通过使用回调将C库（GSL）包装在cython代码中

Question

我是一个新手cython和c。我想使用cython来提高代码的性能。我想gsl_integration在我的代码中使用库进行集成。更新：
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)

此.pyx代码是使用以下setup.py文件编译的，不会引发任何错误消息：

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})

甚至使用命令行：

cython test_gsl.pyx
gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/vol/anaconda/lib/python2.7/site-packages -I/usr/include -I/vol/anaconda/include/python2.7 -c test_gsl.c `pkg-config --cflags gsl` 
gcc -pthread -shared test_gsl.o -L/usr/lib -L/vol/anaconda/lib -lgsl -lgslcblas -lpython2.7 `pkg-config --libs gsl` -o test_gsl.so

当以如下方式在python中导入时，它确实引发错误：

>>> import pyximport; pyximport.install()
(None, <pyximport.pyximport.PyxImporter object at 0x7f0c7e888150>)
>>> import gsl
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/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 "/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 gsl failed: ['ImportError: /users/dalek/.pyxbld/lib.linux-x86_64-2.7/gsl.so: undefined symbol: gsl_integration_qags\n']

gsl_integration_qags 已经正确定义，我不明白为什么我再次遇到此错误？

Answer 1

使用以下命令编译后：

cython test_gsl.pyx
gcc -m64 -pthread -fno-strict-aliasing -Wstrict-prototypes -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/include -I/vol/dalek/anaconda/include/python2.7 -c test_gsl.c -o build/temp.linux-x86_64-2.7/test_gsl.o
gcc -pthread -shared -L/usr/lib/ -L/vol/dalek/anaconda/lib -o test_gsl.so  build/temp.linux-x86_64-2.7/test_gsl.o -lpython2.7  -lgsl -lgslcblas -lm

如果我test_gsl不带python导入pyximport，则效果很好。由于pyximport不支持与外部库的链接。