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I have a startup problem with the backrub application:
The -ntrials option gives me an error: “ERROR: Unique best command line context option match not found for -ntrials” as if this option was given twice? I checked this so what am I doing wrong?
Try calling it backrub:ntrials.
The problem is that there is also an option jd2:ntrials, and the command line parser doesn’t know which one you meant to use.
This may fail; there are known issues with application-defined options (backrub) whose names conflict with centrally-defined options (jd2). I can offer further troubleshooting if this doesn’t work.