LinearAlgebra incredibly slow for eigenvalue problems

drife daranrife at yahoo.com
Fri Jan 28 23:55:51 CET 2005


Hi David,

I performed the above check, and sure enough, Numeric
is --not-- linked to the ATLAS libraries.

I followed each of your steps outlined above, and Numeric
still is not linking to the ATLAS libraries.

My setup.py file is attached below.

Thanks ,

Daran

--#!/usr/bin/env python
# To use:
#       python setup.py install
# or:
#       python setup.py bdist_rpm (you'll end up with RPMs in dist)
#
import os, sys, string, re
from glob import glob
if not hasattr(sys, 'version_info') or sys.version_info <
(2,0,0,'alpha',0):
raise SystemExit, "Python 2.0 or later required to build Numeric."
import distutils
from distutils.core import setup, Extension

# Get all version numbers
execfile(os.path.join('Lib','numeric_version.py'))
numeric_version = version

execfile(os.path.join('Packages', 'MA', 'Lib', 'MA_version.py'))
MA_version = version

headers = glob (os.path.join ("Include","Numeric","*.h"))
extra_compile_args = []  # You could put "-O4" etc. here.
mathlibs = ['m']
define_macros = [('HAVE_INVERSE_HYPERBOLIC',None)]
undef_macros = []
# You might need to add a case here for your system
if sys.platform in ['win32']:
mathlibs = []
define_macros = []
undef_macros = ['HAVE_INVERSE_HYPERBOLIC']
elif sys.platform in ['mac', 'beos5']:
mathlibs = []

# delete all but the first one in this list if using your own
LAPACK/BLAS
sourcelist = [os.path.join('Src', 'lapack_litemodule.c')]
# set these to use your own BLAS;

library_dirs_list = ['/d2/lib/atlas']
libraries_list = ['lapack', 'ptcblas', 'ptf77blas', 'atlas', 'g2c']

# set to true (1), if you also want BLAS optimized
matrixmultiply/dot/innerproduct
use_dotblas = 1
include_dirs = ['/d2/include']
# You may need to set this to find cblas.h
#  e.g. on UNIX using ATLAS this should be
['/usr/include/atlas']
extra_link_args = []

# for MacOS X to link against vecLib if present
VECLIB_PATH = '/System/Library/Frameworks/vecLib.framework'
if os.path.exists(VECLIB_PATH):
extra_link_args = ['-framework', 'vecLib']
include_dirs = [os.path.join(VECLIB_PATH, 'Headers')]

# The packages are split in this way to allow future optional inclusion
# Numeric package
packages = ['']
package_dir = {'': 'Lib'}
include_dirs.append('Include')
ext_modules = [
Extension('_numpy',
[os.path.join('Src', '_numpymodule.c'),
os.path.join('Src', 'arrayobject.c'),
os.path.join('Src', 'ufuncobject.c')],
extra_compile_args = extra_compile_args),
Extension('multiarray',
[os.path.join('Src', 'multiarraymodule.c')],
extra_compile_args = extra_compile_args),
Extension('umath',
[os.path.join('Src', 'umathmodule.c')],
libraries = mathlibs,
define_macros = define_macros,
undef_macros = undef_macros,
extra_compile_args = extra_compile_args),
Extension('arrayfns',
[os.path.join('Src', 'arrayfnsmodule.c')],
extra_compile_args = extra_compile_args),
Extension('ranlib',
[os.path.join('Src', 'ranlibmodule.c'),
os.path.join('Src', 'ranlib.c'),
os.path.join('Src', 'com.c'),
os.path.join('Src', 'linpack.c')],
extra_compile_args = extra_compile_args),
Extension('lapack_lite', sourcelist,
library_dirs = library_dirs_list,
libraries = libraries_list,
extra_link_args = extra_link_args,
extra_compile_args = extra_compile_args)
]

# add FFT package (optional)
packages.append('FFT')
package_dir['FFT'] = os.path.join('Packages','FFT','Lib')
include_dirs.append(os.path.join('Packages','FFT','Include'))
ext_modules.append(Extension('FFT.fftpack',
[os.path.join('Packages','FFT','Src',
'fftpackmodule.c'),
os.path.join('Packages', 'FFT', 'Src',
'fftpack.c')],
extra_compile_args = extra_compile_args))

# add MA package (optional)
packages.append('MA')
package_dir['MA'] = os.path.join('Packages', 'MA', 'Lib')

# add RNG package (optional)
packages.append('RNG')
packages.append('RNG')
package_dir['RNG'] = os.path.join('Packages', 'RNG', 'Lib')
include_dirs.append(os.path.join('Packages', 'RNG', 'Include'))
ext_modules.append(Extension('RNG.RNG',
[os.path.join('Packages', 'RNG', 'Src',
'RNGmodule.c'),
os.path.join('Packages', 'RNG', 'Src',
'ranf.c'),
os.path.join('Packages', 'RNG', 'Src',
'pmath_rng.c')],
extra_compile_args = extra_compile_args))
# add dotblas package (optional)
if use_dotblas:
packages.append('dotblas')
package_dir['dotblas'] = os.path.join('Packages', 'dotblas',
'dotblas')
ext_modules.append(Extension('_dotblas',
[os.path.join('Packages', 'dotblas',
'dotblas', '_dotblas.c')],
library_dirs = library_dirs_list,
libraries = libraries_list,

extra_compile_args=extra_compile_args))




long_description = """
Numerical Extension to Python with subpackages.

The authors and maintainers of the subpackages are:

FFTPACK-3.1
maintainer = "Numerical Python Developers"
maintainer_email = "numpy-discussion at lists.sourceforge.net"
description = "Fast Fourier Transforms"
url = "http://numpy.sourceforge.net"

MA-%s
author = "Paul F. Dubois"
description = "Masked Array facility"
maintainer = "Paul F. Dubois"
maintainer_email = "dubois at users.sf.net"
url = "http://sourceforge.net/projects/numpy"

RNG-3.1
author = "Lee Busby, Paul F. Dubois, Fred Fritsch"
maintainer = "Paul F. Dubois"
maintainer_email = "dubois at users.sf.net"
description = "Cray-like Random number package."
""" % (MA_version, )

# Oops, another bug in Distutils!?
# Write rpm_build.sh pointing to this python
rpm_build_text="""env CFLAGS="$RPM_OPT_FLAGS" %setup.py build\n""" %
sys.executable
rpm_script = open("rpm_build.sh", "w")
rpm_script.write(rpm_build_text)
rpm_script.close()

# Write rpm_install.sh pointing to this python
rpm_install_text=sys.executable +""" setup.py install
--root=$RPM_BUILD_ROOT

cat >INSTALLED_FILES <<EOF
%doc Demo
EOF
find $RPM_BUILD_ROOT -type f | sed -e "s|$RPM_BUILD_ROOT||g"
>>INSTALLED_FILES

"""
rpm_script = open("rpm_install.sh", "w")
rpm_script.write(rpm_install_text)
rpm_script.close()

setup (name = "Numeric",
version = numeric_version,
maintainer = "Numerical Python Developers",
maintainer_email = "numpy-developers at lists.sourceforge.net",
description = "Numerical Extension to Python",
long_description = long_description,
url = "http://numpy.sourceforge.net",

# distutils allows you to fix or fudge anything :-)
extra_path = 'Numeric',
packages = packages,
package_dir = package_dir,
headers = headers,
include_dirs = include_dirs,
ext_modules = ext_modules
)

print 'MA Version', MA_version
print 'Numeric Version', numeric_version




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