Did you try x64 version of PyPy? x86 version is necessarily much slower (both CPython and PyPy) if your program is long-heavy. SymPy is actually part of benchma

Did you try x64 version of PyPy? x86 version is necessarily much slower (both CPython and PyPy) if your program is long-heavy. SymPy is actually part of benchmark used by PyPy and PyPy should be faster if you compare x64 to x64.