[Numpy-discussion] Help building numpy

Ian Goodfellow goodfellow.ian@gmail....
Fri Oct 8 10:58:26 CDT 2010


Here's the output on my atlas library:
file -L /usr/local/atlas/lib/libatlas.so
/usr/local/atlas/lib/libatlas.so: ELF 64-bit LSB shared object, x86-64,
version 1 (SYSV), dynamically linked, not stripped

It looks mostly the same as yours except it says "not stripped" while yours
says "stripped." Do you know what that means?

Here's my timing code (but the difference between installations is pretty
obvious even without a timer, 8 full seconds on my machine versus .2 seconds
on a slower machine at work):

import numpy as N
import time
rng = N.random.RandomState([0,1,2])
A = rng.randn(1000,1000)
t1 = time.time(); x = N.dot(A,A); t2 = time.time()
print t2-t1




On Fri, Oct 8, 2010 at 11:49 AM, Bruce Southey <bsouthey@gmail.com> wrote:

>  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> 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
>>
>>
>> _______________________________________________
>> NumPy-Discussion mailing list
>> 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
>> >>>
>>
>>
>>
>> _______________________________________________
>> NumPy-Discussion mailing list
>> NumPy-Discussion@scipy.org
>> http://mail.scipy.org/mailman/listinfo/numpy-discussion
>>
>>
>
> _______________________________________________
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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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> NumPy-Discussion@scipy.org
> http://mail.scipy.org/mailman/listinfo/numpy-discussion
>
>
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