[Numpy-discussion] Help building numpy

Ian Goodfellow goodfellow.ian@gmail....
Fri Oct 8 10:01:28 CDT 2010


I'm using 64-bit Ubuntu 10.04. I originally tried building without site.cfg
and got the same result. After that I removed the installation and the
numpy/build directory and tried again with site.cfg.

Here's the otuput of my show_config(). Does this mean it's actually using
atlas? I ran 'make time' in the atlas directory and got higher % of clock
speed numbers than the reference so I would be surprised if my atlas build
is this slow.

atlas_threads_info:
    libraries = ['lapack', 'lapack', 'f77blas', 'cblas', 'atlas']
    library_dirs = ['/usr/local/atlas/lib']
    define_macros = [('ATLAS_INFO', '"\\"None\\""')]
    language = f77
    include_dirs = ['/usr/include']
blas_opt_info:
    libraries = ['lapack', 'f77blas', 'cblas', 'atlas']
    library_dirs = ['/usr/local/atlas/lib']
    define_macros = [('ATLAS_INFO', '"\\"None\\""')]
    language = c
    include_dirs = ['/usr/include']
atlas_blas_threads_info:
    libraries = ['lapack', 'f77blas', 'cblas', 'atlas']
    library_dirs = ['/usr/local/atlas/lib']
    define_macros = [('ATLAS_INFO', '"\\"None\\""')]
    language = c
    include_dirs = ['/usr/include']
lapack_opt_info:
    libraries = ['lapack', 'lapack', 'f77blas', 'cblas', 'atlas']
    library_dirs = ['/usr/local/atlas/lib']
    define_macros = [('ATLAS_INFO', '"\\"None\\""')]
    language = f77
    include_dirs = ['/usr/include']
lapack_mkl_info:
  NOT AVAILABLE
blas_mkl_info:
  NOT AVAILABLE
mkl_info:
  NOT AVAILABLE


On Fri, Oct 8, 2010 at 10:53 AM, Bruce Southey <bsouthey@gmail.com> wrote:

>  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>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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> NumPy-Discussion@scipy.orghttp://mail.scipy.org/mailman/listinfo/numpy-discussion
>
>
> 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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>
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