Cython Error linking Shared Library? - cython

Question

I'm trying to use the Cuhre routine provided in the Cuba library. I previously encountered some errors linking a static library to Cython, so I tried to create a shared library with the Cuhre attribute. To do this, I have three files: cuhre.c, cuhre.h, and libcuhre.so (created by compiling cuhre.c).
cuhre.c has a routine tryCuhre that essentially calls on the Cuhre routing provided in the Cuba library. For simplicity, it is just for 2D integration:
double tryCuhre(integrand_t t, void * ud)
{
int comp, nregions, neval, fail;
cubareal integral[NCOMP], error[NCOMP], prob[NCOMP];
Cuhre(2, 1, t, ud, 1,
EPSREL, EPSABS, VERBOSE | LAST,
MINEVAL, MAXEVAL, 13,
STATEFILE, SPIN,
&nregions, &neval, &fail, integral, error, prob);
return (double)integral[0];
}
The variables in all caps (e.g. MINEVAL and SPIN) are all predefined at compile time and constant.
This is my cuhre.h file, which is included by cuhre.c:
#ifndef CUHRE_H_
#define CUHRE_H_
#ifdef __cplusplus
extern "C" {
#endif
typedef double cubareal;
typedef int (*integrand_t)(const int *ndim, const cubareal x[], const int
*ncomp, cubareal f[], void *userdata);
double tryCuhre(integrand_t t, void * ud);
#ifdef __cplusplus
}
#endif
#endif
And after running the set of commands
gcc -Wall -fPIC -c cuhre.c
gcc -shared -o libcuhre.so cuhre.o
I am able to create the shared library libcuhre.so. So far so good. It should be noted that up to this point, the routine works just as I want, i.e. making the executable cuhre from cuhre.c performs correctly.
I am trying to use the tryCuhre routine in a cython file now (execute.pyx). At the top, I have the declarations:
cdef extern from "math.h":
double sin(double x)
double cos(double x)
double sqrt(double x)
double atan(double x)
double exp(double x)
double log(double x)
cdef extern from "cuhre.h":
ctypedef double cubareal
ctypedef int (*integrand_t)(const int *ndim, const cubareal x[], const int *ncomp, cubareal f[], void *userdata)
double tryCuhre(integrand_t t, void * ud)
Finally, to compile, I am using the command
python setup.py build_ext --inplace
on setup.py, which is as follows:
from distutils.core import setup, Extension
from Cython.Distutils import build_ext
from Cython.Build import cythonize
from distutils.extension import Extension
sourcefiles = ['execute.pyx']
ext_modules = [Extension("execute", sourcefiles, library_dirs =
['~/Documents/project/libcuhre.so'],)]
setup(
name = 'execute',
cmdclass = {'build_ext': build_ext},
ext_modules = ext_modules
)
which compiles the file. However, whenever I try the statement
import execute
in the python shell, it raises the error:
/Documents/project/execute.so: undefined symbol: tryCuhre
I have looked all around for ways to link my artificially created libcuhre.so library, but so far none have worked. How can this issue be fixed? Furthermore, how come my program is able to find all of the methods from the math library (sin, cos, exp, etc.) but not any from my libcuhre.so? (It should also be noted that all of these files are in the same directory, ~/Documents/project.)
Thank you so much for any help!

Answer 1

Dependent source code and libraries need to be included in the Extension, either as libraries to link against, or source files to compile with.
library_dirs only adds to the directories the linker will search for a library but does not link anything so is not sufficient.
In this case, since the C code is self-built and a single .c, it is easiest to compile it together as a source. This also means cuhre.c will be compiled by setuptools itself, automating its compilation on the target distribution.
from setuptools import setup, Extension
from Cython.Distutils import build_ext
from Cython.Build import cythonize
sourcefiles = ['execute.pyx', 'cuhre.c']
ext_modules = [Extension("execute", sourcefiles,
include_dirs=['.'],
depends='cuhre.h',
)]
setup(
name='execute',
cmdclass = {'build_ext': build_ext},
ext_modules = ext_modules
)
Code also changed to use setuptools, distutils is deprecated and now part of setuptools.