TL;DR - Nuitka (which has been garnering some attention on HN today - https://news.ycombinator.com/item?id=8771925) is not as fast as CPython and less faster than PyPy for the chosen scenario (enumeration of a fat graph and computing their graph homology).

A year and a half down the line after this paper was published (Apr 2013), Nuitka's main strengths seem to be the convenience in packaging the code into an executable which a number of readers have reported success in. If runtime and memory usage are more important, you are better off sticking with the interpreters for now.