[Numpy-discussion] Help building numpy
Bruce Southey
bsouthey at gmail.com
Fri Oct 8 11:49:21 EDT 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 at gmail.com
> <mailto:bsouthey at 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 at gmail.com <mailto:goodfellow.ian at 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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>
>
>
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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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