using pbspro

Using PBSpro

IS&T Advanced Campus Services

04/22/23 Using PBSpro, IS&T Advanced Campus Services 2

Syllabus Introduction to PBS Submitting a job Job examples Checking job/system status Working with PBS jobs Some tips Summary


Introduction PBS: Portable Batch System PBSpro: PBS Professional

Enhanced commercial version Originally developed for NASA Altair Grid Technology www.pbspro.com

http://www.pbspro.com/


Why use PBS? Features and benefits

Enterprise-wide resource sharing Cross-system scheduling Automatic load-leveling Distributed clustering Computational grid support Parallel job support Broad platform availability …


PBS components Commands: command

line & graphic interface Server: job server

daemon/service—central focus of PBS

Job executor (MOM): which actually places jobs into execution

Scheduler: implements the site’s policy controlling when each job is run and on which resources


Submitting a job To run a PBS job, we use the

command: qsub

Two ways of job submission Job without a job script Submitting with a job script


Job without a job script PBS reads input from the keyboard

Stop reading input and submit the job by “control-d” (UNIX) or “control-z”, then “enter” (Windows)

“control-c” (UNIX) or “control-break” (Windows) to terminate the qsub command qsub

[directives] [tasks]ctrl-d


Submitting a job script Type “qsub script_name”

PBS returns a job identifier sequence-number.servername.domain Job identifier is needed for any actions

involving the job, such as checking job status, deleting the job

qsub myjob


Script format A PBS job script consists of:

An optional shell specification (UNIX) The first line of the script Bourne shell (sh) is the default

PBS directives At the top the script Begins with “#PBS” Used to request resources or job control options

Tasks—programs or commands Where the user specifies an application to be run


Job submission options Specify a job name

-N name

Resources related options System resources request

-l resources_list Single-node conditional request

-l resc=resc_spec Multi-node jobs

-l nodes=node_sepc

qsub –N counter myjob


System resources arch: system architecture cput: max, aggregate CPU time file: max disk space requirements host: name of request host/node mem: max amount of physical memory ncpus: number of CPUs nodes: number and/or type of nodes resc: single-node resource specification vmen: max, aggregate amount of virtual memory walltime: max amount of real time …


Single-node conditional request

Use boolean logic in the specification of certain resources within a single node -l resc=resc_spec Provides more control over selecting

nodesqsub –l resc=“(arch==‘UNIX’)&&(ncpus==4)” myjob


Job submission options (cont)

Specify queue and/or server, where to submit

-q [queue[@host]]

Redirect output & error files -o/-e path

Specify job checkpoint interval -c interval (minutes)

qsub –q [email protected] myjob

qsub –o MyOutputFile myjob

qsub –c c=10 myjob


Job submission options (cont)

Specify job user ID at different server -u UserID@server

Specify email notification -m MailOptions

Set email recipient list -M user_list

Set a job’s priority -p priority

qsub -u astcxx@node1,cscxx@node2 myjob

qsub –m abe myjob

qsub –M astcxx@node1,cscxx@node2 myjob

qsub –p 300 myjob


Examples Submitting a job through command

line:qsub –l walltime=5 –l mem=100mb –j oe awk 'BEGIN {for(i=0;i<10000;i++)for(j=0;j<10000;j++);}‘ctrl-d


Examples (cont) Submitting a using a job script

Below is the contents of script file myjob#!/bin/sh

#PBS –l walltime=5#PBS –l mem=100mb#PBS –j oe awk 'BEGIN {for(i=0;i<10000;i++)for(j=0;j<10000;j++);}'

qsub myjob


Check job status Display job information

qstat


Check server status Display

the status of the specified PBS server qstat –Bf


Check queue status Display the status of all queues on

the PBS server qstat -Qf


View job information Print all

information known about the job qstat –f

job_identifier


List user-specific jobs Display jobs owned by specified user

name qstat –u user_name


Modify job attributes Change an attribute on a job

previously submitted qalter job_resources job_list

If any of the specified attributes cannot be modified for a job for any reason, none of that job’s attributes will be modified

qalter –l walltime=20:00 –N Example 56


Hold, release & delete jobs

Hold a job qhold [-h hold_list] job_identifier

Release a job qrls [-h hold_list] job_identifier

Delete jobs from the system qdel job_identifier

qhold –h u 56

qrls –h u 56

qdel 56


Change order of jobs in queue

Change the order (reorder) two jobs qorder job_identifier1 job_identifier2


Move jobs between queues

Move jobs between different queues (even queues on different servers) qmove destination job_identifier(s)

qmove queue@node1 56


Some tips Directives inputed in command lines

override those in job scripts Use “” to brace directive values

which contains one or more blanks Difference between

“==”(comparison) and “=”(assignment)


Summary How to submit a job Job examples How to check job/system status How to work with PBS jobs


References PBS Professional 7 Quick Start PBS Professional 7 User Guide PBS Professional 7 Administration

Guide www.pbspro.com

http://www.pbspro.com/

Thank you!

Contacts: Bill Xie

[email protected] Victor Bolet [email protected]

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