speed up execution time of script (Cython or other...)

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Cython is not necessarilly the first optimization to try. It may be worth to ensure first that your algorithm has an good complexity. Also, you can check whether you are using the right types/classes ; for example, if you use Sage real numbers in your simulations, RDF will in general be much faster than using RR. And so on. So, it really depends on the current state of your code, if it is not too long, could you please paste it here ?

Take a look at the last section of this. As it is quoted there, «Premature optimization is the root of all evil». So use the profiler (or put prints in the appropriate places) to find out what parts of your calculation are taking the most, and the we will be able to give you more specific answers. Good luck!