ImportError: undefined symbol: _Py_ZeroStruct

Question

I am trying to run a Python script that is supposed to import some Cython code, and I get the following error:

ImportError: 'path to my .so file': undefined symbol: _Py_ZeroStruct

I have read that this could be due to a mismatch between Python versions. However, I have tried to compile with Python 2.7 and 3.8 (on Visual Studio code) and I always get the same error. I am using try to run this Ubuntu 20.04. I should also add that the code worked fine with older versions of Ubuntu, before I upgraded it a few days ago (I had Ubuntu 16 before).

Any idea how I can solve the problem?

How are you compiling it? I suspect you should be using a setup.py file and not trying to do it manually in vscode — DavidW, Mar 05 '21 at 13:03
How do I do that? Sorry, I should have also mentioned that I am not very proficient at compiling python code, as I am quite new at this. — Giampaolo Pitruzzello, Mar 05 '21 at 14:14
https://cython.readthedocs.io/en/latest/src/userguide/source_files_and_compilation.html#basic-setup-py — DavidW, Mar 05 '21 at 14:26

score 0 · Answer 1 · answered Mar 05 '21 at 15:24

So the issue was probably that I was trying to import the .so file that was compiled with the old version of Ubuntu prior to upgrade (probably a beginner's mistake!).

I fixed it by re-compiling my .pyx file as suggested here. I initially got the error numpy/arrayobject.h: No such file or directory. I fixed this with include_dirs=[numpy.get_include()]. So in the end I compiled my .pyx with:

from distutils.core import setup
from Cython.Build import cythonize
import numpy

setup(
    ext_modules = cythonize("cython_all_fit.pyx"),
    include_dirs=[numpy.get_include()]
)

I run python setup.py build_ext --inplace, which generated my .so file. I was then able to import "cython_all_fit" in my main python code without errors.

ImportError: undefined symbol: _Py_ZeroStruct

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