[SciPy-user] Compile scipy from SVN on OS X: no clapack ?
Pierre GM
pgmdevlist at gmail.com
Tue Apr 7 17:52:00 EDT 2009
All,
I'm working on a piece of code that requires numerous calls to
scipy.linalg.eigvals. I was surprised by the slowness of the code, so
I figured I'd check whether my installation of scipy was correct.
Turns out it's probably not: running the tests, I end up w/ some
messages indicating that clapack is empty. That never really mattered
until now...
Could anybody try and hold my hand on this one (I'm still a newbie on
Mac) ?
* I do have an Accelerate framework in my /System/Library
* The python I use is the 2.5.4 from macports
* I have a macports atlas (v3.8.2)
* I do want to compile from source: I usually install scipy/numpy w/
python -c "import setuptools; execfile('setup.py')" develop in virtual
environments (that way, I can get the latest changes I make straight
away).
* extra config info below
Obviously I'm missing some configuration step somewhere, or I'm mixing
things that shouldn't be.
Note that following the info in INSTALL.txt, I tried to run
python setup_atlas_version.py build_ext --inplace --force
but failed w/ a
Traceback (most recent call last):
File "setup_atlas_version.py", line 7, in <module>
from numpy.distutils.misc_util import get_path, default_config_dict
ImportError: cannot import name get_path
Any help welcome.
Thanks an awful lot in advance
P.
__________
>>> python setup.py build 2>&1 | tee build.log
File downloadable at
http://rapidshare.com/files/218658464/build.log.html
__________
>>> python -c "from numpy.f2py.diagnose import run; run()"
------
os.name='posix'
------
sys.platform='darwin'
------
sys.version:
2.5.4 (r254:67916, Apr 1 2009, 17:15:22)
[GCC 4.0.1 (Apple Inc. build 5490)]
------
sys.prefix:
/Users/pierregm/Computing/.pythonenvs/default/bin/..
------
sys.path=':/Users/pierregm/Computing/.pythonenvs/default/lib/python2.5/
site-packages/setuptools-0.6c9-py2.5.egg:/Users/pierregm/
Computing/.pythonenvs/default/lib/python2.5/site-packages/
ipython-0.9.1-py2.5.egg:/Users/pierregm/Computing/workspace/svn_numpy:/
Users/pierregm/Computing/.pythonenvs/default/lib/python2.5/site-
packages/nose-0.10.4-py2.5.egg:/Users/pierregm/Computing/workspace/
svn_scipy:/Users/pierregm/Computing/.pythonenvs/default/lib/python2.5/
site-packages/BeautifulSoup-3.1.0.1-py2.5.egg:/Users/pierregm/
Computing/.pythonenvs/default/lib/python2.5/site-packages/xlrd-0.6.1-
py2.5.egg:/Users/pierregm/Computing/.pythonenvs/default/lib/python2.5/
site-packages/Sphinx-0.6.1-py2.5.egg:/Users/pierregm/
Computing/.pythonenvs/default/lib/python2.5/site-packages/Jinja2-2.1.1-
py2.5-macosx-10.5-i386.egg:/Users/pierregm/Computing/.pythonenvs/
default/lib/python2.5/site-packages/SquareMap-1.0.0b23-py2.5.egg:/
Users/pierregm/Computing/.pythonenvs/default/lib/python2.5/site-
packages/RunSnakeRun-2.0.0b4-py2.5.egg:/opt/local/Library/Frameworks/
Python.framework/Versions/2.5/lib/python2.5/site-packages/Jinja-1.2-
py2.5-macosx-10.3-i386.egg:/opt/local/Library/Frameworks/
Python.framework/Versions/2.5/lib/python2.5/site-packages/
Pygments-0.11.1-py2.5.egg:/opt/local/Library/Frameworks/
Python.framework/Versions/2.5/lib/python2.5/site-packages/yolk-0.4.1-
py2.5.egg:/opt/local/Library/Frameworks/Python.framework/Versions/2.5/
lib/python2.5/site-packages/Sphinx-0.5-py2.5.egg:/opt/local/Library/
Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/
cocos2d-0.3.0-py2.5.egg:/opt/local/Library/Frameworks/Python.framework/
Versions/2.5/lib/python2.5/site-packages/virtualenv-1.3.2-py2.5.egg:/
Users/pierregm/Computing/workspace/hydroclimpy:/Users/pierregm/
Computing/workspace/svn_scikits_timeseries:/Library/Frameworks/
GDAL.framework/Versions/1.6/lib:/Users/pierregm/Computing/.pythonenvs/
default/lib/python25.zip:/Users/pierregm/Computing/.pythonenvs/default/
lib/python2.5:/Users/pierregm/Computing/.pythonenvs/default/lib/
python2.5/plat-darwin:/Users/pierregm/Computing/.pythonenvs/default/
lib/python2.5/plat-mac:/Users/pierregm/Computing/.pythonenvs/default/
lib/python2.5/plat-mac/lib-scriptpackages:/Users/pierregm/
Computing/.pythonenvs/default/lib/python2.5/lib-tk:/Users/pierregm/
Computing/.pythonenvs/default/lib/python2.5/lib-dynload:/opt/local/
Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5:/opt/
local/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/
lib-tk:/opt/local/Library/Frameworks/Python.framework/Versions/2.5/lib/
python2.5/plat-darwin:/opt/local/Library/Frameworks/Python.framework/
Versions/2.5/lib/python2.5/plat-mac:/opt/local/Library/Frameworks/
Python.framework/Versions/2.5/lib/python2.5/plat-mac/lib-
scriptpackages:/Users/pierregm/Computing/.pythonenvs/default/lib/
python2.5/site-packages:/opt/local/Library/Frameworks/Python.framework/
Versions/2.5/lib/python2.5/site-packages:/opt/local/Library/Frameworks/
Python.framework/Versions/2.5/lib/python2.5/site-packages/Numeric:/opt/
local/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/
site-packages/PyObjC:/opt/local/Library/Frameworks/Python.framework/
Versions/2.5/lib/python2.5/site-packages/gtk-2.0:/opt/local/lib/
python2.5/site-packages:/opt/local/lib/svn-python2.5:/opt/local/
Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-
packages/wx-2.8-mac-unicode'
------
Failed to import numarray: No module named numarray
Found Numeric version '24.2' in /opt/local/Library/Frameworks/
Python.framework/Versions/2.5/lib/python2.5/site-packages/Numeric/
Numeric.pyc
Found new numpy version '1.4.0.dev' in /Users/pierregm/Computing/
workspace/svn_numpy/numpy/__init__.pyc
Found f2py2e version '2' in /Users/pierregm/Computing/workspace/
svn_numpy/numpy/f2py/f2py2e.pyc
Found numpy.distutils version '0.4.0' in '/Users/pierregm/Computing/
workspace/svn_numpy/numpy/distutils/__init__.pyc'
------
Importing numpy.distutils.fcompiler ... ok
------
Checking availability of supported Fortran compilers:
Using built-in specs.
Target: powerpc-apple-darwin8
Configured with: /Builds/unix/gcc/gcc-4.2/configure --prefix=/usr/
local --mandir=/share/man --program-transform-name=/^[cg][^.-]*$/s/
$/-4.2/ --build=i686-apple-darwin8 --host=i686-apple-darwin8 --
target=powerpc-apple-darwin8 --enable-languages=fortran
Thread model: posix
gcc version 4.2.3
Using built-in specs.
Target: i686-apple-darwin8
Configured with: /Builds/unix/gcc/gcc-4.2/configure --prefix=/usr/
local --mandir=/share/man --program-transform-name=/^[cg][^.-]*$/s/
$/-4.2/ --build=i686-apple-darwin8 --host=i686-apple-darwin8 --
target=i686-apple-darwin8 --enable-languages=fortran
Thread model: posix
gcc version 4.2.3
Using built-in specs.
Target: powerpc-apple-darwin8
Configured with: /Builds/unix/gcc/gcc-4.2/configure --prefix=/usr/
local --mandir=/share/man --program-transform-name=/^[cg][^.-]*$/s/
$/-4.2/ --build=i686-apple-darwin8 --host=i686-apple-darwin8 --
target=powerpc-apple-darwin8 --enable-languages=fortran
Thread model: posix
gcc version 4.2.3
Using built-in specs.
Target: i686-apple-darwin8
Configured with: /Builds/unix/gcc/gcc-4.2/configure --prefix=/usr/
local --mandir=/share/man --program-transform-name=/^[cg][^.-]*$/s/
$/-4.2/ --build=i686-apple-darwin8 --host=i686-apple-darwin8 --
target=i686-apple-darwin8 --enable-languages=fortran
Thread model: posix
gcc version 4.2.3
Gnu95FCompiler instance properties:
archiver = ['/usr/local/bin/gfortran', '-cr']
compile_switch = '-c'
compiler_f77 = ['/usr/local/bin/gfortran', '-Wall', '-ffixed-
form', '-
fno-second-underscore', '-arch', 'ppc', '-arch',
'i686', '
-fPIC', '-O3', '-funroll-loops']
compiler_f90 = ['/usr/local/bin/gfortran', '-Wall', '-fno-second-
underscore', '-arch', 'ppc', '-arch', 'i686', '-
fPIC', '-
O3', '-funroll-loops']
compiler_fix = ['/usr/local/bin/gfortran', '-Wall', '-ffixed-
form', '-
fno-second-underscore', '-Wall', '-fno-second-
underscore',
'-arch', 'ppc', '-arch', 'i686', '-fPIC', '-O3', '-
funroll
-loops']
libraries = ['gfortran']
library_dirs = []
linker_exe = ['/usr/local/bin/gfortran', '-Wall', '-Wall']
linker_so = ['/usr/local/bin/gfortran', '-Wall', '-arch',
'ppc', '-
arch', 'i686', '-Wall', '-undefined',
'dynamic_lookup', '-
bundle']
object_switch = '-o '
ranlib = ['/usr/local/bin/gfortran']
version = LooseVersion ('4.2.3')
version_cmd = ['/usr/local/bin/gfortran', '--version']
Fortran compilers found:
--fcompiler=gnu95 GNU Fortran 95 compiler (4.2.3)
Compilers available for this platform, but not found:
--fcompiler=absoft Absoft Corp Fortran Compiler
--fcompiler=g95 G95 Fortran Compiler
--fcompiler=gnu GNU Fortran 77 compiler
--fcompiler=ibm IBM XL Fortran Compiler
--fcompiler=intel Intel Fortran Compiler for 32-bit apps
--fcompiler=nag NAGWare Fortran 95 Compiler
Compilers not available on this platform:
--fcompiler=compaq Compaq Fortran Compiler
--fcompiler=hpux HP Fortran 90 Compiler
--fcompiler=intele Intel Fortran Compiler for Itanium apps
--fcompiler=intelem Intel Fortran Compiler for EM64T-based apps
--fcompiler=intelev Intel Visual Fortran Compiler for Itanium apps
--fcompiler=intelv Intel Visual Fortran Compiler for 32-bit apps
--fcompiler=lahey Lahey/Fujitsu Fortran 95 Compiler
--fcompiler=mips MIPSpro Fortran Compiler
--fcompiler=none Fake Fortran compiler
--fcompiler=pg Portland Group Fortran Compiler
--fcompiler=sun Sun or Forte Fortran 95 Compiler
--fcompiler=vast Pacific-Sierra Research Fortran 90 Compiler
For compiler details, run 'config_fc --verbose' setup command.
------
Importing numpy.distutils.cpuinfo ... ok
------
CPU information: CPUInfoBase__get_nbits getNCPUs is_32bit is_i386 ------
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