[Numpy-discussion] Building Numeric+numarray with atals on Fedora Core 4

[Chris Barker]

It looks like I'm managing to maintain this thread all by myself!

I thought I'd  post this final note, so that anyone searching the 
archives can see my solution. It's a bit ugly, but it seems to work.

First the summary:

I'm trying to build both Numeric and numarray on a new installation of 
Linux Fedora Core 4 on a Pentium M laptop.

Fedora helpfully provides a full lapack and blas rpms, but they don't 
appear to be at all optimized. In fact, when I used them, it was slower 
than the built-in lapack-lite.

I haven't been able to find a complete atlas+lapack distribution for 
Fedora core 4 (or anything like it), so this is what I did:

Got the atlas binaries from the atlas site:

https://sourceforge.net/projects/math-atlas/

I downloaded:
atlas3.6.0_Linux_P4SSE2.tar.gz

NOTE: these are pretty old...should I be using the 3.7.10 unstable 
version instead?

I then merged these with the Fedora lapack (should be in 
/usr/lib/liblapack.a) by following the directions in the atlas README:

"""******** GETTING A FULL LAPACK LIB **************************
ATLAS does not provide a full lapack library.  However, there is a 
simple way
to get ATLAS to provide its faster LAPACK routines to a full LAPACK library.
ATLAS's internal routines are distinct from LAPACK's, so it is safe to 
compile
ATLAS's LAPACK routines directly into a netlib-style LAPACK library.
First, obtain the LAPACK src from netlib and build the LAPACK library as
normal.  Then, in this directory (where you should have a liblapack.a),
issue the following commands:
   mkdir tmp
   cd tmp
   ar x ../liblapack.a
   cp <your LAPACK path & lib> ../liblapack.a
   ar r ../liblapack.a *.o
   cd ..
   rm -rf tmp

Just linking in ATLAS's liblapack.a first will not get you the best LAPACK
performance, mainly because LAPACK's untuned ILAENV will be used instead
of ATLAS's tuned one.
"""

I installed them in:

/usr/local/lib/atlas
and
/usr/local/include/atlas

Then I set up the numarray and Numeric build process to use them. For 
numarray, I edited cfg_packages.py, and put in:

USE_LAPACK = True

near the top, and edited on of the blocks to read:

	print "Adding paths for lapack/blas"
         lapack_dirs = ['/usr/local/lib/atlas']
         lapack_libs = ['lapack', 'cblas', 'f77blas', 'atlas', 'g2c', 
'gfortran']
	lapack_include_dirs += ['/usr/local/include/atlas/']

NOTE: the gfortran lib is something I hadn't seen before, but I needed 
it to resolve missing symbols. I'm guess that the fedora lapack used 
gfortran.

then a setup.py build, setup.py install, and it seems to work, and is 
about twice as fast as lapack-lite on my simple test case. In the past, 
I got about a 7 times speed-up with the atlas that I got from Gentoo. 
I'm a bit disappointed, but it's OK, and I'm not really doing anything 
where it matters much.

For Numeric, I edited customize.py:

#  Using ATLAS blas in /usr/local
if 1:
     use_system_lapack = 1
     lapack_library_dirs = ['/usr/local/lib/atlas']
     lapack_libraries = ['lapack', 'cblas', 'f77blas', 'atlas', 'g2c', 
'gfortran']

And that did it.

-Chris


-- 
Christopher Barker, Ph.D.
Oceanographer
                                     		
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Chris.Barker at noaa.gov