Python may just not be good choice of language for your problem. Have you looked at Julia? It claims to be fast for the kinds of things you're doing, and it sha

Python may just not be good choice of language for your problem. Have you looked at Julia? It claims to be fast for the kinds of things you're doing, and it shares a lot of the Python ecosystem -- the Ju in Jupyter is from Julia, i.e., you can work in notebooks, and you can use existing Python (and C/Fortran) libraries directly. Also, Cython might be an option to speed up your code.