Theano fails due to NumPy Fortran mixup under Ubuntu

I had the same problem, and after reviewing the source code, user212658's answer seemed like it would work (I have not tried it). I then looked for a way to deploy user212658's hack without modifying the source code.

Put these lines in your theanorc file:

[blas]ldflags = -lblas -lgfortran

This worked for me.

Have you tried to recompile NumPy from the sources?

I'm not familiar with the Ubuntu package system, so I can't check what's in your dist-packages/numpy. With a clean archive of the NumPy sources, you should have a setup.py at the same level as the directories numpy, tools and benchmarks (among others). I'm pretty sure that's the one you want to use for a python setup.py build.

[EDIT]

Now that you have recompiled numpy with the proper --fcompiler option, perhaps could you try to do the same with Theano, that is, compiling directly from sources without relying on a apt-get or even pip. You should have a better control on the build process that way, which will make debugging/trying to find a solution easier.

I had the same problem. The solution I found is to add a hack in theano/gof/cmodule.py to link against gfortran whenever 'blas' is in the libs. That fixed it.

class GCC_compiler(object):   ...    @staticmethod    def compile_str(module_name, src_code, location=None,                    include_dirs=None, lib_dirs=None, libs=None,                    preargs=None):        ...        cmd.extend(['-l%s' % l for l in libs])        if 'blas' in libs:            cmd.append('-lgfortran')