How to check BLAS/LAPACK linkage in NumPy and SciPy?

Question

I am builing my numpy/scipy environment based on blas and lapack more or less based on this walk through.

When I am done, how can I check, that my numpy/scipy functions really do use the previously built blas/lapack functionalities?

Answer 1

What you are searching for is this: system info

I compiled numpy/scipy with atlas and i can check this with:

import numpy.distutils.system_info as sysinfo
sysinfo.get_info('atlas')

Check the documentation for more commands.

Answer 2

The method numpy.__config__.show() outputs information about linkage gathered at build time. My output looks like this. I think it means I am using the BLAS/LAPACK that ships with Mac OS.

>>>import numpy as np
>>>np.__config__.show()

lapack_opt_info:
    extra_link_args = ['-Wl,-framework', '-Wl,Accelerate']
    extra_compile_args = ['-msse3']
    define_macros = [('NO_ATLAS_INFO', 3)]
blas_opt_info:
    extra_link_args = ['-Wl,-framework', '-Wl,Accelerate']
    extra_compile_args = ['-msse3', '-I/System/Library/Frameworks/vecLib.framework/Headers']
    define_macros = [('NO_ATLAS_INFO', 3)]

Answer 3

As it uses the dynamically loaded versions, you can just do this:

$ ldd anyoftheCmodules.so

where anyoftheCmodules.so could be, for example, numpy/core/_dotblas.so, which links to libblas.so.

Answer 4

You can use the link loader dependency tool to look at the C level hook components of your build and see whether they have external dependencies on your blas and lapack of choice. I am not near a linux box right now, but on an OS X machine you can do this inside the site-packages directory which holds the installations:

$ otool -L numpy/core/_dotblas.so 
numpy/core/_dotblas.so:
    /System/Library/Frameworks/Accelerate.framework/Versions/A/Accelerate (compatibility version 1.0.0, current version 4.0.0)
    /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 125.2.0)
    /System/Library/Frameworks/vecLib.framework/Versions/A/vecLib (compatibility version 1.0.0, current version 268.0.1)

$ otool -L scipy/linalg/flapack.so 
scipy/linalg/flapack.so (architecture i386):
    /System/Library/Frameworks/Accelerate.framework/Versions/A/Accelerate (compatibility version 1.0.0, current version 4.0.0)
    /usr/local/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0)
    /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 111.1.4)
    /System/Library/Frameworks/vecLib.framework/Versions/A/vecLib (compatibility version 1.0.0, current version 242.0.0)
scipy/linalg/flapack.so (architecture ppc):
    /System/Library/Frameworks/Accelerate.framework/Versions/A/Accelerate (compatibility version 1.0.0, current version 4.0.0)
    /usr/local/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0)
    /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 111.1.4)

$ otool -L scipy/linalg/fblas.so 
scipy/linalg/fblas.so (architecture i386):
    /System/Library/Frameworks/Accelerate.framework/Versions/A/Accelerate (compatibility version 1.0.0, current version 4.0.0)
    /usr/local/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0)
    /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 111.1.4)
    /System/Library/Frameworks/vecLib.framework/Versions/A/vecLib (compatibility version 1.0.0, current version 242.0.0)
scipy/linalg/fblas.so (architecture ppc):
    /System/Library/Frameworks/Accelerate.framework/Versions/A/Accelerate (compatibility version 1.0.0, current version 4.0.0)
    /usr/local/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0)
    /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 111.1.4)

substitute ldd in place of otool on a gnu/Linux system and you should get the answers you need.

Answer 5

You can display BLAS, LAPACK, MKL linkage using show_config():

import numpy as np
np.show_config()

Which for me gives output:

mkl_info: libraries = ['mkl_rt', 'pthread'] library_dirs = ['/my/environment/path/lib'] define_macros = [('SCIPY_MKL_H', None), ('HAVE_CBLAS', None)] include_dirs = ['/my/environment/path/include'] blas_mkl_info: libraries = ['mkl_rt', 'pthread'] library_dirs = ['/my/environment/path/lib'] define_macros = [('SCIPY_MKL_H', None), ('HAVE_CBLAS', None)] include_dirs = ['/my/environment/path/include'] blas_opt_info: libraries = ['mkl_rt', 'pthread'] library_dirs = ['/my/environment/path/lib'] define_macros = [('SCIPY_MKL_H', None), ('HAVE_CBLAS', None)] include_dirs = ['/my/environment/path/include'] lapack_mkl_info: libraries = ['mkl_rt', 'pthread'] library_dirs = ['/my/environment/path/lib'] define_macros = [('SCIPY_MKL_H', None), ('HAVE_CBLAS', None)] include_dirs = ['/my/environment/path/include'] lapack_opt_info: libraries = ['mkl_rt', 'pthread'] library_dirs = ['/my/environment/path/lib'] define_macros = [('SCIPY_MKL_H', None), ('HAVE_CBLAS', None)] include_dirs = ['/my/environment/path/include']