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How-to for clearing a job in R state that is not running, no SessID or Elapsed time

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Clear a hung (zombie) vnode

22-April-2014:  PBS Pro version 12.0 installed on SLES 11 SP2 running on an SGI UV1000



PBS Pro qstat reports a job or jobs in R state without a SessID or Elapsed Time

  • The job is not running on the OS nor is there an existing vnode cpuset, look in /dev/cpuset/PBSPro, there will not be a cpuset directory for the affected Job
  • The qdel is ineffective


How-to resolve:

  1. Use  “qstat –r“ to list the affected jobs
  2. Use  “qalter –r y PBS_JobID“ to mark the job rerunable
  3. You can check it is now marked rerunable, “qstat –f PBS_JobID | grep Rerunable”  should return  “Rerunable = True
  4. Use  “qrerun –W force PBS_JobID”  to re-queue job
  5. You can check it is re-queued,  “qstat –a” will list the job in Q state
  6. Use  “qdel PBS_JobID” to terminate job



               Fixing several nodes at the same time, targeting a particular user:


                        qstat –ru a_users_id


                        qalter –r –y PBS_JobID_1  PBS_JobID_2  PBS_JobID_3  PBS_JobID_4


                qstat –f PBS_JobID_1  PBS_JobID_2  PBS_JobID_3  PBS_JobID_4 | grep Rerunable


                qrerun –W force PBS_JobID_1 PBS_JobID_2  PBS_JobID_3  PBS_JobID_4


                qstat –au a_users_id


                qdel PBS_JobID_1  PBS_JobID_2  PBS_JobID_3  PBS_JobID_4

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