[SciPy-User] site.cfg problems : scipy can't find BLAS

John Reid j.reid@mail.cryst.bbk.ac...
Fri Apr 9 03:04:27 CDT 2010

josef.pktd@gmail.com wrote:
> On Thu, Apr 8, 2010 at 3:18 PM, John Reid <j.reid@mail.cryst.bbk.ac.uk> wrote:
>> josef.pktd@gmail.com wrote:
>>> On Thu, Apr 8, 2010 at 8:38 AM, John Reid <j.reid@mail.cryst.bbk.ac.uk> wrote:
>>>> Hi,
>>>> I'm trying to build numpy and scipy from the latest svn source. I have
>>>> followed the instructions in site.cfg.example to configure my own
>>>> site.cfg and I'm using the same site.cfg for both numpy and scipy. numpy
>>>> builds and installs fine and the tests pass. scipy won't build and
>>>> throws out lots of warnings about the BLAS libraries and source. I have
>>>> GotoBLAS2 installed in /usr/local/lib but it doesn't seem to find it.
>>>> Here is my site.cfg:
>>>> # Defaults
>>>> # ========
>>>> # The settings given here will apply to all other sections if not
>>>> overridden.
>>>> # This is a good place to add general library and include directories like
>>>> # /usr/local/{lib,include}
>>>> #
>>>> [DEFAULT]
>>>> library_dirs =
>>>> /usr/local/lib:/home/john/local/src/SuiteSparse-3.4.0/UMFPACK/Lib:/home/john/local/src/SuiteSparse-3.4.0/AMD/Lib
>>>> include_dirs =
>>>> /usr/local/include:/home/john/local/src/SuiteSparse-3.4.0/AMD/Include:/home/john/local/src/SuiteSparse-3.4.0/UMFPACK/Include
>>> I don't know Linux nor gotblas, but I think that here you are telling
>>> numpy distutils that all libraries and include are under AMD and
>> I do have /usr/local/lib at the front of these library lists. That is
>> where the libgoto.a and libgoto.so are stored. How else should I tell it
>> where these libraries are?
> My mistake, I didn't know : works as separator
> the only other thing, I can think of, is whether it looks for the
> correct filenames, is goto2_penrynp-r1.13
> the actual filename?
Yes. Well I have both libgoto2_penrynp-r1.13.a and 
libgoto2_penrynp-r1.13.so in /usr/local/lib

> my impression is that
> #[blas_opt]
> #libraries = ptf77blas, ptcblas, atlas
> #
> #[lapack_opt]
> #libraries = lapack, ptf77blas, ptcblas, atlas
> refer to actual filenames of the libraries (maybe minus prefix and extension).
> But I'm usually debugging by trial and error (and I'm not too bad on
> it on Windows), so the guess in your case might be as bad as my first
> guess.
That's what I find frustrating : python setup.py produces all these 
warnings and errors but they don't seem to relate directly to the 
sections in site.cfg. As far as I can tell from the documentation on the 
website, I've done the right thing. Unfortunately its not working and 
the error messages aren't constructive enough to help me fix it.

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