PBS: How to submit jobs that depend on previously submitted jobs?

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

You can also automate this step using a simple 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)