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This wiki page is devoted to questions for users of the simulator. There is a similar Developer_FAQ page for ns-3 software developers and maintainers.
What is the difference between ns-2 and ns-3?
ns-2 is a popular discrete-event network simulator developed under several previous research grants and activities. It remains in active use and will continue to be maintained.
ns-3 is a new software development effort focused on improving upon the core architecture, software integration, models, and educational components of ns-2. The project commenced in July 2006 and there have not yet been any releases (pre-alpha stage).
If you are looking for a simulator to currently use for research, please use ns-2.
Will ns-2 scripts run on ns-3?
No. ns-2 uses OTcl as its scripting environment. ns-3 will use C++ programs or python scripts to define simulations.
I found a bug in ns-3. How do I report it?
Please consult this page. Also, please consider fixing the bug, not just reporting it :)