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

Dennis Williams dennis.williams at bjss.co.uk
Thu Jul 19 17:28:54 BST 2007


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Hello,

 

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

 

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

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