The qsub man page says that command line options can be used to
override options embedded in the script. I just submitted a script
that contained a -masterq option with a different -masterq option on
the command line. Rather than the command line overriding the
embedded option they appear to have been combined and the job appears
to be eligible to run with either masterq. Given that qsub/submit
calls for this to override I'd say this was at least a documentation
bug. Using version 6.2u3
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