkjob displays detailed job state information
showq displays information about active, eligible, blocked, and/or recently completed jobs
showbf shows what resources are available for immediate use

1 Job Submission

Batch jobs are submitted using the command msub. The main purpose of the msub command is to specify the resources that are needed to run the job. msub will then queue the job into the input queue. The jobs are organized into different job classes. For each job class there are specific limits for the available resources (number of nodes, number of CPUs, maximum CPU time, maximum memory etc.).

1.1 msub Command

The syntax and use of msub can be displayed via:

$ man msub

msub options can be used from the command line or in your job script.

msub Options
Command line Script Purpose
-l resources #MSUB -l resources Defines the resources that are required by the job. See the description below for this important flag.
-N name #MSUB -N name Gives a user specified name to the job.
-I Declares the the job is to be run interactively.
-o filename #MSUB -o filename Defines the path to be used for the standard output stream of the batch job.
-V #MSUB -V Declares that all environment variables in the msub environment are exported to the batch job.

1.1.1 msub -l resource_list

The -l option is one of the most important msub options. It is used to specify a number of resource requirements for your job. Multiple resource strings are separated by commas.

msub -l resource_list
resource Purpose
-l nodes=1
-l nodes=2:ppn=8
Number of nodes
Number of nodes and number of processes per node
-l walltime=600
-l walltime=1:30:00
Wall-clock time. Default units are seconds.
HH:MM:SS format is also accepted.
-l feature=tree
-l feature=blocking
-l feature=fat
For jobs that span over several nodes
For sequential jobs
For jobs that require up to 1 TB memory
-l pmem=1000mb Memory per process, allowed units are kb,mb,gb.

1.2 msub Examples

1.2.1 Serial Programs

To submit a serial job that runs the script and that requires 5000 MB of main memory and 3 hours of wall clock time execute:

$ msub -N test -l nodes=1:ppn=1,walltime=3:00:00,pmem=5000mb

or add to the script the lines:

#MSUB -l nodes=1:ppn=1
#MSUB -l walltime=3:00:00
#MSUB -l pmem=5000mb
#MSUB -N test

and execute the modified

$ msub

1.2.2 Multithreaded Programs

1.2.3 Parallel MPI Programs

2 Display Status of submitted Jobs

3 Environment Variables for Batch Jobs