Cython Compilation Error: dynamic module does not define module export function

Question

I am building a package in Cython. I am using the following as the structure for setup.py:

from distutils.core import setup
from distutils.extension import Extension
from Cython.Build import cythonize
import numpy
import scipy

extensions = [
    Extension("xxxxx",["xxxx/xxxxx.pyx"],
    include_dirs=[numpy.get_include(),"."]),
    Extension("nnls",["xxxxx/xxxxx.pyx"],
              include_dirs=[numpy.get_include(),"."]),
]

setup(
    name='xxxxxx',
    version='0.0.0',
    description='''********''',
    url='xxxxxxx',
    author='xxxxx',
    author_email='xxxxx',
    packages=[
        'xxxxx',
    ],
    install_requires=[
        'cython',
        'numpy',
        'scipy',
    ],
    ext_modules=cythonize(extensions),
)

However, I am getting an error upon installation in Python 3. It is working in Python 2 however, it is not compiling in Python 3 having the following error:

dynamic module does not define module export function

How can I solve this problem? Is the structure of the setup.py the reason why this is not compiling?

DavidW · Accepted Answer · 2018-10-05T08:51:12.090

You need to call setup.py with Python 3 (python3 setup.py build_ext, maybe --inplace). It's because Python 3 defines a different name for the init function called when the module starts, and so you need to build it using Python 3 to ensure the correct name is generated.

See dynamic module does not define init function (PyInit_fuzzy) and How to specify Python 3 source in Cython's setup.py? for slightly more detail (it's bordering on a duplicate of these questions, but isn't quite in my view)

score 6 · Answer 2 · answered Nov 14 '19 at 13:27

6

I experienced this and found that I had to use the same name of .pyx as the module name, e.g.

makefile:

# (default)
# INSTALL_DIR:=/usr/lib/python3.6/site-packages
# (my venv)
INSTALL_DIR:=/home/<username>/python3_venv/lib/python3.6/site-packages
all:
    sudo python3 setup_myproj.py install --install-lib ${INSTALL_DIR}

setup_myproj.py

from distutils.core import setup, Extension
from Cython.Build import cythonize

ext = Extension("myproj",
                sources=["myproj.pyx", "myCppProjFacade.cpp"],
                <etc>
                language="c++"
               )

setup(name="myproj",
      version="0.0.1",
      ext_modules=cythonize(ext))

client module, run after installing to venv

import myproj as myCppProjWrapper
...

I also found that if the "myproj" names are different, under <python-lib-dir>/<python-vers>/site-packages the .so and .egg-info names are different and the client fails to load it.

In addition I found that the client's environment does not need to have the cython package installed.

answered Nov 14 '19 at 13:27

Den-Jason

2,395
1
22
17

Would you comment on what OS you were on? – jxramos Mar 03 '20 at 22:46
@jxramos Debian Linux – Den-Jason Mar 04 '20 at 11:09
holiness, the same thing here, not allowed to change the name of the .so file – Dee Oct 26 '21 at 13:56
You saved my life, thanks! But why this is required? – mando May 12 '22 at 16:57
I've no idea; it just happened to be what I found to work. – Den-Jason May 16 '22 at 07:41

score 0 · Answer 3 · answered Jul 13 '20 at 12:27

0

I had the same error for torchvision. FIxed it by downgrading the installation versions:

pip install torch==1.2.0+cu92 torchvision==0.4.0+cu92 -f https://download.pytorch.org/whl/torch_stable.html

answered Jul 13 '20 at 12:27

tsveti_iko

6,834
3
47
39

Non relevant to the question – David I. Rock Apr 19 '23 at 22:57

Cython Compilation Error: dynamic module does not define module export function

3 Answers3

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