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

genarohjr Genaro.Hernandez at nih.gov
Thu Sep 24 20:21:47 BST 2009


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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