[Numpy-discussion] Help building numpy

Bruce Southey bsouthey@gmail....
Fri Oct 8 09:53:43 CDT 2010


  On 10/08/2010 09:06 AM, Benjamin Root wrote:
> On Fri, Oct 8, 2010 at 8:47 AM, Ian Goodfellow 
> <goodfellow.ian@gmail.com <mailto:goodfellow.ian@gmail.com>> wrote:
>
>     Can anyone explain how to get numpy to recognize atlas? I have
>     atlas built and installed, and I put what I thought should be
>     sufficient, based on numpy's INSTALL.TXT, to make numpy use atlas
>     in my site.cfg then ran python setup.py install. The resulting
>     build is incredibly slow. Multiplying a 1,000 x 1,000 matrix takes
>     8 seconds. The default packages take .8 . On a computer at work
>     with a similar but slower cpu to mine, it only takes .2, so I know
>     I should be able to get a lot more speed out of numpy.
>
>     This is my site.cfg:
>
>     [atlas]
>     atlas_libs = lapack, f77blas, cblas, atlas
>
>     [DEFAULT]
>     library_dirs = /usr/local/atlas/lib
>     include_dir = /usr/local/atlas/include
>
>     Thanks in advance,
>     Ian
>
>
> Ian, it would be very helpful if you could post the output from the 
> build of numpy.  That log can tell us whether it found the libraries 
> or not when building.
>
> Ben Root
>
>
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I do not use a 'site.cfg' even though I build my own numpy but use the 
standard Fedora (13) packages for atlas. So try it without defining it - 
remove the installation and build directories first!

Can you please provide the operating system (including 32bit or 64 bit), 
Python version and numpy version?

What is the output of the numpy function 'show_config()'?
I added mine below from a 64-bit linux system so you can see that numpy 
is looking in the '/usr/lib64' directory.

Bruce

 >>> import numpy as np
 >>> np.show_config()
atlas_threads_info:
     libraries = ['lapack', 'ptf77blas', 'ptcblas', 'atlas']
     library_dirs = ['/usr/lib64/atlas']
     define_macros = [('ATLAS_INFO', '"\\"3.8.3\\""')]
     language = f77
     include_dirs = ['/usr/include']
blas_opt_info:
     libraries = ['ptf77blas', 'ptcblas', 'atlas']
     library_dirs = ['/usr/lib64/atlas']
     define_macros = [('ATLAS_INFO', '"\\"3.8.3\\""')]
     language = c
     include_dirs = ['/usr/include']
atlas_blas_threads_info:
     libraries = ['ptf77blas', 'ptcblas', 'atlas']
     library_dirs = ['/usr/lib64/atlas']
     define_macros = [('ATLAS_INFO', '"\\"3.8.3\\""')]
     language = c
     include_dirs = ['/usr/include']
lapack_opt_info:
     libraries = ['lapack', 'ptf77blas', 'ptcblas', 'atlas']
     library_dirs = ['/usr/lib64/atlas']
     define_macros = [('ATLAS_INFO', '"\\"3.8.3\\""')]
     language = f77
     include_dirs = ['/usr/include']
lapack_mkl_info:
   NOT AVAILABLE
blas_mkl_info:
   NOT AVAILABLE
mkl_info:
   NOT AVAILABLE
 >>>


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