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Batch System

The PPE group maintains a PBS cluster for running small quantities of jobs. If you need to run large numbers of jobs, you should investigate the possibility of running on ScotGrid. The current composition of the batch system is as follows:

Nodes Operating System Total CPU Cores
node007 Scientific Linux 6 40
node008 Scientific Linux 5 4
node013 to node017 Scientific Linux 5 20
node019 Scientific Linux 6 4
node034 Scientific Linux 6 56
tempnode001 to tempnode006 Scientific Linux 5 24
tempnode007 to tempnode015 Scientific Linux 6 36

The following queues are provided:

Name Operating System Maximum runtime
short5 Scientific Linux 5 1 hour
medium5 Scientific Linux 5 6 hours
long5 Scientific Linux 5 1 day
vlong5 Scientific Linux 5 5 days
short6 Scientific Linux 6 1 hour
medium6 Scientific Linux 6 6 hours
long6 Scientific Linux 6 1 day
vlong6 Scientific Linux 6 5 days

Jobs running in the vlong* queues can be pre-empted by jobs in the short* and medium* queues. A pre-empted job is placed in the suspended state; it remains in memory on the compute node, but is no longer being executed. Once the pre-empting job has finished, the pre-empted job will be allowed to continue.

The PBS headnode is, and you will see this name in the output of various PBS commands.

Using PBS

Batch jobs can be submitted and managed from any Linux desktop using the commands described in this section. Further information on these commands can be found in the linked documentation and Linux man pages at the bottom of this page.

Create a submission script

Jobs are defined using a submission script, which is like a shell script with the addition of certain directives (indicated by the #PBS prefix) which tell PBS how the job should be handled. A simple submission script might look like the following:

#PBS -N TestJob
#PBS -l walltime=1,mem=1024Mb
#PBS -m abe
#PBS -M user@machine
echo "This is a test..."

Submit a job

Jobs are submitted using the qsub command:

$ qsub <FILENAME>

After running this command, the ID of the newly-submitted will be output. For example, to submit a job defined by the submission script test.pbs:

$ qsub test.pbs

The numerical portion of this ID (1000150 in this example) can be used to manage the job in the future.

Show running jobs

You can view details of submitted jobs using the qstat command:

$ qstat
                                                                         Req'd  Req'd   Elap
Job ID               Username Queue    Jobname          SessID NDS   TSK Memory Time  S Time
-------------------- -------- -------- ---------------- ------ ----- --- ------ ----- - -----
1000151.offler.p     rrabbit  medium6  maus_sim_814      56289     1   1    --  05:59 R 03:21   node034
1000152.offler.p     bbunny   long6    test_job          29669     1   1    --  24:00 R 01:24   node007



There are currently eight queues on the batch system. The four queues ending in '4' will run jobs on SL4 machines and the four queues ending in '5' will run jobs on SL5 machines:

Queue            Memory CPU Time Walltime Node  Run Que Lm  State
---------------- ------ -------- -------- ----  --- --- --  -----
short4             --      --    01:00:00   --    0   0 --   E R
medium4            --      --    06:00:00   --    0   0 --   E R
long4              --      --    24:00:00   --    0   0 --   E R
vlong4             --      --    120:00:0   --    0   0 --   E R
short5             --      --    01:00:00   --    0   0 --   E R
medium5            --      --    06:00:00   --    0   0 --   E R
long5              --      --    24:00:00   --    0   0 --   E R
vlong5             --      --    120:00:0   --    0   0 --   E R

where short5 is the default queue and Walltime is the maximum walltime allowed on each queue.

While it is possible to view your own jobs with qstat, the command will not display all jobs. To display all jobs use the Maui client command showq

To see the current priorities of waiting jobs use the command showq -i.

Job Priority

The priority of a job is the sum of several weighting factors.

  • There is a constant weighting given to short jobs and smaller weighting given to medium and long jobs. So that if all other factors are equal short jobs will have priority.
  • The primary weighting is user fairshare. As a users jobs run their usage increases and the priority of their queued jobs decreases. This is balanced so that a user who uses exactly their fairshare allotment (currently 20% of the cpu averaged over the previous 48 days) will have their medium job priority decreased such that the medium job priority is equal to someone else's vlong job priority who has not used the batch system in the previous 48 days.
  • Waiting jobs priority slowly increases as a function of time waiting in the queue. Currently a vlong job would have to wait several weeks to match the priority of a medium queue job all other things being equal.

Delete a job

Jobs are deleted using the qdel command:

$ qsub <JOB_ID>

To delete the job with ID 12345:

$ qdel 12345


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Topic revision: r13 - 2016-04-22 - GordonStewart
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