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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 batch system uses the TORQUE resource manager (based on OpenPBS) and the Maui scheduler. It can be accessed from any Linux desktop using the commands described below.

The current composition of the batch system is as follows:

Nodes Operating System Total CPU Cores
node123 to node456 SL5 999

The following queues are provided:

Name Operating System Maximum runtime
short5 SL5 1 hour
medium5 SL5 6 hours
long5 SL5 1 day
vlong5 SL5 5 days
short6 SL6 1 hour
medium6 SL6 6 hours
long6 SL6 1 day
vlong6 SL6 5 days

Using PBS

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>

To submit a job defined by the submission script test.pbs:

$ qsub test.pbs

More details can be found in the qsub man page.

Show running jobs

Queues

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 Pre-emption

Jobs in the vlong4 and vlong5 queues can be preempted by jobs waiting in the short4, short5, medium4 or medium5 queues. A preempted job is placed in the suspended state - it remains in memory but is not longer being executed. Once the preempting job has finished the preempted job starts executing again.

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.

Killing a job

Jobs may be terminated by executing qdel JOBID where the JOBID is the numerical ID code returned in the qstat listing.

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Topic revision: r12 - 2016-04-22 - GordonStewart
 
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