[GE users] Failure when trying to submit java job to SGE 5.3

Reuti reuti at staff.uni-marburg.de
Thu Jul 19 19:36:22 BST 2007


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Am 19.07.2007 um 18:28 schrieb Dennis Williams:

> I?m operating SGE 5.3 on Linux (Fedora 6). I?m trying to work out  
> how to submit a batch script job to a sun grid engine 5.3.  The job  
> can be executed from the command line using the following command:
>
> ./job.sh <a number> <a xml file name>
>
> e.g.
>
> ./job.sh 1 workflow.xml
>
> The job.sh script executes a java process and looks something like  
> this?
>
> #! /bin/sh
>
> CLASSPATH=/home/LinuxNode1/Java/lib/commons-collections-3.2.jar:/ 
> home/LinuxNode1/Java/lib/commons-beanutils.jar:/home/LinuxNode1/ 
> Java/lib/application.jar
>
> java -cp $CLASSPATH uk.co.bjss.prototype.jobs.JobProcess $1 $2
>
> I?ve tried submitting the job to the grid engine using the following:
>
> qsub ?N job.sh 1 workflow.xml
Is this a typo? If you set -N, this will give the job a special name.  
You could either use:

qsub ?N my_special_job job.sh 1 workflow.xml

or

qsub job.sh 1 workflow.xml


I assume, the real problem is in your queue setup. Try:

shell_start_mode      unix_behavior

-- Reuti

> Unfortunately this yields the following errors in
>
> Standard output
>
> Warning: no access to tty (Bad file descriptor).
>
> Thus no job control in this shell.
>
> Standard Error
>
> CLASSPATH=/home/LinuxNode1/Java/lib/commons-collections-3.2.jar:/ 
> home/LinuxNode1/Java/lib/commons-beanutils.jar:/home/LinuxNode1/ 
> Java/lib/application.jar
>
> : Command not found.
>
> CLASSPATH: Undefined variable.
>
> I understand that I may be using the wrong qsub syntax.
>
> Any suggestions welcome.
>
>
>
> Thanks
>
>
>
> Dennis
>
>
>
> BJSS Limited, 1st Floor Coronet House, Queen Street, Leeds LS1 2TW.
> Registered in England with company number 2777575.
> http://www.bjss.co.uk
>
>

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