SARA Reken- en Netwerkdiensten ToPoS | 3 juni 2007

More efficient job submission

Evert Lammerts

SARA Computing and Networking Services

High Performance Computing and Visualization

e-Science Support

SARA Reken- en Netwerkdiensten

Job submission works!

But it’s up to YOU to monitor the cycle of a jobstrange return codes

does the job status (Success, Failed) really mean what you think it does

resubmit failed jobs

Etc, etc, etc…

Success rate: 70%

ToPoS | 3 juni 2007

SARA Reken- en Netwerkdiensten

Pilot Jobs I

Normally:

With Pilot jobs:

ToPoS | 3 juni 2007

SARA Reken- en Netwerkdiensten

Pilot Jobs II

Pilot jobs:Are basically loops

Find out what to do by fetching tasks

Run till there are no more tasks, or…

Run till they are out of Wall Time

Tasks:Contain parameters

Are served by ToPoS from a webserver

When there are no more tasks, you’re sure that you’re done!

ToPoS| 3 juni 2007

SARA Reken- en Netwerkdiensten

ToPoS

is a service

is based on HTTP

can be queried by any HTTP client!

is strong because it’s simple!

Has task realms and pools

https://topos.grid.sara.nl/3/

ToPos| 3 juni 2007

SARA Reken- en Netwerkdiensten

Great! But now what…

A trivial example: matrix multiplication

ToPoS | 3 juni 2007

SARA Reken- en Netwerkdiensten

Approach

1 file per row of matrix A

1 file per column of matrix B

The Task:Contains an A[row] and B[col]

Is a shell script that can be sourced

The Pilot job:Fetches a task (None? Exit!)

Sources the task

Calculates the result

Puts the result in a file ([row]-[col].txt)

Deletes the task

ToPoS | 3 juni 2007

SARA Reken- en Netwerkdiensten

Upload files to UI

Wget https://hpcv.projects.sara.nl/wiki/images/0/06/ToposDemo.zip

WinSCP?

ToPoS | 3 juni 2007

SARA Reken- en Netwerkdiensten

Lets go! I

Login to UIssh [user]@gb-se-ams.els.sara.nl (or putty!)

Create proxystartGridSession [VO]

Enter certificate password

Unpack the demo:tar -xvvf toposDemo.tar.gz

Unzip -xvvf toposDemo.zip

ToPoS | 3 juni 2007

SARA Reken- en Netwerkdiensten

Transfer input data

export LFC_HOST='lfc.grid.sara.nl‘

lfc-mkdir /grid/[VO]/[USERNAME]

inputdata/copyFiles.sh:

#!/bin/bash

if [ $# -ne 2 ]

then

echo "Supply your VO name and your username!"

exit 0

fi

for x in *.txt

do

lcg-cr --vo ${1} -d srm://srm.grid.sara.nl:8443/pnfs/grid.sara.nl/data/${1}/${2}/${x} -l lfn:/grid/${1}/${2}/${x} "file://${PWD}/${x}"

done

ToPoS | 3 juni 2007

SARA Reken- en Netwerkdiensten

Pilot Job

Pilotjob.sh

ToPoS | 3 juni 2007

SARA Reken- en Netwerkdiensten

JDL

pilotjob.jdl:

Type = "Job";

JobType = "Normal";

Executable = "/bin/sh";

Arguments = "pilotjob.sh [REALM_URL] [VO] [USER]";

StdOutput = "stdout.log";

StdError = "stderr.log";

InputSandbox = {"pilotjob.sh"};

OutputSandbox = {"stdout.log","stderr.log"};

ShallowRetryCount = 1;

ToPoS | 3 juni 2007

SARA Reken- en Netwerkdiensten

Submit 10 pilot jobs

submit.sh:

#!/bin/bash

touch jobids.txt

for i in {1..10}do glite-wms-job-submit –d $USER pilotjob.jdldone

ToPoS | 3 juni 2007

SARA Reken- en Netwerkdiensten

Check status

glite-wms-job-status --input jobids.txt

ToPoS | 3 juni 2007