[SciPy-user] Problems while trying to build scipy with umfpack on Intel MacBook Pro

Rick Muller rpmuller@gmail....
Sun Jul 20 13:24:43 CDT 2008


I'm trying to get a scipy build that contains umfpack on an Intel MacBook
Pro. I believe that I've compiled and installed umfpack correctly.


I appended the output I get from the build to this message. In short, I get
some warnings about having multiply defined "-arch" flags, but I'm not clear
whether this is the fatal error or not. At the end of the install process, I
have what looks like a umfpack directory:

$ ls  /Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/
site-packages/scipy/linsolve/umfpack/
__init__.py     _umfpack.py     info.pyc        tests/
__init__.pyc    _umfpack.pyc    setup.py        umfpack.py
__umfpack.so    info.py         setup.pyc       umfpack.pyc

But for some reason I can't import it:

s886301{rmuller}[1]: import scipy.linsolve.umfpack as um
---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call
last)

/Users/rmuller/<ipython console> in <module>()
AttributeError: 'module' object has no attribute 'umfpack'


Any suggestions?


mkl_info:
  libraries mkl,vml,guide not found in
/Library/Frameworks/Python.framework/Versions/2.5/lib
  libraries mkl,vml,guide not found in /usr/local/lib
  libraries mkl,vml,guide not found in /usr/lib
  NOT AVAILABLE

fftw3_info:
  libraries fftw3 not found in
/Library/Frameworks/Python.framework/Versions/2.5/lib
  libraries fftw3 not found in /usr/local/lib
  libraries fftw3 not found in /usr/lib
  fftw3 not found
  NOT AVAILABLE

fftw2_info:
  libraries rfftw,fftw not found in
/Library/Frameworks/Python.framework/Versions/2.5/lib
  libraries rfftw,fftw not found in /usr/local/lib
  libraries rfftw,fftw not found in /usr/lib
  fftw2 not found
  NOT AVAILABLE

dfftw_info:
  libraries drfftw,dfftw not found in
/Library/Frameworks/Python.framework/Versions/2.5/lib
  libraries drfftw,dfftw not found in /usr/local/lib
  libraries drfftw,dfftw not found in /usr/lib
  dfftw not found
  NOT AVAILABLE

djbfft_info:
  NOT AVAILABLE

blas_opt_info:
  FOUND:
    extra_link_args = ['-Wl,-framework', '-Wl,Accelerate']
    define_macros = [('NO_ATLAS_INFO', 3)]
    extra_compile_args = ['-faltivec',
'-I/System/Library/Frameworks/vecLib.framework/Headers']

lapack_opt_info:
  FOUND:
    extra_link_args = ['-Wl,-framework', '-Wl,Accelerate']
    define_macros = [('NO_ATLAS_INFO', 3)]
    extra_compile_args = ['-faltivec']

non-existing path in 'scipy/linsolve': 'tests'
umfpack_info:
  libraries umfpack not found in
/Library/Frameworks/Python.framework/Versions/2.5/lib
amd_info:
  libraries amd not found in
/Library/Frameworks/Python.framework/Versions/2.5/lib
  libraries amd not found in /usr/local/lib
  libraries amd not found in /usr/lib
  NOT AVAILABLE

  FOUND:
    libraries = ['umfpack']
    library_dirs = ['/usr/local/lib']
    swig_opts = ['-I/usr/local/include']
    define_macros = [('SCIPY_UMFPACK_H', None)]
    include_dirs = ['/usr/local/include']

running build
running scons
customize UnixCCompiler
Found executable /usr/bin/gcc
customize NAGFCompiler
Could not locate executable f95
customize AbsoftFCompiler
Could not locate executable f90
Could not locate executable f77
customize IBMFCompiler
Could not locate executable xlf90
Could not locate executable xlf
customize IntelFCompiler
Could not locate executable ifort
Could not locate executable ifc
customize GnuFCompiler
Could not locate executable g77
customize Gnu95FCompiler
Found executable /usr/local/bin/gfortran
customize Gnu95FCompiler
customize UnixCCompiler
customize UnixCCompiler using scons
running config_cc
unifing config_cc, config, build_clib, build_ext, build commands --compiler
options
running config_fc
unifing config_fc, config, build_clib, build_ext, build commands --fcompiler
options
running build_src
building py_modules sources
building library "dfftpack" sources
building library "linpack_lite" sources
building library "mach" sources
building library "quadpack" sources
building library "odepack" sources
building library "fitpack" sources
building library "superlu_src" sources
building library "odrpack" sources
building library "minpack" sources
building library "rootfind" sources
building library "c_misc" sources
building library "cephes" sources
building library "mach" sources
building library "toms" sources
building library "amos" sources
building library "cdf" sources
building library "specfun" sources
building library "statlib" sources
building extension "scipy.cluster._vq" sources
building extension "scipy.fftpack._fftpack" sources
f2py options: []
  adding 'build/src.macosx-10.3-fat-2.5/fortranobject.c' to sources.
  adding 'build/src.macosx-10.3-fat-2.5' to include_dirs.
building extension "scipy.fftpack.convolve" sources
f2py options: []
  adding 'build/src.macosx-10.3-fat-2.5/fortranobject.c' to sources.
  adding 'build/src.macosx-10.3-fat-2.5' to include_dirs.
building extension "scipy.integrate._quadpack" sources
building extension "scipy.integrate._odepack" sources
building extension "scipy.integrate.vode" sources
f2py options: []
  adding 'build/src.macosx-10.3-fat-2.5/fortranobject.c' to sources.
  adding 'build/src.macosx-10.3-fat-2.5' to include_dirs.
building extension "scipy.interpolate._fitpack" sources
building extension "scipy.interpolate.dfitpack" sources
f2py options: []
  adding 'build/src.macosx-10.3-fat-2.5/fortranobject.c' to sources.
  adding 'build/src.macosx-10.3-fat-2.5' to include_dirs.
  adding
'build/src.macosx-10.3-fat-2.5/scipy/interpolate/dfitpack-f2pywrappers.f' to
sources.
building extension "scipy.io.numpyio" sources
building extension "scipy.lib.blas.fblas" sources
f2py options: ['skip:', ':']
  adding 'build/src.macosx-10.3-fat-2.5/fortranobject.c' to sources.
  adding 'build/src.macosx-10.3-fat-2.5' to include_dirs.
  adding
'build/src.macosx-10.3-fat-2.5/build/src.macosx-10.3-fat-2.5/scipy/lib/blas/fblas-f2pywrappers.f'
to sources.
building extension "scipy.lib.blas.cblas" sources
  adding 'build/src.macosx-10.3-fat-2.5/scipy/lib/blas/cblas.pyf' to
sources.
f2py options: ['skip:', ':']
  adding 'build/src.macosx-10.3-fat-2.5/fortranobject.c' to sources.
  adding 'build/src.macosx-10.3-fat-2.5' to include_dirs.
building extension "scipy.lib.lapack.flapack" sources
f2py options: ['skip:', ':']
  adding 'build/src.macosx-10.3-fat-2.5/fortranobject.c' to sources.
  adding 'build/src.macosx-10.3-fat-2.5' to include_dirs.
building extension "scipy.lib.lapack.clapack" sources
  adding 'build/src.macosx-10.3-fat-2.5/scipy/lib/lapack/clapack.pyf' to
sources.
f2py options: ['skip:', ':']
  adding 'build/src.macosx-10.3-fat-2.5/fortranobject.c' to sources.
  adding 'build/src.macosx-10.3-fat-2.5' to include_dirs.
building extension "scipy.lib.lapack.calc_lwork" sources
f2py options: []
  adding 'build/src.macosx-10.3-fat-2.5/fortranobject.c' to sources.
  adding 'build/src.macosx-10.3-fat-2.5' to include_dirs.
building extension "scipy.lib.lapack.atlas_version" sources
building extension "scipy.linalg.fblas" sources
  adding 'build/src.macosx-10.3-fat-2.5/scipy/linalg/fblas.pyf' to sources.
f2py options: []
  adding 'build/src.macosx-10.3-fat-2.5/fortranobject.c' to sources.
  adding 'build/src.macosx-10.3-fat-2.5' to include_dirs.
  adding
'build/src.macosx-10.3-fat-2.5/build/src.macosx-10.3-fat-2.5/scipy/linalg/fblas-f2pywrappers.f'
to sources.
building extension "scipy.linalg.cblas" sources
  adding 'build/src.macosx-10.3-fat-2.5/scipy/linalg/cblas.pyf' to sources.
f2py options: []
  adding 'build/src.macosx-10.3-fat-2.5/fortranobject.c' to sources.
  adding 'build/src.macosx-10.3-fat-2.5' to include_dirs.
building extension "scipy.linalg.flapack" sources
  adding 'build/src.macosx-10.3-fat-2.5/scipy/linalg/flapack.pyf' to
sources.
f2py options: []
  adding 'build/src.macosx-10.3-fat-2.5/fortranobject.c' to sources.
  adding 'build/src.macosx-10.3-fat-2.5' to include_dirs.
  adding
'build/src.macosx-10.3-fat-2.5/build/src.macosx-10.3-fat-2.5/scipy/linalg/flapack-f2pywrappers.f'
to sources.
building extension "scipy.linalg.clapack" sources
  adding 'build/src.macosx-10.3-fat-2.5/scipy/linalg/clapack.pyf' to
sources.
f2py options: []
  adding 'build/src.macosx-10.3-fat-2.5/fortranobject.c' to sources.
  adding 'build/src.macosx-10.3-fat-2.5' to include_dirs.
building extension "scipy.linalg._flinalg" sources
f2py options: []
  adding 'build/src.macosx-10.3-fat-2.5/fortranobject.c' to sources.
  adding 'build/src.macosx-10.3-fat-2.5' to include_dirs.
building extension "scipy.linalg.calc_lwork" sources
f2py options: []
  adding 'build/src.macosx-10.3-fat-2.5/fortranobject.c' to sources.
  adding 'build/src.macosx-10.3-fat-2.5' to include_dirs.
building extension "scipy.linalg.atlas_version" sources
building extension "scipy.linalg._iterative" sources
f2py options: []
  adding 'build/src.macosx-10.3-fat-2.5/fortranobject.c' to sources.
  adding 'build/src.macosx-10.3-fat-2.5' to include_dirs.
building extension "scipy.linsolve._zsuperlu" sources
building extension "scipy.linsolve._dsuperlu" sources
building extension "scipy.linsolve._csuperlu" sources
building extension "scipy.linsolve._ssuperlu" sources
building extension "scipy.linsolve.umfpack.__umfpack" sources
  adding 'scipy/linsolve/umfpack/umfpack.i' to sources.
building extension "scipy.odr.__odrpack" sources
building extension "scipy.optimize._minpack" sources
building extension "scipy.optimize._zeros" sources
building extension "scipy.optimize._lbfgsb" sources
f2py options: []
  adding 'build/src.macosx-10.3-fat-2.5/fortranobject.c' to sources.
  adding 'build/src.macosx-10.3-fat-2.5' to include_dirs.
building extension "scipy.optimize.moduleTNC" sources
building extension "scipy.optimize._cobyla" sources
f2py options: []
  adding 'build/src.macosx-10.3-fat-2.5/fortranobject.c' to sources.
  adding 'build/src.macosx-10.3-fat-2.5' to include_dirs.
building extension "scipy.optimize.minpack2" sources
f2py options: []
  adding 'build/src.macosx-10.3-fat-2.5/fortranobject.c' to sources.
  adding 'build/src.macosx-10.3-fat-2.5' to include_dirs.
building extension "scipy.signal.sigtools" sources
building extension "scipy.signal.spline" sources
building extension "scipy.sparse._sparsetools" sources
building extension "scipy.special._cephes" sources
building extension "scipy.special.specfun" sources
f2py options: ['--no-wrap-functions']
  adding 'build/src.macosx-10.3-fat-2.5/fortranobject.c' to sources.
  adding 'build/src.macosx-10.3-fat-2.5' to include_dirs.
building extension "scipy.stats.statlib" sources
f2py options: ['--no-wrap-functions']
  adding 'build/src.macosx-10.3-fat-2.5/fortranobject.c' to sources.
  adding 'build/src.macosx-10.3-fat-2.5' to include_dirs.
building extension "scipy.stats.futil" sources
f2py options: []
  adding 'build/src.macosx-10.3-fat-2.5/fortranobject.c' to sources.
  adding 'build/src.macosx-10.3-fat-2.5' to include_dirs.
building extension "scipy.stats.mvn" sources
f2py options: []
  adding 'build/src.macosx-10.3-fat-2.5/fortranobject.c' to sources.
  adding 'build/src.macosx-10.3-fat-2.5' to include_dirs.
  adding 'build/src.macosx-10.3-fat-2.5/scipy/stats/mvn-f2pywrappers.f' to
sources.
building extension "scipy.ndimage._nd_image" sources
building data_files sources
running build_py
copying build/src.macosx-10.3-fat-2.5/scipy/__config__.py ->
build/lib.macosx-10.3-fat-2.5/scipy
creating build/lib.macosx-10.3-fat-2.5/scipy/linsolve/umfpack
copying scipy/linsolve/umfpack/__init__.py ->
build/lib.macosx-10.3-fat-2.5/scipy/linsolve/umfpack
copying scipy/linsolve/umfpack/info.py ->
build/lib.macosx-10.3-fat-2.5/scipy/linsolve/umfpack
copying scipy/linsolve/umfpack/setup.py ->
build/lib.macosx-10.3-fat-2.5/scipy/linsolve/umfpack
copying scipy/linsolve/umfpack/umfpack.py ->
build/lib.macosx-10.3-fat-2.5/scipy/linsolve/umfpack
copying build/src.macosx-10.3-fat-2.5/scipy/linsolve/umfpack/_umfpack.py ->
build/lib.macosx-10.3-fat-2.5/scipy/linsolve/umfpack
running build_clib
customize UnixCCompiler
customize UnixCCompiler using build_clib
customize NAGFCompiler
customize AbsoftFCompiler
customize IBMFCompiler
customize IntelFCompiler
customize GnuFCompiler
customize Gnu95FCompiler
customize Gnu95FCompiler
customize Gnu95FCompiler using build_clib
running build_ext
customize UnixCCompiler
customize UnixCCompiler using build_ext
library 'mach' defined more than once, overwriting build_info
{'sources': ['scipy/integrate/mach/d1mach.f',
'scipy/integrate/mach/i1mach.f', 'scipy/integrate/mach/r1mach.f',
'scipy/integrate/mach/xerror.f'], 'config_fc': {'noopt':
('scipy/integrate/setup.pyc', 1)}, 'source_languages': ['f77']}...
with
{'sources': ['scipy/special/mach/d1mach.f', 'scipy/special/mach/i1mach.f',
'scipy/special/mach/r1mach.f', 'scipy/special/mach/xerror.f'], 'config_fc':
{'noopt': ('scipy/special/setup.pyc', 1)}, 'source_languages': ['f77']}...
extending extension 'scipy.linsolve._zsuperlu' defined_macros with
[('USE_VENDOR_BLAS', 1)]
extending extension 'scipy.linsolve._dsuperlu' defined_macros with
[('USE_VENDOR_BLAS', 1)]
extending extension 'scipy.linsolve._csuperlu' defined_macros with
[('USE_VENDOR_BLAS', 1)]
extending extension 'scipy.linsolve._ssuperlu' defined_macros with
[('USE_VENDOR_BLAS', 1)]
customize UnixCCompiler
customize UnixCCompiler using build_ext
customize NAGFCompiler
customize AbsoftFCompiler
customize IBMFCompiler
customize IntelFCompiler
customize GnuFCompiler
customize Gnu95FCompiler
customize Gnu95FCompiler
customize Gnu95FCompiler using build_ext
building 'scipy.linsolve.umfpack.__umfpack' extension
compiling C sources
C compiler: gcc -arch ppc -arch i386 -isysroot
/Developer/SDKs/MacOSX10.4u.sdk -fno-strict-aliasing -Wno-long-double
-no-cpp-precomp -mno-fused-madd -fno-common -dynamic -DNDEBUG -g -O3

compile options: '-DSCIPY_UMFPACK_H -DNO_ATLAS_INFO=3 -I/usr/local/include
-I/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/numpy/core/include
-I/Library/Frameworks/Python.framework/Versions/2.5/include/python2.5 -c'
extra options: '-faltivec
-I/System/Library/Frameworks/vecLib.framework/Headers'
gcc -arch i386 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -g
-bundle -undefined dynamic_lookup
build/temp.macosx-10.3-fat-2.5/build/src.macosx-10.3-fat-2.5/scipy/linsolve/umfpack/_umfpack_wrap.o
-L/usr/local/lib -Lbuild/temp.macosx-10.3-fat-2.5 -lumfpack -o
build/lib.macosx-10.3-fat-2.5/scipy/linsolve/umfpack/__umfpack.so
-Wl,-framework -Wl,Accelerate
/usr/bin/ld: for architecture ppc
/usr/bin/ld: warning /usr/local/lib/libumfpack.a archive's cputype (7,
architecture i386) does not match cputype (18) for specified -arch flag: ppc
(can't load from it)
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