CODEWITHSUNDEEP
cythonanaconda
uday
uday

Reputation: 6723

cython works fine on winpython but not on anaconda - linking issue

I have a Cython code that runs and works fine under WinPython but giving me issues when I switch from WinPython to Anaconda3. I am using Python 3.4

The test code is :

# cython: boundscheck=False
# cython: wraparound=False
# cython: cdivision=True

cimport cython
cimport numpy as np
import numpy as np
from numpy cimport ndarray as ar
from libc.math cimport *


cpdef ar[double, ndim=1, mode='c'] test(ar[double, ndim=1, mode='c'] x):
    cdef:
        int n = x.shape[0]
        Py_ssize_t i
        ar[double, ndim=1, mode='c'] y = np.zeros(n)*np.nan
    with nogil:
        for i in range(0, n):
            y[i] = x[i]+1
    return y

The compilation code is:

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

ext_modules = [Extension('test', ['tech/test.pyx'], include_dirs=[np.get_include()],
                         define_macros=[('NPY_NO_DEPRECATED_API', None)],
                         extra_compile_args=['-O3', '-march=native', '-ffast-math'],
                         libraries=['m']
                         )]

setup(
    name="Test Function",
    cmdclass={'build_ext': build_ext},
    ext_modules=ext_modules
)

I am using MinGw to compile, so under the ...\Anaconda3\Lib\distutils folder I have a file that has 

[build]
compiler = mingw32

In addition in the PATH environment variables, I have:

default: ...\Anaconda3 ...\Anaconda3\Scripts

also added: ...\Anaconda3\libs (this contains python34)

also added: mingw32 files copied from WinPython that contain gcc etc: ...\Anaconda3\Tools\tools\mingw32\bin (this contains gcc) ...\Anaconda3\Tools\tools\mingw32\x86_64-w64-mingw32\bin

when I try:

python setup.py build_ext --inplace

the code runs fine until the test.c, test.o and test.def have been generated. thereafter this is what I get: 

C:\Anaconda3\Tools\tools\mingw32\bin\gcc.exe -shared -s build\temp.win-amd64-3.4\Release\tech\test.o build\temp.win-amd64-3.4\Release\tech\test.def -LC:\Anaconda3\libs -LC:\Anaconda3\PCbuild\amd64 -lm -lpython34 -lmsvcr100 -

o P:\Documents\Temp\python-master\python-master\common\test.pyd

build\temp.win-amd64-3.4\Release\tech\test.o:test.c:(.text+0x8e): undefined reference to `__imp_PyExc_TypeError'

build\temp.win-amd64-3.4\Release\tech\test.o:test.c:(.text+0x10e): undefined reference to `__imp_PyExc_ValueError'

build\temp.win-amd64-3.4\Release\tech\test.o:test.c:(.text+0x259): undefined reference to `__imp__PyThreadState_Current'
....
....
C:/Anaconda3/Tools/tools/mingw32/bin/../lib/gcc/x86_64-w64-mingw32/4.9.2/../../../../x86_64-w64-mingw3                ild\temp.win-amd64-3.4\Release\tech\test.o: bad reloc address 0x0 in section `.data'
collect2.exe: error: ld returned 1 exit status                                                                        
error: command 'C:\\Anaconda3\\Tools\\tools\\mingw32\\bin\\gcc.exe' failed with exit status 1

  1. First of all, I couldn't find a Anacond3\PCBuild\amd64 directory/file anywhere.

  2. I tried to look all over the internet, but I couldn't find any reference to __imp_PyExc_TypeError, __imp__PyThreadState_Current, __imp_PyExc_ValueError.

What could be going wrong with the final conversion to *.pyd file?

Upvotes: 2

Views: 373

Answers (2)

asmeurer
asmeurer

Reputation: 91630

You can run 

conda remove libpython

to make Anaconda use Visual Studio instead of mingw, which may work better.

Upvotes: 1

stonebig
stonebig

Reputation: 1191

I suspect Anaconda doesn't support mingw-64 yet.

Historically mingw-64 was indeed a hopeless idea until Cark Kleffner came with his static version.

Things may (should ?) change when Carl's updated version will be available as mingwpy wheel.

Upvotes: 1

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