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PBS Commands

A list of useful PBS Pro commands can be found below.

If HPC users would like more information, a very useful PBS Pro User Guide (320 pages) can be found at http://www.pbsworks.com/documentation/support/PBSProUserGuide11.2.pdf and a PBS Pro reference guide (592 pages) can also be found at http://www.pbsworks.com/documentation/support/PBSProRefGuide11.1.pdf.

CommandDescriptionUsage ExampleEffect
qsub Submit a jobqsub myjobSubmits the job "myjob" for the execution.
qstat  Show status of batch jobsqstat -u belljShow the status of all the jobs submitted by the user bellj (Jason Bell).
qdel Delete a jobqdel 3221.pbsserverDeletes the job with job id 3221.
qalter  Alter a job's attributesqalter -l ncpus = 4 : mem: 512 230.pbsserverChanges the attributes of the job 230.
qhold  Place a hold on a job to keep it from being scheduled for runningqhold 54.pbsserverPuts the user hold on job 54.
qmove  Move a job to a different queue or serverqmove test_queue 43.pbsserverMoves job 43 from original queue to test_queue ( may require privileges).
qmsg  Append a message to the output of an executing jobqmsg -o "output file message" 54.pbsserverWrites the message to the output file of job 54.
qrerun  Terminate an executing job and return it to a queueqrerun 54.pbsserverTerminates the running job 54 and returns it into the queue.
qrls  Remove a hold from a jobqrls -h u 54.pbsserverReleases the user type hold from the job 54.
qselect  Obtain a list of jobs that meet certain criteriaqselect -u barry -l ncpus.gt. 16.pbsserverGives a list of jobs that are owned by user barry and have used cpu's > 16.
qsig  Send a signal to an existing jobqsig -s Kill 34.pbsserverThis command would send kill signal to the job 34.
xpbs  GUI front to PBS commandsxpbsRuns the GUI interface to the PBS.

qsub options

OptionDescription
-I

Declares that the job is to be run "interactively".

Default: Run in a batch job, if the option is not specified.

-j
{oe,eo,n}
  • oe merges standard error to standard output;
  • eo merges standard output to standard error.

Default n, or if the option is not specified, standard output and standard error are two separate files

-o path 

The name of the file for standard output.

Default: job_name.osequence_number if the option is not specified.

-e path 

The name of the file for standard error.

Default: job_name.esequence_number if the option is not specified.

-l resource_list 
-m
{a,b,e,n}

Mail is sent:

  • a when the job is aborted by PBS
  • b when the job begins execution
  • e when the job terminates.

Default n or if option is not specified: no mail is sent.

-M user_list 

List of users for the option -m.

Give here mail address(es).

Default: job owner if unset.

-N job_name 

The job name.

Default: is based on the name of the job script if the option is not specified, STDIN if no script and it was read from standard input.

-q destinationDestination of the job. destination names a queue, a server or a queue at a server
-v variable_list Environment variables exported to the job. variable_list is a comma separated list of the form variable or variable=value
-V All environment variables in the qsub command's environment are to be exported to the batch job.

qstat options

OptionDescription
(no options)Displays all jobs
-f Displays full status of jobs
-aDisplays all jobs in alternative format
-iDisplays jobs (non-running mainly) in alternative format
-rDisplays jobs (mainly running and suspended)
-nIn addition to the basic information, nodes  allocated  to  a  job  are  listed
-u user(s) Displays jobs of a user or users
-Q Status  of queues
-Q -f Full status of queues (configuration also)
-q Status of queues in the alternative format
-B Batch server status
-B -f Full batch server status (configuration also)

Job identifiers, queue names, PBS server names or named queues on named servers can be given as additional operands for these options. These restrict displayed information only to these items. For more information about these operands and the qstat command see the manual page qstat(1B).

Job status
Job status is displayed by the command qstat without options, or in an alternative format by using, e.g. the options -a, -i, -r, -n and -u without  -f.
When option -f is included, full job status, i.e., attributes including requested and used (if job is running) resources, is displayed.

Queue status
Queue status is displayed by options -q and -Q. Full queue status, i.e., queue attributes including resources (minimum and maximum limits and defaults), is displayed with options -Q -f.

Server status
Server status is displayed by the option  -B.
Full server status, i.e., server attributes including resources (limits and defaults), is shown by options -B -f.