compilation error of gsl library callback in cython

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I am trying to compile the following cython code : test_gsl.pyx

cdef extern from "math.h":
    double log(double x) nogil

cdef extern from "gsl/gsl_math.h":
    ctypedef struct gsl_function:
        double (* function) (double x, void * params)
        void * params

cdef extern from "gsl/gsl_integration.h":
    ctypedef struct gsl_integration_workspace
    gsl_integration_workspace *  gsl_integration_workspace_alloc(size_t n)
    void  gsl_integration_workspace_free(gsl_integration_workspace * w)
    int  gsl_integration_qags(const gsl_function * f, double a, double b, double epsabs, double epsrel, size_t limit, gsl_integration_workspace * workspace, double *result, double *abserr)


cdef double do_callback(double x, void* params):
    return (<MyCallback>params).eval(x)

cdef class MyCallback:
    cdef double a
    def __init__(self, a):
        self.a = a
    cpdef double eval(self, double x):
        return self.a * log(x+1) * x
    def call_gsl(self):
        cdef gsl_integration_workspace* w =gsl_integration_workspace_alloc (1000)

        cdef gsl_function F
        F.function = &do_callback
        F.params = <void*>self

        cdef double result = 3, error = 5
        gsl_integration_qags(&F, 0, 1, 0, 1e-7, 1000, w, &result, &error)
        print result, error

        gsl_integration_workspace_free(w)

So I have written a setup.py script with given gsl libraries header directory and libgsl.so and etc ..

from distutils.core import setup
from distutils.extension import Extension
from Cython.Distutils import build_ext
import numpy
import sys

ext = Extension("test_gsl", ["test_gsl.pyx"],
    include_dirs=[numpy.get_include(),
                  "/usr/include/"],
    library_dirs=["/usr/lib/"],
    libraries=["gsl"])

setup(ext_modules=[ext],
    cmdclass = {'build_ext': build_ext})

The code gets compiled with this setup.py script even with the command line given as following:

cython test_gsl.pyx
gcc -shared -pthread -fPIC -fwrapv -O2 -Wall -fno-strict-aliasing -I /users/dapple/anaconda/pkgs/numpy-1.7.1-py27_2/lib/python2.7/site-packages/numpy/core/include/ -I /users/dapple/anaconda/include/python2.7/ -I /usr/include/ -c test_gsl.c -o test_gsl.so -lpython2.7 -lgsl -lgslcblas

but when I import the .pyx or .so in python it raises the following error message:

>>> import pyximport
>>> pyximport.install()
(None, <pyximport.pyximport.PyxImporter object at 0x7f9d54c5f0d0>)
>>> import test_gsl
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/vol/anaconda/lib/python2.7/site-packages/Cython-0.20.1-py2.7-linux-x86_64.egg/pyximport/pyximport.py", line 431, in load_module
    language_level=self.language_level)
  File "/vol/anaconda/lib/python2.7/site-packages/Cython-0.20.1-py2.7-linux-x86_64.egg/pyximport/pyximport.py", line 210, in load_module
    mod = imp.load_dynamic(name, so_path)
ImportError: Building module test_gsl failed: ['ImportError: /users/dalek/.pyxbld/lib.linux-x86_64-2.7/test_gsl.so: undefined symbol: gsl_integration_qags\n']

why the code couldn't access to the gsl_integration in C library??

asked 40 secs ago

Dalek

167