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Grid Engine provides two ways to run your jobs, the first is directly from the command line or through theQMON GUI, and it's up to the user to choose what is convenient for her.
However, if the job is simple and consists on only few commands then the submission is more easily done done via the command line. If the job requires the setup of many options and special requests, the use of the GUI is helpful (at least first time when you are writing your script), and facilitates the navigation through the available options.