On an HPC system, why wouldn't you use normal HPC-type performance tools? It will probably give you better analysis tools and allow you to profile/trace the libraries which are probably providing the performance. At least Score-p, Extrae, and TAU have Python support and have sophisticated viewers with support for call trees and inclusive/exclusive views. When I looked (maybe a couple of years ago) I couldn't find anything in the Python ecosystem to do that, though there may be now.