[GE users] Can someone help me? I'm having problems with running a java program on the Sun Grid Engine (SGE).

templedf dan.templeton at sun.com
Thu Sep 24 21:28:36 BST 2009


Grid Engine does not interfere with the application itself.  The only 
difference between running it by hand and submitting it to the cluster 
is the environment in which it runs.  Check that your directories exist 
on the execution node.  Check that the working directory for the job is 
where you expect it to be (see -cwd and -wd in qsub(1)).  Try "qrsh env" 
to show the list of environment variables that are being set for your job.

Daniel

genarohjr wrote:
>
> To: SGE users
>
> From: Genaro
>
>  
>
> Hi there! I am hoping someone can help me.
>
>  
>
> *_The Problem:_*
>
> I am new to using the SGE. However, I have successfully used it to run 
> several java programs. But there is one java program that does not 
> give me the correct output when I submit it to the SGE. I noticed that 
> if I do not submit this job to the SGE, it generates the correct 
> output. The only difference between this java program and other java 
> programs I have submitted to the SGE is that it passes a command to 
> the bash shell. Therefore, it employs the java exec() method 
> (http://java.sun.com/j2se/1.4.2/docs/api/java/lang/Runtime.html).
>
>  
>
> *_What my java program does:_*
>
> My java program uses a directory, D1, as input. That directory 
> contains a list of files. Those files are in a specific format known 
> as N-Triples. The output of the program is a directory, D2, that has a 
> list of files. These files are created from taking each file in D1 and 
> converting it to another format known as RDF/XML.
>
>  
>
> *_How I submit my job to the SGE:_*
>
> qsub -q all.q at sungrid01 <mailto:all.q at sungrid01> -o /rhome/hernange 
> run_NT_to_RDF_XML.sh
>
>  
>

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