DataScience Workbook / 06. High-Performance Computing (HPC) / 5. Introduction to Job Scheduling / 5.2 PBS: Portable Batch System / 5.2.2 Submitting Dependency Jobs using PBS


Submitting dependency jobs using PBS-Torque

To submit jobs one after the other (i.e., run second job after the completion of first), we can use depend function of qsub.

First submit the firstjob, like normal

qsub first_job.sub

You will get the output (jobid#)


Second submit the second job following way,

qsub -W depend=afterok:1234567 second_job.sub

Both job will be queued, but second job won’t start till the first job is finished.

The other dependencies that can be used with -W depend=dependency:jobid are

Argument Description
after this job can be scheduled after job jobid begins execution.
afterok this job can be scheduled after job jobid finishes successfully.
afternotok this job can be scheduled after job jobid finishes unsucessfully.
afterany this job can be scheduled after job jobid finishes in any state.
before this job must begin execution before job jobid can be scheduled.
beforeok this job must finish successfully before job jobid begins
beforenotok this job must finish unsuccessfully before job jobid begins
beforeany this job must finish in any state before job jobid begins

Simple way to automate this with a bash script:

FIRST=`qsub first_job.sub`
SECOND=`qsub -W depend=afterok:$FIRST second_job.sub`
THIRD=`qsub -W depend=afterok:$SECOND third_job.sub`
FOURTH=`qsub -W depend=afterok:$THIRD fourth_job.sub`

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