Link MKL to an installed Numpy in Anaconda?

Question

>>> numpy.__config__.show()
atlas_threads_info:
  NOT AVAILABLE
blas_opt_info:
    libraries = ['f77blas', 'cblas', 'atlas']
    library_dirs = ['/home/admin/anaconda/lib']
    define_macros = [('ATLAS_INFO', '"\\"3.8.4\\""')]
    language = c
atlas_blas_threads_info:
  NOT AVAILABLE
openblas_info:
  NOT AVAILABLE
lapack_opt_info:
    libraries = ['lapack', 'f77blas', 'cblas', 'atlas']
    library_dirs = ['/home/admin/anaconda/lib']
    define_macros = [('ATLAS_INFO', '"\\"3.8.4\\""')]
    language = f77
openblas_lapack_info:
  NOT AVAILABLE
atlas_info:
    libraries = ['lapack', 'f77blas', 'cblas', 'atlas']
    library_dirs = ['/home/admin/anaconda/lib']
    define_macros = [('ATLAS_INFO', '"\\"3.8.4\\""')]
    language = f77
lapack_mkl_info:
  NOT AVAILABLE
blas_mkl_info:
  NOT AVAILABLE
atlas_blas_info:
    libraries = ['f77blas', 'cblas', 'atlas']
    library_dirs = ['/home/admin/anaconda/lib']
    define_macros = [('ATLAS_INFO', '"\\"3.8.4\\""')]
    language = c
mkl_info:
  NOT AVAILABLE

This is numpy.config.show()

And this numpy is based on Anaconda.

in /home/admin/anaconda/lib/python2.7/site-packages/numpy

And meanwhile, I have installed MKL in /opt/intel/mkl.

Also it seems that, I can use MKL, when I used Theano with this Anaconda and this numpy.

Thank you~

Answer 1

To do this, you'll have to get the Numpy source code and create a site.cfg file in the main folder that tells Numpy where to look for the MKL libraries. Use the site.cfg.example file as a guide; there's a section in there on MKL that should tell you the exact lines you need.

Once you have a site.cfg file, run python setup.py config. This will spit out the configuration info (it looks like the output of numpy.config.show()). You should see the paths to your MKL libraries in there (if not, you'll have to play around with the site.cfg file until you do).

Then, you can build and install with python setup.py build and python setup.py install. You may want to uninstall your old Numpy first.

I have a blog post on installing Numpy with OpenBLAS. While your situation is a little different, a lot of steps are similar I think.