I chose to use NetLogo for this class because it lets us build models very quickly without having to worry about all the graphical, GUI, or plotting code. There are many agent-based modeling libraries and platforms out there. NetLogo is the best at getting a novice from knowing nothing to having fun with his custom-built model.
The Mason Java library is good for large-scale simulations, of the type you would run on a 'supercomputer'. The Repast Java library and IDE is another popular library that integrates with eclipse. Obviously, you have to know Java to use either one of these.