The Cython wrapper cannot find the symbols defined by BLAS

[argoncloud]

I am having an issue with cython. The cython file compiles correctly to C, and the C file also compiles correctly to .so (see first target of the Makefile on branch caa_devel). However, when I import the .so in python, python complains that ImportError: ./pasgd.so: undefined symbol: cblas_sdsdot

I am not using cblas_sdsdot in python, and also the function is in fact defined (either in simple_blas.c or from libcblas.so). This sounds like a silly issue, like me not giving some necessary parameter to Python. Did you ever encounter something like this? Suggestions?

[npinto]

How did you link the shared library ?

Here is an example of setup.py (the one you call with python setup.py build_ext --inplace):

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

import numpy

ext_modules=[
    Extension("fbcorr_cython", ["fbcorr_cython.pyx"],
              include_dirs = [numpy.get_include(),'.'],
              libraries=['cblas'],
              extra_compile_args = \
              ["-O3", "-Wall",
               "-pthread",
               "-fopenmp",
               #"-ffast-math",
               #"-funroll-all-loops",
               "-msse2",
               "-msse3",
               "-msse4",
               #"-fomit-frame-pointer",
               "-march=native",
               "-mtune=native",
               "-ftree-vectorize",
               "-ftree-vectorizer-verbose=2",
               #"-fwrapv",
              ],
              ),
]

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

The relevant line is in the libraries kwarg.

[argoncloud]

Nevermind, the problem is that I accidentally misnamed the shared library as .o instead of .so - changing that solved it.

I am not using setup.py, I am compiling the files manually via Makefile with the same calls specified at http://wiki.cython.org/tutorials/numpy it's more convenient because with the Makefile variables you can use the same parameters for compiling everything.

On 11/13/2011 10:56 PM, Nicolas Pinto wrote:

How did you link the shared library ?

Here is an example of setup.py (the one you call with python setup.py build_ext --inplace):

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

import numpy

ext_modules=[
    Extension("fbcorr_cython", ["fbcorr_cython.pyx"],
              include_dirs = [numpy.get_include(),'.'],
              libraries=['cblas'],
              extra_compile_args = \
              ["-O3", "-Wall",
               "-pthread",
               "-fopenmp",
               #"-ffast-math",
               #"-funroll-all-loops",
               "-msse2",
               "-msse3",
               "-msse4",
               #"-fomit-frame-pointer",
               "-march=native",
               "-mtune=native",
               "-ftree-vectorize",
               "-ftree-vectorizer-verbose=2",
               #"-fwrapv",
              ],
              ),
]

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

The relevant line is in the libraries kwarg.

---

Reply to this email directly or view it on GitHub: https://github.com/npinto/asgd/issues/10#issuecomment-2726461

[npinto]

For Cython modules, please use setup.py or we'll have many issues in the future.