Linking numpy/scipy to serial ATLAS

Question

My operating system is Fedora 16 (although I have had the same issue on other distros).

I want to build numpy/scipy linking to serial ATLAS (rather than threaded). It would seem this involves uncommenting the following lines in my site.cfg file:

[DEFAULT]
library_dirs = /usr/lib64/atlas
include_dirs = /usr/local/include
[blas_opt]
libraries = f77blas, cblas, atlas
[lapack_opt]
libraries = lapack, f77blas, cblas, atlas

I have done this, but when I build the package via

python setup.py build

It still links to the threaded libraries eg.

Setting PTATLAS=ATLAS
  FOUND:
    libraries = ['ptf77blas', 'ptcblas', 'atlas']
    library_dirs = ['/usr/lib64/atlas']
    language = c
    define_macros = [('ATLAS_INFO', '"\\"3.8.4\\""')]

Any ideas?

Tomas Tomecek · Accepted Answer · 2013-09-24 07:15:17Z

1

I know that this is already one year old, so I'm writing this answer in case anyone would have same problem.

I would probably manually remove/rename threaded atlas libs. It's a bit ugly but it should work.

Another solution could be to configure numpy like this:

[atlas]
library_dirs = /usr/lib64/atlas
atlas_libs = lapack, f77blas, cblas, atlas

There was also this commit in numpy saying that {blas,lapack}_opt sections are not actually read.

answered Sep 24, 2013 at 7:15

Tomas Tomecek

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