Job Submission

1
Job Submission

• Using PBSPro and
• Globus Job Commands

2
Overview

• Computational Resources
• Queuing Systems
• PBSPro
• Globus Toolkit

3
Computational Resources

• Hard Disks (permanent storage)
• Number of CPUs (processing power)
• CPU time (processing time)
• Physical memory (program size)
• All computers have limited resources
• These resources may span across multiple
  processors/machines
• How to allocate these resources fairly, amongst
  the many users?

4
Queuing Systems

• Holding area for pending requests
• A method for allocating the needed resources
  based on a user request
• Processing of requests dynamically, quickly and
  fairly
• Many differentimplementations

5
PBSPro

• Queuing System used to control the allocation of
  computational resources to user submitted jobs
• Allows optimal sharing of all resources
• Ensures that the limited resources arent
  over-run and exceeded
• Unattended processing of requests

6
PBS Queues

• Allows distribution of resources into clearly
  defined groups, called queues
• Queues can be defined by
• Maximum CPU time
• Number of CPUs available
• Memory needed
• Concurrently executing jobs
• Queuing schemes evolve over time as user requests
  and workload vary

7
Interacting With PBS

• qsub Submit a job to the queues
• qstat Check the status of a job
• qdel Delete a job from the queues
• qmgr Create/modify queue settings
• xpbs Monitor all queues and jobs

8
qsub Submit A Job

• To submit a job to the Queuing System, use qsub
• E.g. qsub test.sub
• Test.sub is a script file containing the commands
  to be executed
• qsub returns your QueueID, if the job was
  submitted successfully61606.master

9
Submit File For A Serial Job

• !/bin/bashPBS -l walltime20000PBS -l
  mem5mbPBS -j oePBS m becd Serial./test

10
Submit File For A Parallel Job

• !/bin/shPBS -l nodes4ppn2PBS -l
  walltime480000PBS -j oecd
  ./MPI/Examplesmpiexec ./test

11
qstat Check Job Status

• To check the status of a job submitted to the
  Queuing System, use qstatJob id
  Name User Time S
  Queue------------------ ----------
  ------------ ------------ -
  --------61395.master G5D2C ngs0140
  700040 R cpu1661494.master STDIN
  ngs0227 175840 R cpu161495.master
  STDIN ngs0227 181542 R
  cpu161496.master STDIN ngs0227
  181502 R cpu161497.master STDIN
  ngs0227 181342 R cpu161498.master
  STDIN ngs0227 181413 R
  cpu861555.master Co_V ngs0133
  205753 R cpu2461567.master 20_12
  ngs0234 003117 R cpu161576.master
  20_21 ngs0234 001159 R
  cpu461578.master 20_23 ngs0234
  000551 R cpu161580.master 20_25
  ngs0234 000309 R cpu1

12
qdel Delete A Job

• To delete a job submitted to the Queuing System,
  use qdel
• E.g. qdel QueueID qdel QueueID1 QueueID2

13
Globus Toolkit

• An open source toolkit for developing Grid based
  applications and connectivity
• Allocating computational resources on remote
  (Globus aware) machines for the execution of user
  submitted jobs

14
Globus Job Commands

• globus-job-run ltoptionsgt
• globus-job-submit ltoptionsgt
• globus-job-status URL
• globus-job-get-output URL

15
globus-job-run

• Allows you to run a job as though it were
  interactive, on a local or remote machine
• Dont actually need to log on to the machine
  itself
• Not submitted to the Queuing System
• Returns the programs output as though you were
  running interactively

16
globus-job-run Examples

• globus-job-run grid-data.man.ac.uk /bin/date
• globus-job-run grid-data.rl.ac.uk ./test
• globus-job-run \grid-compute.leeds.ac.uk/jobmanag
  er-pbs \-np 8 -x (jobtypempi)(environment
  \(NGSMODULES clusteruser)) ./MPI/test
• globus-job-run grid-data.rl.ac.uk -s ./test

17
globus-job-submit

• To submit a job through a Globus Job Manager
• Commands returns a URL to the programs
  outputhttps//grid-compute.leeds.ac.uk64167/5291
  /1094639422/
• The status and output of the job can be tested
  through this URL

18
globus-job-submit Examples

• globus-job-submit \grid-data.rl.ac.uk/jobmanager-
  pbs ./test
• globus-job-submit \grid-compute.leeds.ac.uk/jobma
  nager-pbs \-x (jobtypempi)(directory/home/bob/
  mpi) \(environment(NGSMODULES clusteruser))
  \(count8) ./mpi_program
• globus-job-submit \grid-data.man.ac.uk/jobmanager
  -pbs -s ./test

19
globus-job-status URL

• To get the status of a submitted job
• globus-job-status \https//gridcompute.leeds.ac.u
  k64167/5291/1094639422/
• Returns
• Pending, Active, Done, Failed

20
globus-job-get-output URL

• To retrieve the output of a job submitted through
  a Globus Job Manager
• globus-job-get-output \https//gridcompute.leeds.
  ac.uk64167/5291/1094639422/
• Returns the output of the program to the console