[Numpy-discussion] Help building numpy

Bruce Southey bsouthey@gmail....
Fri Oct 8 10:49:21 CDT 2010


  On 10/08/2010 10:01 AM, Ian Goodfellow wrote:
> 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 
> <mailto: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 <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
>>
>>
>>     _______________________________________________
>>     NumPy-Discussion mailing list
>>     NumPy-Discussion@scipy.org <mailto:NumPy-Discussion@scipy.org>
>>     http://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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It appears to finding something but I do not know enough about that aspect.

I presume that you installed your own version of atlas since you are 
using /usr/local. So you need to be careful of the flags used especially 
that it is 64-bit and uses the appropriate SSE instructions for your 
processor. For example, on my system:

$ file -L /usr/lib64/atlas/libatlas.so
/usr/lib64/atlas/libatlas.so: ELF 64-bit LSB shared object, x86-64, 
version 1 (SYSV), dynamically linked, stripped

Can you please provide the code you are using for timing for the 'slow' 
system?

By the way, there was this thread:
'HOWTO build NumPy without external math libs'
http://mail.scipy.org/pipermail/numpy-discussion/2010-July/051513.html

BLAS=None LAPACK=None ATLAS=None python setup.py build


Bruce
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