Deprecated: please see new documentation site.

Useful PBS commands

qsub for submitting job

The command qsub is used to send a batch job to PBS. The basic usage is

qsub pbs.script 

where pbs.script is the scrip users write to specify their needs. qsub also accept command line arguments, which will overwrite those specified in the script, for example, the following command

qsub myscript -A my_LONI_allocation2

will direct the system to charge SUs (service units) to the allocation my_LONI_allocation2 instead of the allocation specified in myscript.

qstat for checking job status

The command qstat is used to check the status of PBS jobs. The simplest usage is


which would give informations similar to the following:

Job id              Name             User            Time Use S Queue
------------------- ---------------- --------------- -------- - -----
2572.eric2          s13pic           cott            00:00:00 R checkpt
2573.eric2          s13pib           cott            00:00:00 R checkpt
2574.eric2          BHNS02_singleB   palenzuela             0 Q checkpt
2575.eric2          BHNS02_singleC   palenzuela      00:00:00 R checkpt
2576.eric2          BHNS02_singleE   palenzuela      00:00:00 R checkpt
2577.eric2          BHNS02_singleF   palenzuela      00:00:00 R checkpt
2578.eric2          BHNS02_singleD   palenzuela      00:00:00 R checkpt
2580.eric2          s13pia           cott                   0 Q workq

The first column to the six column show the id of each job, the name of each job, the owner of each job, the time consummed by each job, the status of each job (R corresponds to running, Q correcponds to in queue ), and which queue each job is in. qstat also accepts command line arguments, for instance, the following usage gives more detailed information regarding jobs.

[ou@eric2 ~]$ qstat -a
                                                                   Req'd  Req'd   Elap
Job ID               Username Queue    Jobname    SessID NDS   TSK Memory Time  S Time
-------------------- -------- -------- ---------- ------ ----- --- ------ ----- - -----
2572.eric2           cott     checkpt  s13pic      28632     6   1    --  48:00 R 24:51
2573.eric2           cott     checkpt  s13pib      13753     6   1    --  48:00 R 15:29
2574.eric2           palenzue checkpt  BHNS02_sin    --      8   1    --  48:00 Q   --
2575.eric2           palenzue checkpt  BHNS02_sin  10735     8   1    --  48:00 R 08:04
2576.eric2           palenzue checkpt  BHNS02_sin  30726     8   1    --  48:00 R 07:52
2577.eric2           palenzue checkpt  BHNS02_sin  24719     8   1    --  48:00 R 07:51
2578.eric2           palenzue checkpt  BHNS02_sin  23981     8   1    --  48:00 R 07:31
2580.eric2           cott     workq    s13pia        --      6   1    --  48:00 Q   --

qdel for cancelling a job

To cancel a PBS job, enter the following command.

qdel job_id [job_id] ...

qfree to qury free nodes in PBS

One useful command for users to schedule their jobs in an optimal way is "qfree", which shows free nodes in each queue. For example,

[ou@eric2 ~]$ qfree
PBS total nodes: 128,  free: 14,  busy: 111 *3,  down: 3,  use: 86%
PBS checkpt nodes: 128,  free: 14,  busy: 98
PBS workq nodes: 64,  free: 14,  busy: 10
PBS single nodes: 16,  free: 14,  busy: 1
(Highest priority job on queue workq will start in 6:47:09)

shows that there total 14 free nodes in PBS, they are available in all the three queues: checkpt, workq and single.

showstart for estimating the starting time for a job

The command showstart can be used to get an approximate estimation of the starting time of your job, the basic usage is

showstart job_id

The following shows an simple example:

[ou@eric2 ~]$ showstart 2928.eric2
job 2928 requires 16 procs for 1:00:00:00 
Estimated Rsv based start in                 7:28:18 on Wed Jun 27 16:46:21
Estimated Rsv based completion in         1:07:28:18 on Thu Jun 28 16:46:21 
Best Partition: base

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