How to clear a PBS job dependency using qalter?

Question

Say I sent a job with a dependency using qsub -W depend=afterok:JOBID to the cluster, how to I clear it with qalter command (using PBSpro scheduler)? I found Some info in the qalter man page, but couldn't find how to clear it, just how to create a new dependency.

Answer 1

With a little help from some friends I got an answer, apparently I had to submit a qalter command to alter the dependency, but instead of specifying a new JOBID, just omitting the :JOBID.

Example:

Submit a job that depends on successful completion of a previous job (say 1234)

qsub -q my_queue -l ... -W depend=afterok:1234 file.pbs

The newly submitted job will stay on-hold until job 1234 finishes with ExitStatus:0. We can check the JobId and status of the newly submitted job using the qstat command (its status should be H for Hold and say its Id is 1235). Then if we decide that we don't need to wait for the first command to finish, we can clear the dependency:

qalter -W depend=afterok 1235

Note that I ommited the colon and the dependency Id after afterok and that qalter requires the JobId it's altering as its last argument.