python - 使用回调将 C 库 (GSL) 包装在 cython 代码中

Question

我是 cython 和 c 的新手。我想使用 cython 来加速我的代码的性能。我想在我的代码中使用 gsl_integration 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

当它在 python 中导入如下时，它确实会引发错误:

>>> 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 已经正确定义了，我不明白为什么我又报错了？

Answer 1

First Rule: Premature optimization is the root of all evil.

Second Rule: Follow first rule at all cost.

Third Rule: Do not use C++ complex features ( complex in comparison to C - this includes classes) if there is no need for that (even if you are a C++ fanatic like I am). This is especially true if you are mixing C++ with C libraries.

我看不出有任何理由在您的示例中需要 C++ 类，尤其是因为您通过这样做创建了不必要的间接(包装器)!如果您为了性能而使用编译语言进行编码，那么您一定要避免不必要的步骤和间接访问!你无缘无故地让你的生活变得困难，特别是因为 C 中的 GSL 例程将完成你程序中 99.9% 的计算。为什么不使用类似 cython-gsl 的东西呢？并将您的代码恢复为类似的代码(取自 cython-gsl 示例文件夹)。这要短得多，更干净，而且我看不出为什么它不能很好地执行，因为 python 没有做任何繁重的工作(假设函数 foo() 将被转换为 C，这似乎是这种情况)!

from cython_gsl cimport *

ctypedef double * double_ptr ctypedef void * void_ptr

cdef double foo(double x, void * params) nogil:
    cdef double alpha, f
    alpha = (<double_ptr> params)[0]
    f = log(alpha*x) / sqrt(x)
    return f


def main():
    cdef gsl_integration_workspace * w
    cdef double result, error, expected, alpha
    w = gsl_integration_workspace_alloc (1000)

    expected = -4.0
    alpha = 1

    cdef gsl_function F
    F.function = &foo
    F.params = &alpha

    gsl_integration_qags (&F, 0, 1, 0, 1e-7, 1000, w, &result, &error)
    print "result          = % .18f\n" % result
    print "estimated error          = % .18f\n" % error