Determining batch parameters

Before you submit dwarves.pl for batch processing, you need to determine the parameters for this submission. To use the Condor system for batch processing, you must define these parameters by assigning values to submit file arguments, which describe the jobs that you choose to submit for processing.

In the RCE, you always use the vanilla environment.

To determine the remaining submit file arguments, answer the following questions:

  • What is the executable path and file name?

    For any shell script or statistical application installed in the RCE, the condor_submit_util script can determine the full path for the executable. At the script prompt, you type in the name of your script, program, or application. The default executable in the RCE is the R language, and the path and executable name are /usr/bin/R.

  • Do you have any arguments to supply to the executable?

    Arguments are parameters that you specify for your executable. For example, the default arguments in the condor_submit_util script are --no-save and --vanilla, which specify how to launch and exit the R program. The argument --no-save specifies not to save the R workspace at exit. The argument --vanilla instructs R to not read any user or site profiles or restored data at start up and to not save data files at exit.

  • What are the input file names?

    If you are using the R program, your input file(s) will be whatever R script you want to execute.

  • What do you plan to name the output files?

    A general rule for batch processing is that you have one output file for each input file. Therefore, if you have seven input files, you expect to have seven output files after processing is complete. A useful practice is to correlate the names of input and output files.

  • How many times do you need to execute this script or program?

    A general rule for batch processing is that you execute your job one time for each input file that you use.