Cython: Link to library and call function

Question

I am trying to write a Cython wrapper for a C Library. I have read through the docs carefully but I must be missing something since I cannot get the following simple Cython code to work.

I created a shared library from the following:

mathlib.c

#include "mathlib.h"

int add_one(int x){
  return x + 1;
}

mathlib.h

extern int add_one(int x);

Then I created the library like so:

gcc -c mathlib.c gcc -shared -o libmathlib.so mathlib.o -lm

My Cython files are mathlib.pyx, cmathlib.pyd, and setup.py

cymathlib.pyx

from mathlib cimport add_one  

def add_one_c(int x):  
   print add_one(x)  
   return x

mathlib.pyd

cdef extern from "mathlib.h":  
    int add_one(int x)

setup.py

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

setup(
    ext_modules = cythonize([Extension("cymathlib", ["cymathlib.pyx"])], libraries ["mathlib"])
)

The module cymathlib.so is created but when I attempt to import it in Python I get the following error: ImportError: dlopen(./cymathlib.so, 2): Symbol not found: _add_one Referenced from: ./cymathlib.so Expected in: flat namespace in ./cymathlib.so"

score 4 · Accepted Answer · answered Dec 28 '14 at 22:16

4

It looks like something went wrong with your Extension specification, which should be something like:

ext_modules = cythonize([Extension("cymathlib", 
                                   ["cymathlib.pyx"], 
                                   libraries=["mathlib"],
                                   library_dirs=["/place/path/to/libmathlib.so/here"]
                                   )])

To be able to use the module, it must be able to find libmathlib.so at run time, since it will look in that file for the actual implementation of add_one. Apart from copying the file to /usr/lib or /usr/local/lib (and running ldconfig again), you can also set an environment variable to make sure the library can be found:

export LD_LIBRARY_PATH=/place/full/path/to/libmathlib.so/here

It's also possible to add the C code into the python module you're creating (so no libmathlib.so will need to be compiled or used anymore). You just need to add the mathlib.c file to the list of cython sources:

ext_modules = cythonize([Extension("cymathlib", 
                                   ["cymathlib.pyx","mathlib.c"]
                                   )])

answered Dec 28 '14 at 22:16

brm

3,706
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14

I have tried everything you suggested here. export LD_LIBRARY_PATH=/usr/local/lib and put libmathlib.so in /usr/local/lib and /usr/lib. and added library_dirs=["/usr/local/lib"] I am getting the same error – ktizzel Dec 29 '14 at 00:07
In your original `cythonize` line, the `libraries` was in the wrong place (had to be inside `Extension()`), did you fix that? – brm Dec 29 '14 at 07:08
I've put some code that works for me at https://bitbucket.org/brmtron/mathlibcythontest . Hope that helps. – brm Dec 29 '14 at 07:36
Thanks that did it! My Extension() had the wrong syntax. – ktizzel Dec 31 '14 at 21:45
if you're getting `ImportError: libxyz.so: cannot open shared object file: No such file or directory`, [you need to set `LD_LIBRARY_PATH` before starting Python interpreter](https://stackoverflow.com/questions/36827871/cython-unable-to-find-shared-object-file) – Yibo Yang Jun 21 '17 at 16:31

Cython: Link to library and call function

1 Answers1