[Numpy-discussion] building numpy/scipy
Mike Landis
mlandis001 at comcast.net
Fri Jan 2 13:29:26 EST 2009
Some of the install instructions are kind of ambiguous.
When a library name ends in .a or .dll, it's obvious what it is, but
'library' is sometimes used generically without indicating whether
you're talking about static or dynamic, e.g. how does numpy/scipy
link to MKL? Is it statically or dynamically linked?
It's not clear where things should go or how things are found. After
downloading numpy and putting numpy-1.2.1 into a directory named
numpy-1.2.1 in python2.5/Lib/site-packages/ and running python
setup.py install from the numpy-1.2.1 directory, you get a numpy
directory in site-packages. Later, the install instructions refer to
the numpy directory generically. Which numpy directory are you
talking about? Should the numpy-1.2.1 directory not be in
site-packages in the first place? Ditto for scipy. E.g. are you
referring to the site.cfg in the distribution directory (numpy-1.2.1)
or the installed directory (numpy without version notation). Maybe
you should give names to these directories (e.g. distribution and
install) and always refer to them with leading adjectives.
It should be possible to create a script that keeps track of all of
these extra lib configuration steps, so installs won't be so involved
and error prone.
I built ATLAS (they need better documentation of processor types and
how to use what CPU-Z tells you) and I have MKL installed. A quarter
of my MKL evaluation days have already ticked away, and I've come to
the disappointing realization that 30 days is probably not going to
be enough to get the scipy/MKL install right.
What's compatible with what? There is mention of MKL, ATLAS, LAPACK
and CLAPACK (I also downloaded CLAPACK 3.1.1.1). It seems like
CLAPACK would be naturally compatible because python uses C-style
matrix addressing, but does Python (or numpy) flip indexes around if
you have LAPACK instead of CLAPACK, so it works anyway, if slower?
There is mention of ".numpy-site.cfg" in the user's home directory
(which I created), but it didn't seem to have any effect on installing.
I created the following site.cfg in the numpy (install) directory:
[mkl]
include_dirs = D:\Programs\Intel\MKL\10.1.0.018\include
library_dirs = D:\Programs\Intel\MKL\10.1.0.018\ia32\lib
mkl_libs = mkl_ia32, mkl_c_dll, libguide40
lapack_libs = mkl_lapack
Do numpy AND scipy each need a site.cfg in their respective install
directories? If so, does one take precedence over the other?
When I run 'python setup.py install' from the numpy install directory, I get:
Warning: No configuration returned, assuming unavailable.
blas_opt_info:
blas_mkl_info:
libraries mkl, vml, guide not found in d:\Programs\Python25\lib
libraries mkl, vml, guide not found in C:\
libraries mkl, vml, guide not found in d:\Programs\Python25\libs
NOT AVAILABLE
atlas_blas_threads_info:
Setting PTATLAS=ATLAS
libraries mkl, vml, guide not found in d:\Programs\Python25\lib
libraries mkl, vml, guide not found in C:\
libraries mkl, vml, guide not found in d:\Programs\Python25\libs
NOT AVAILABLE
atlas_blas_info:
libraries mkl, vml, guide not found in d:\Programs\Python25\lib
libraries mkl, vml, guide not found in C:\
libraries mkl, vml, guide not found in d:\Programs\Python25\libs
NOT AVAILABLE
D:\Programs\Python25\lib\site-packages\numpy\disutils\system_info.py:1340:
UserWarning:
Atlas (http://math-atlas.sourceforgr.net/) libraries not found
Directories to search for the libraries can be specified in the
numpy/disutils/site.cfg file (section [atlas]) or by setting the
ATLAS environment variable.
warnings.warn(AtlasNotFoundError.__doc__)
blas_info:
libraries blas not found in d:\Programs\Python25\lib
-----------------------------------------------------------------
Where is it looking for blas_opt_info, blas_mkl_info,
atlas_blas_threads_info, and atlas_blas_info? Is it actually looking
on sourceforge for Atlas? FYI, when I try using make in
...MKL/10.1.0.018/examples/cblas, I get a "missing separator" error
on the "!INCLUDE cblas.lst" line (first significant line in the
file). There are no spaces on this line. Could cygwin make be
complaining about something inside the cblas.lst file, or is
complaining about the line not being terminated the way it expects it
to be (I see carriage return, line feed pairs in the file).
HELP!!!!
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