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#)
1234567.computername
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:
#!/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`