WestGrid Seminar Series Copyright © 2006 University of Alberta. All rights reserved Integrating...

Copyright © 2006 University of Alberta. All rights reserved

WestGrid Seminar Series

Integrating GridstoreInto The Job Submission

ProcessWith GSUB

Edmund Sumbar

University of Alberta

Copyright © 2006 University of Alberta. All rights reserved create deleteJanuary 25, 2006 2

GSUB

Gridstore…• close proximity to vizserver

• does not impose quotas

• has a large capacity

• performs backups


GSUB

time gcp gridstore:largefile .

glacier lattice *matrix nexus cortex

10MB 4 5 8 6 5

100MB 14 7 70 40 170

1GB 120 55 ~600 440 ~4000

Data collected January 11, 2006.

* Using scp, gcp not installed yet.


GSUB

Job submission protocol…• copy files from gridstore to execution site (gcp)

• submit job (qsub)

• wait for job to end (qstat)

• copy files from execution site to gridstore (gcp)


GSUB

desktop

user


GSUB

{execution nodes

desktop

user

head node

exec site


GSUB

{execution nodes

desktop

user

head node

exec site

gridstore


GSUB

{execution nodes

desktop

user

head node

exec site

head node

home site

gridstore


GSUB

ssh {execution nodes

desktop

user

head node

exec site

head node

home site

gridstore


GSUB


desktop

user

head node

exec site

head node

home site

grid-proxy-init

gridstore


GSUB


desktop

user

head node

exec site

head node

home site

grid-proxy-init

ssh

gridstore


GSUB


desktop

user

head node

exec site

gridstore

head node

home site

grid-proxy-init

ssh

gcp


GSUB


desktop

user

head node

exec site

gridstore

head node

home site

grid-proxy-init

ssh qsub

gcp


GSUB


desktop

user

head node

exec site

gridstore

head node

home site

grid-proxy-init

ssh qsub

gcp gcp


GSUB


desktop

user

head node

exec site

gridstore

head node

home site

grid-proxy-init

ssh qsub

gcp gc

p

1

2

3

4

5

6


GSUB

Becomes tedious/inefficient/error-prone

Automate process with scripts…


GSUB

Consider gsub…


GSUB

Consider gsub…• No changes are required to your existing Torque (PBS)

job scripts


GSUB

Consider gsub…• No changes are required to your existing Torque (PBS)

job scripts

• All qsub command-line options are supported


GSUB

{execution nodes

desktop

user

head node

exec site

gridstore

head node

home site


GSUB


desktop

user

head node

exec site

head node

home site

gridstore


GSUB


desktop

user

head node

exec site

head node

home site

grid-proxy-init

gridstore


GSUB


desktop

user

head node

exec site

head node

home site

grid-proxy-init

ssh

gridstore


GSUB

{execution nodes

head node

exec site

ssh

desktop

user

gridstore

head node

home site

grid-proxy-init

ssh gsub


GSUB


desktop

user

head node

exec site

gridstore

head node

home site

grid-proxy-init

ssh gsub

gcp


GSUB


desktop

user

head node

exec site

gridstore

head node

home site

grid-proxy-init

ssh gsub

gcp

stage in


GSUB


desktop

user

head node

exec site

gridstore

head node

home site

grid-proxy-init

ssh qsub

gcp gcp


GSUB


desktop

user

head node

exec site

gridstore

head node

home site

grid-proxy-init

ssh qsub

gcp gcp

stage out


GSUB


desktop

user

head node

exec site

gridstore

head node

home site

grid-proxy-init

ssh gsub

gcp

gcp

1

2

3

4


GSUB

Demonstration…


GSUB


GSUB


desktop

user

head node

exec site

gridstore

head node

home site

grid-proxy-init

ssh gsub

gcp

gcp


GSUB


desktop

user

head node

exec site

gridstore

head node

home site

grid-proxy-init

ssh gsub

gcp

gcp

blackhole(gridstore head node)

ssh• prepare input

• analyze output


GSUB

Submit jobs directly from blackhole…


GSUB

desktop

user {execution nodes

head node

gridstore

head node

home site


GSUB

desktop


head node

gridstore

head node

home site


GSUB

desktop


head nodeblackhole

gridstore


GSUB

desktop


head nodeblackhole

ssh

gridstore


GSUB

desktop


head nodeblackhole

ssh

myproxy-get-delegation

gridstore


GSUB

head nodeblackholedesktop


ssh


gridstore

gsub


GSUB

desktop


head nodeblackhole

ssh


gsub gsub

gridstore


GSUB

desktop


head nodeblackhole

ssh


gsub gsub

gridstore

gcp


GSUB

desktop


head nodeblackhole

ssh


gsub gsub

gridstore

gcp gc

p


GSUB

desktop


head nodeblackhole

ssh


gsub gsub

gridstore

gcp

gcp

1

2

3


GSUB

Demonstration…


GSUB


GSUB

Tools for monitoring and managing jobs• gstat

• gdel

• glog


GSUB

Demonstration…


GSUB


GSUB

View WestGrid like a scaled-up execution

site…


GSUB

desktop


head node


GSUB

desktop

user

{


GSUB

desktop

user

{{


GSUB

desktop

user

{{{


GSUB

{desktop

user

{{{


GSUB

{desktop

user

{{{

blackhole

super head node


GSUB

{desktop

user

{{{

blackhole

super head node

myproxy

credential server


GSUB

{desktop

user

{{{

blackhole

super head node

myproxy

credential server

gridstore

file system


GSUB

{desktop

user

{{{

blackhole

super head node

myproxy

credential server

gridstore

file system

WestGrid


GSUB

DISCLAIMER

The opinions expressed herein are those of

the author and do not necessarily represent

the views of WestGrid management.


GSUB

Gsub implements programmable workflow

Specify actions to be executed at various

times (phases) during the life of a job• before stage in

• after stage in

• job start

• job end

• before stage out

• after stage out


GSUB

Workflow programmed as a case statement

case $phase in beforestagein ) exit ;; afterstagein ) exit ;; jobstarted ) exit ;; jobended ) exit ;; beforestageout ) exit ;; afterstageout ) if some condition is true; then resubmit fi exit ;;esac


GSUB

Predefined workflows• email

• prevent

• tidy

• autoresub

• exclusive

• aggressive


GSUB

No script modifications required

Specified at submission time• gsub jobscript=workflow

Cascade workflows• gsub jobscript=workflow1+workflow2


GSUB

Demonstration…


GSUB


GSUB

Gsub is unsuitable for…• very short jobs

• developing, testing, debugging programs

• staging very large or very many files


GSUB

Gsub is not officially accepted by WestGrid

Still needs testing in the real world…


GSUB

Gsub is not officially accepted by WestGrid

Still needs testing in the real world…

…any volunteers?


GSUB

Questions…

WestGrid Seminar Series Copyright © 2006 University of Alberta. All rights reserved Integrating...

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