Cython in Windows 64 with GSL

Question

I am attempting to compile the following pyx code:

#declaring external GSL functions to be used
cdef extern from "math.h":
    double sqrt(double)

cdef double Sqrt(double n):
   return sqrt(n)

cdef extern from "gsl/gsl_rng.h":
   ctypedef struct gsl_rng_type:
       pass
   ctypedef struct gsl_rng:
       pass
   gsl_rng_type *gsl_rng_mt19937
   gsl_rng *gsl_rng_alloc(gsl_rng_type * T)

cdef gsl_rng *r = gsl_rng_alloc(gsl_rng_mt19937)

cdef extern from "gsl/gsl_randist.h":
   double gamma "gsl_ran_gamma"(gsl_rng * r,double,double)
   double gaussian "gsl_ran_gaussian"(gsl_rng * r,double)

# original Cython code
def gibbs(int N=20000,int thin=500):
   cdef double x=0
   cdef double y=0
   cdef int i, j
   samples = []
   #print "Iter  x  y"
   for i in range(N):
       for j in range(thin):
           x = gamma(r,3,1.0/(y*y+4))
           y = gaussian(r,1.0/Sqrt(x+1))
       samples.append([x,y])
   return samples

smp = gibbs()

Here is what my setup.py file looks like:

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

import numpy
import sys

if sys.platform == "win32":
    include_gsl_dir = sys.exec_prefix+"\gsl\include"
    lib_gsl_dir = sys.exec_prefix+"\gsl\lib"
else:
    include_gsl_dir = sys.exec_prefix+"\include"
    lib_gsl_dir = sys.exec_prefix+"\lib"

ext = Extension("samplers", ["samplers.pyx"],
    include_dirs=[numpy.get_include(), 
                  include_gsl_dir],
    library_dirs=[lib_gsl_dir],
    libraries=["gsl","gslcblas","m"]
)
setup(ext_modules=[ext],
    cmdclass = {'build_ext': build_ext})

The GSL files are contained in C:\Users\MyName\Anaconda\gsl\include\gsl, C:\Users\MyName\Anaconda\gsl\lib\ and C:\Users\MyName\Anaconda\gsl\bin. Hence why the setup.py file contains reference to sys.exec_prefix to get the main Anaconda folder where the python executable is.

Is there anything wrong with how I am linking GSL with Cython? When I run:

 python setup.py build_ext --inplace

a PYD file is created, but I get the dreadful "ImportError: DLL load failed: The specified module could not be found" when I try to import samplers from the python environment in the same folder where the pyd is created.

I believe it is compiled wrong either because it could not communicate with the GSL files, or something is wrong with the pyx code. I ruled out the latter since it successfully compiles a pyd file without error.

I have also attempted to link with CythonGSL module, but if you look at init.py, for win32 gsl needs to be located in c:\Program Files\GnuWin32\include and I prefer to have the gsl library in the Anaconda folder. Nonetheless, putting them in c:\Program Files\GnuWin32\include still gives me the same error of ImportError: DLL...

Answer 1

I believe I figured out the issue.

My PATH variable did not have access to the GSL folders. In run-time, it needs to access the gsl/bin folder, so I need to add C:\Users\MyName\Anaconda\gsl\bin to the system path variable. I have tried setx PATH "%PATH%;C:\Users\MyName\Anaconda\gsl\bin", and this DOES work. But when I close the CMD window, and redo it, it no longer works.

As I am using this to distribute, is there anyway to permanently set this via a batch file? I have the bld.bat file for conda build, but even there the setx command does not work.

Answer 2

Current version of CythonGSL uses an environmental variable LIB_GSL to recognize the location of GSL. It uses the hard-coded c:\Program Files\GnuWin32\include only when LIB_GSL does not exist. So you can put your GSL installation in a different location as long as you have LIB_GSL set. I think you should use / instead of \ when you set LIB_GSL.

So you need to create/modify two environmental variables for CythonGSL to work: LIB_GSL and PATH. I think you can use setlocal in your batch file. For example, I think you can do the following (I have gsl installed at C:\lib64\gsl) to set it temporarily:

setlocal
SET LIB_GSL=C:/lib64/gsl
SET PATH=%PATH%;C:\lib64\gsl\bin;
Python

Hope this is helpful.