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Change into the yourpath/mytemplate1 directory and perform your changes modifications in the job_settings file and the other scripts. Then perform a clean to get rid of any unnecessary files that may have transferred during the copying of sp001.
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Change into the yourpath/mytemplate2 directory and perform your changes modifications in the job_settings file and the other scripts. Then perform a clean to get rid of any unnecessary files that may have transferred during the copying of sp002.
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