topic in Intel® oneAPI Math Kernel Library

Numpy and Scipy with MKL: installation troubles

Garnier__Maxime — Mon, 04 Jun 2018 15:46:18 GMT

Hi,

I am currently trying to build Numpy and Scipy with MKL on Ubuntu 18.04 following your tutorial (but not using the Intel compilers). It seems that everything works for Numpy. Here is the

np.__config__.show()

blas_mkl_info:
    libraries = ['mkl_rt', 'pthread']
    library_dirs = ['/opt/intel/compilers_and_libraries_2018/linux/mkl/lib/intel64']
    define_macros = [('SCIPY_MKL_H', None), ('HAVE_CBLAS', None)]
    include_dirs = ['/opt/intel/compilers_and_libraries_2018/linux/mkl/include']
blas_opt_info:
    libraries = ['mkl_rt', 'pthread']
    library_dirs = ['/opt/intel/compilers_and_libraries_2018/linux/mkl/lib/intel64']
    define_macros = [('SCIPY_MKL_H', None), ('HAVE_CBLAS', None)]
    include_dirs = ['/opt/intel/compilers_and_libraries_2018/linux/mkl/include']
lapack_mkl_info:
    libraries = ['mkl_rt', 'pthread']
    library_dirs = ['/opt/intel/compilers_and_libraries_2018/linux/mkl/lib/intel64']
    define_macros = [('SCIPY_MKL_H', None), ('HAVE_CBLAS', None)]
    include_dirs = ['/opt/intel/compilers_and_libraries_2018/linux/mkl/include']
lapack_opt_info:
    libraries = ['mkl_rt', 'pthread']
    library_dirs = ['/opt/intel/compilers_and_libraries_2018/linux/mkl/lib/intel64']
    define_macros = [('SCIPY_MKL_H', None), ('HAVE_CBLAS', None)]
    include_dirs = ['/opt/intel/compilers_and_libraries_2018/linux/mkl/include']

but when trying to build SciPy, it happens that my system cannot find mutiarray which seems to be due to the fact that it cannot find

libmkl_rt.so

I don't know how to work around that. I have tried following this tutorial too https://www.elliottforney.com/blog/npspmkl/

Any hints would be appreciated!

Thanks in advance

YHi Maxime,

Ying_H_Intel — Wed, 06 Jun 2018 02:14:56 GMT

YHi Maxime,

what is the exact message you are seeing at which exact step? do you mean

When run

$python setup.py build 2>&1 | less

# for python3

#python3 setup.py build 2>&1 | less

Note: If you re-build for any reason (including for python3) you will need to clean up with python setup.py clean –all In the output that is piped to less, you can't see something like this telling you that MKL was found ? :

blas_mkl_info:
FOUND:
library_dirs = ['/opt/intel/mkl/lib/intel64']
include_dirs = ['/opt/intel/mkl/include']
libraries = ['mkl_def', 'mkl_intel_lp64', 'mkl_gnu_thread', 'mkl_core', 'mkl_mc3', 'pthread']
define_macros = [('SCIPY_MKL_H', None)]

FOUND:
library_dirs = ['/opt/intel/mkl/lib/intel64']
include_dirs = ['/opt/intel/mkl/include']
libraries = ['mkl_def', 'mkl_intel_lp64', 'mkl_gnu_thread', 'mkl_core', 'mkl_mc3', 'pthread']
define_macros = [('SCIPY_MKL_H', None)]

blas_mkl_info:

FOUND:

library_dirs = ['/opt/intel/mkl/lib/intel64']

include_dirs = ['/opt/intel/mkl/include']

libraries = ['mkl_def', 'mkl_intel_lp64', 'mkl_gnu_thread', 'mkl_core', 'mkl_mc3', 'pthread']

define_macros = [('SCIPY_MKL_H', None)]

FOUND:

library_dirs = ['/opt/intel/mkl/lib/intel64']

include_dirs = ['/opt/intel/mkl/include']

libraries = ['mkl_def', 'mkl_intel_lp64', 'mkl_gnu_thread', 'mkl_core', 'mkl_mc3', 'pthread']

define_macros = [('SCIPY_MKL_H', None)]

Or let's check the environment

1. You may check if you set the environment for MKL before build the scipy , run

$ source /opt/intel/compilers_and_libraries_2018/linux/mkl/bin/mklvars.sh intel64?

2. what is the output
$export
or
3. ldd ~/.local/lib/python2.7/site-packages/numpy/core/_dotblas.so

We’ll also need to set our LD_LIBRARY_PATH so that the MKL libraries can be found at run time. This should be added to your .bashrc (or whichever bash init scripts you use).

1	export LD_LIBRARY_PATH=/opt/intel/mkl/lib/intel64:${LD_LIBRARY_PATH}

Best Regards,
Ying

Garnier__Maxime — Mon, 16 Jul 2018 17:10:27 GMT

Dear Ying,

Sorry for the very late reply but I managed to solve my problems thanks to your post.

Thanks again,

Best regards,