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 <[email protected]
<mailto:[email protected]>> wrote:
On 10/08/2010 09:06 AM, Benjamin Root wrote:
On Fri, Oct 8, 2010 at 8:47 AM, Ian Goodfellow
<[email protected] <mailto:[email protected]>> 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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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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