DataScience Workbook / 06: High-Performance Computing (HPC) / 5. Introduction to job scheduling / 5.2. PBS: Portable Batch System / 5.2.3. 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.

Submit the first job, like usual:

qsub first_job.sub

You will get the output (jobid#):

1234567.computername

Then, submit the second job like this:

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.

other dependency types

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

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

automate the process

here is an example on how to automate the sequence of job execution within a bash script:

#!/bin/bash
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`

Submitting dependency jobs using PBS

Arun Seetharam

Submitting dependency jobs using PBS-Torque

other dependency types

automate the process

Further Reading