Installing numpy on Mac OS X Mavericks with alternate LAPACK/BLAS

Question

I'm trying to parallelize some Python code that uses NumPy extensively with the Python multiprocessing package. Unfortunately, as noted here, the default linear algebra libraries provided by Apple (Accelerate/Veclib) cannot be run in parallel. So I'm trying to link an alternate LAPACK/BLAS when installing NumPy, in the hopes that my code can then be parallelized without crashes!

I downloaded and compiled an alternative LAPACK/BLAS. Then, following instructions here, I did:

export LAPACK=/usr/local/Cellar/lapack/3.4.2/lib/liblapack.dylib
export BLAS=/usr/local/Cellar/lapack/3.4.2/lib/libblas.dylib
export ATLAS=None
pip install numpy

which ran fine. However, if I run

numpy.show_config()

in Python, I get

atlas_threads_info:
  NOT AVAILABLE
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)]
atlas_blas_threads_info:
  NOT AVAILABLE
openblas_info:
  NOT AVAILABLE
lapack_opt_info:
    extra_link_args = ['-Wl,-framework', '-Wl,Accelerate']
    extra_compile_args = ['-msse3']
    define_macros = [('NO_ATLAS_INFO', 3)]
atlas_info:
  NOT AVAILABLE
lapack_mkl_info:
  NOT AVAILABLE
blas_mkl_info:
  NOT AVAILABLE
atlas_blas_info:
  NOT AVAILABLE
mkl_info:
  NOT AVAILABLE

indicating NumPy is still using Apple's LAPACK/BLAS! And indeed crashes still abound. Could anyone help me?

Do you have either of the Fortran compilers, g77 or gfortran installed? I do not and see pretty much the same as what you are seeing - installed using Anaconda. — Fred Mitchell
To correct you slightly, the default linear algebra libraries provided by Apple "run in parallel" just fine; the problem is with calling them on both sides of a fork-without-exec (and I should note that there's no really good reason to expect that would work). — Stephen Canon
These instructions worked for me: stackoverflow.com/a/14391693/777706 — Oriol Nieto

Fred Mitchell Fred Mitchell · Accepted Answer · 2014-02-25T03:28:30

I have no idea if either of these will be any help: https://github.com/obspy/obspy/wiki/Notes-on-Parallel-Processing-with-Python-and-ObsPy

Multiprocessing with numpy makes Python quit unexpectedly on OSX

I remember seeing something about lapack/blas on a Mac forum as well, but have not located it, but the author seemed to know what she was talking about.

Installing numpy on Mac OS X Mavericks with alternate LAPACK/BLAS

1 Answers