[SciPy-Dev] Mountain Lion Scipy-dev build fails

Aaron Andalman nerduno.list@gmail....
Wed Aug 8 15:32:03 CDT 2012


Dear scipy-dev list,

Scipy is failing to build on Mountain Lion, despite my using the latest
fixes on github.  I'm using pip install -e git+
https://github.com/scipy/scipy#egg=scipy-dev

The installation crashes on the line:

/usr/bin/llvm-gcc -fno-strict-aliasing -fno-common -dynamic -arch i386
-arch x86_64 -O3 -w -pipe -march=core2 -msse4 -DNDEBUG -g -fwrapv -O3 -Wall
-Wstrict-prototypes -Iscipy/sparse/linalg/eigen/arpack/ARPACK/SRC
-I/usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/include
-c scipy/sparse/linalg/eigen/arpack/ARPACK/FWRAPPERS/veclib_cabi_c.c -o
build/temp.macosx-10.5-intel-2.7/scipy/sparse/linalg/eigen/arpack/ARPACK/FWRAPPERS/veclib_cabi_c.o"
failed with exit status 1


With the error:

In file included from
/System/Library/Frameworks/vecLib.framework/Headers/vecLib.h:43,
                 from
/System/Library/Frameworks/Accelerate.framework/Headers/Accelerate.h:20,
                 from
scipy/sparse/linalg/eigen/arpack/ARPACK/FWRAPPERS/veclib_cabi_c.c:2:
/System/Library/Frameworks/vecLib.framework/Headers/vfp.h:51:23: error:
immintrin.h: No such file or directory
In file included from
/System/Library/Frameworks/vecLib.framework/Headers/vecLib.h:43,
                 from
/System/Library/Frameworks/Accelerate.framework/Headers/Accelerate.h:20,
                 from
scipy/sparse/linalg/eigen/arpack/ARPACK/FWRAPPERS/veclib_cabi_c.c:2:
/System/Library/Frameworks/vecLib.framework/Headers/vfp.h: In function
‘vceilf’:
/System/Library/Frameworks/vecLib.framework/Headers/vfp.h:53: error:
incompatible types in return
...

I can compile veclib_cabi.c.c, if I change the -msse4 compilation flag to
-msse3 (or if I use clang, but this causes other errors).

Thus my questions are:

1) how can I change the compilations flags used by python setup.py to
include -msse3 instead of -msse4?
2) why is -msse4 being selected by python setup.py in the first place?
3) is this a bug with setup.py on mountain lion, or is this a problem with
my installation?

Below is the information requested by the scipy installation readme.

python -c 'from numpy.f2py.diagnose import run; run()'
------
os.name='posix'
------
sys.platform='darwin'
------
sys.version:
2.7.2 (default, Jan 14 2012, 15:51:45)
[GCC 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2335.15.00)]
------
sys.prefix:
/Users/andalman/Documents/Code/_virtualenvs/main_projects/bin/..
------
sys.path=':/Users/andalman/Documents/Code/_virtualenvs/main_projects/lib/python2.7/site-packages/setuptools-0.6c11-py2.7.egg:/Users/andalman/Documents/Code/_virtualenvs/main_projects/lib/python2.7/site-packages/pip-1.1-py2.7.egg:/Users/andalman/Documents/Code/_virtualenvs/main_projects/lib/python27.zip:/usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/distribute-0.6.24-py2.7.egg:/usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pip-1.0.2-py2.7.egg:/Users/andalman/Documents/Code/_virtualenvs/main_projects/lib/python2.7:/Users/andalman/Documents/Code/_virtualenvs/main_projects/lib/python2.7/plat-darwin:/Users/andalman/Documents/Code/_virtualenvs/main_projects/lib/python2.7/plat-mac:/Users/andalman/Documents/Code/_virtualenvs/main_projects/lib/python2.7/plat-mac/lib-scriptpackages:/Users/andalman/Documents/Code/_virtualenvs/main_projects/lib/python2.7/lib-tk:/Users/andalman/Documents/Code/_virtualenvs/main_projects/lib/python2.7/lib-old:/Users/andalman/Documents/Code/_virtualenvs/main_projects/lib/python2.7/lib-dynload:/usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/lib/python2.7:/usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-darwin:/usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-tk:/usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-mac:/usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-mac/lib-scriptpackages:/Users/andalman/Documents/Code/_virtualenvs/main_projects/lib/python2.7/site-packages:/Users/andalman/.local/lib/python2.7/site-packages:/usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages:/usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/setuptools-0.6c11-py2.7.egg-info'
------
Found new numpy version '1.6.2' in
/usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/__init__.pyc
Found f2py2e version '2' in
/usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/f2py/f2py2e.pyc
Found numpy.distutils version '0.4.0' in
'/usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/distutils/__init__.pyc'
------
Importing numpy.distutils.fcompiler ... ok
------
Checking availability of supported Fortran compilers:
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', 'i686', '-arch',
                    'x86_64', '-fPIC', '-O3', '-funroll-loops']
  compiler_f90    = ['/usr/local/bin/gfortran', '-Wall', '-fno-second-
                    underscore', '-arch', 'i686', '-arch', 'x86_64',
'-fPIC',
                    '-O3', '-funroll-loops']
  compiler_fix    = ['/usr/local/bin/gfortran', '-Wall', '-ffixed-form', '-
                    fno-second-underscore', '-Wall',
'-fno-second-underscore',
                    '-arch', 'i686', '-arch', 'x86_64', '-fPIC', '-O3', '-
                    funroll-loops']
  libraries       = ['gfortran']
  library_dirs    = []
  linker_exe      = ['/usr/local/bin/gfortran', '-Wall', '-Wall']
  linker_so       = ['/usr/local/bin/gfortran', '-Wall', '-arch', 'i686', '-
                    arch', 'x86_64', '-Wall', '-undefined',
'dynamic_lookup',
                    '-bundle']
  object_switch   = '-o '
  ranlib          = ['/usr/local/bin/gfortran']
  version         = LooseVersion ('4.2.1')
  version_cmd     = ['/usr/local/bin/gfortran', '--version']
Fortran compilers found:
  --fcompiler=gnu95  GNU Fortran 95 compiler (4.2.1)
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
  --fcompiler=pg      Portland Group Fortran 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 64-bit apps
  --fcompiler=intelev   Intel Visual Fortran Compiler for Itanium apps
  --fcompiler=intelv    Intel Visual Fortran Compiler for 32-bit apps
  --fcompiler=intelvem  Intel Visual Fortran Compiler for 64-bit apps
  --fcompiler=lahey     Lahey/Fujitsu Fortran 95 Compiler
  --fcompiler=mips      MIPSpro Fortran Compiler
  --fcompiler=none      Fake Fortran compiler
  --fcompiler=pathf95   PathScale 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_64bit is_i386 ------
(main_projects)Aaron-Andalmans-MacBook-Pro:scipy andalman$

####################################

ython
/usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/Current/lib/python2.7/site-packages//numpy/distutils/system_info.py
lapack_info:
  libraries lapack not found in
/Users/andalman/Documents/Code/_virtualenvs/main_projects/bin/../lib
  libraries lapack not found in /usr/local/lib
  FOUND:
    libraries = ['lapack']
    library_dirs = ['/usr/lib']
    language = f77

lapack_opt_info:
  FOUND:
    extra_link_args = ['-Wl,-framework', '-Wl,Accelerate']
    define_macros = [('NO_ATLAS_INFO', 3)]
    extra_compile_args = ['-msse3']

wx_info:
Could not locate executable wx-config
File not found: None. Cannot determine wx info.
  NOT AVAILABLE

lapack_atlas_info:
  libraries lapack_atlas,f77blas,cblas,atlas not found in
/Users/andalman/Documents/Code/_virtualenvs/main_projects/bin/../lib
  libraries lapack_atlas not found in
/Users/andalman/Documents/Code/_virtualenvs/main_projects/bin/../lib
  libraries lapack_atlas,f77blas,cblas,atlas not found in /usr/local/lib
  libraries lapack_atlas not found in /usr/local/lib
  libraries lapack_atlas,f77blas,cblas,atlas not found in /usr/lib
  libraries lapack_atlas not found in /usr/lib
__main__.lapack_atlas_info
  NOT AVAILABLE

umfpack_info:
  libraries umfpack not found in
/Users/andalman/Documents/Code/_virtualenvs/main_projects/bin/../lib
amd_info:
  libraries amd not found in
/Users/andalman/Documents/Code/_virtualenvs/main_projects/bin/../lib
  FOUND:
    libraries = ['amd']
    library_dirs = ['/usr/local/lib']
    swig_opts = ['-I/usr/local/include']
    define_macros = [('SCIPY_AMD_H', None)]
    include_dirs = ['/usr/local/include']

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

_pkg_config_info:
Found executable /usr/local/bin/pkg-config
  NOT AVAILABLE

lapack_atlas_threads_info:
Setting PTATLAS=ATLAS
  libraries lapack_atlas,ptf77blas,ptcblas,atlas not found in
/Users/andalman/Documents/Code/_virtualenvs/main_projects/bin/../lib
  libraries lapack_atlas not found in
/Users/andalman/Documents/Code/_virtualenvs/main_projects/bin/../lib
  libraries lapack_atlas,ptf77blas,ptcblas,atlas not found in /usr/local/lib
  libraries lapack_atlas not found in /usr/local/lib
  libraries lapack_atlas,ptf77blas,ptcblas,atlas not found in /usr/lib
  libraries lapack_atlas not found in /usr/lib
__main__.lapack_atlas_threads_info
  NOT AVAILABLE

x11_info:
/usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/Current/lib/python2.7/site-packages//numpy/distutils/system_info.py:538:
UserWarning: Specified path /usr/X11R6/lib64 is invalid.
  warnings.warn('Specified path %s is invalid.' % d)
/usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/Current/lib/python2.7/site-packages//numpy/distutils/system_info.py:538:
UserWarning: Specified path /usr/X11/lib64 is invalid.
  warnings.warn('Specified path %s is invalid.' % d)
/usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/Current/lib/python2.7/site-packages//numpy/distutils/system_info.py:538:
UserWarning: Specified path /usr/lib64 is invalid.
  warnings.warn('Specified path %s is invalid.' % d)
  FOUND:
    libraries = ['X11']
    library_dirs = ['/usr/X11R6/lib']
    include_dirs = ['/usr/X11R6/include']

blas_info:
  libraries blas not found in
/Users/andalman/Documents/Code/_virtualenvs/main_projects/bin/../lib
  libraries blas not found in /usr/local/lib
  FOUND:
    libraries = ['blas']
    library_dirs = ['/usr/lib']
    language = f77

fftw_info:
  libraries fftw3 not found in
/Users/andalman/Documents/Code/_virtualenvs/main_projects/bin/../lib
  libraries fftw3 not found in /usr/local/lib
  libraries fftw3 not found in /usr/lib
  fftw3 not found
  libraries rfftw,fftw not found in
/Users/andalman/Documents/Code/_virtualenvs/main_projects/bin/../lib
  libraries rfftw,fftw not found in /usr/local/lib
  libraries rfftw,fftw not found in /usr/lib
  fftw2 not found
  NOT AVAILABLE

atlas_threads_info:
Setting PTATLAS=ATLAS
  libraries ptf77blas,ptcblas,atlas not found in
/Users/andalman/Documents/Code/_virtualenvs/main_projects/bin/../lib
  libraries lapack_atlas not found in
/Users/andalman/Documents/Code/_virtualenvs/main_projects/bin/../lib
  libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib
  libraries lapack_atlas not found in /usr/local/lib
  libraries ptf77blas,ptcblas,atlas not found in /usr/lib
  libraries lapack_atlas not found in /usr/lib
__main__.atlas_threads_info
  NOT AVAILABLE

f2py_info:
  FOUND:
    sources =
['/usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/f2py/src/fortranobject.c']
    include_dirs =
['/usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/f2py/src']

gdk_pixbuf_xlib_2_info:
  NOT AVAILABLE

dfftw_threads_info:
  libraries drfftw_threads,dfftw_threads not found in
/Users/andalman/Documents/Code/_virtualenvs/main_projects/bin/../lib
  libraries drfftw_threads,dfftw_threads not found in /usr/local/lib
  libraries drfftw_threads,dfftw_threads not found in /usr/lib
  dfftw threads not found
  NOT AVAILABLE

atlas_blas_info:
  libraries f77blas,cblas,atlas not found in
/Users/andalman/Documents/Code/_virtualenvs/main_projects/bin/../lib
  libraries f77blas,cblas,atlas not found in /usr/local/lib
  libraries f77blas,cblas,atlas not found in /usr/lib
  NOT AVAILABLE

fftw3_info:
  libraries fftw3 not found in
/Users/andalman/Documents/Code/_virtualenvs/main_projects/bin/../lib
  libraries fftw3 not found in /usr/local/lib
  libraries fftw3 not found in /usr/lib
  fftw3 not found
  NOT AVAILABLE

blas_opt_info:
  FOUND:
    extra_link_args = ['-Wl,-framework', '-Wl,Accelerate']
    define_macros = [('NO_ATLAS_INFO', 3)]
    extra_compile_args = ['-msse3',
'-I/System/Library/Frameworks/vecLib.framework/Headers']

sfftw_info:
  libraries srfftw,sfftw not found in
/Users/andalman/Documents/Code/_virtualenvs/main_projects/bin/../lib
  libraries srfftw,sfftw not found in /usr/local/lib
  libraries srfftw,sfftw not found in /usr/lib
  sfftw not found
  NOT AVAILABLE

xft_info:
  NOT AVAILABLE

fft_opt_info:
fftw2_info:
  libraries rfftw,fftw not found in
/Users/andalman/Documents/Code/_virtualenvs/main_projects/bin/../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
/Users/andalman/Documents/Code/_virtualenvs/main_projects/bin/../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

  NOT AVAILABLE

gdk_x11_2_info:
  NOT AVAILABLE

agg2_info:
  NOT AVAILABLE

numarray_info:
  NOT AVAILABLE

blas_src_info:
  NOT AVAILABLE

fftw_threads_info:
  libraries rfftw_threads,fftw_threads not found in
/Users/andalman/Documents/Code/_virtualenvs/main_projects/bin/../lib
  libraries rfftw_threads,fftw_threads not found in /usr/local/lib
  libraries rfftw_threads,fftw_threads not found in /usr/lib
  fftw threads not found
  NOT AVAILABLE

_numpy_info:
  NOT AVAILABLE

gdk_info:
  NOT AVAILABLE

gtkp_x11_2_info:
  NOT AVAILABLE

sfftw_threads_info:
  libraries srfftw_threads,sfftw_threads not found in
/Users/andalman/Documents/Code/_virtualenvs/main_projects/bin/../lib
  libraries srfftw_threads,sfftw_threads not found in /usr/local/lib
  libraries srfftw_threads,sfftw_threads not found in /usr/lib
  sfftw threads not found
  NOT AVAILABLE

boost_python_info:
  NOT AVAILABLE

freetype2_info:
  NOT AVAILABLE

gdk_2_info:
  NOT AVAILABLE

lapack_src_info:
  NOT AVAILABLE

atlas_blas_threads_info:
Setting PTATLAS=ATLAS
  libraries ptf77blas,ptcblas,atlas not found in
/Users/andalman/Documents/Code/_virtualenvs/main_projects/bin/../lib
  libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib
  libraries ptf77blas,ptcblas,atlas not found in /usr/lib
  NOT AVAILABLE

gtkp_2_info:
  NOT AVAILABLE

gdk_pixbuf_2_info:
  NOT AVAILABLE

blas_mkl_info:
  libraries mkl,vml,guide not found in
/Users/andalman/Documents/Code/_virtualenvs/main_projects/bin/../lib
  libraries mkl,vml,guide not found in /usr/local/lib
  libraries mkl,vml,guide not found in /usr/lib
  NOT AVAILABLE

atlas_info:
  libraries f77blas,cblas,atlas not found in
/Users/andalman/Documents/Code/_virtualenvs/main_projects/bin/../lib
  libraries lapack_atlas not found in
/Users/andalman/Documents/Code/_virtualenvs/main_projects/bin/../lib
  libraries f77blas,cblas,atlas not found in /usr/local/lib
  libraries lapack_atlas not found in /usr/local/lib
  libraries f77blas,cblas,atlas not found in /usr/lib
  libraries lapack_atlas not found in /usr/lib
__main__.atlas_info
  NOT AVAILABLE

Numeric_info:
  NOT AVAILABLE

numerix_info:
numpy_info:
/usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/Current/lib/python2.7/site-packages//numpy/distutils/system_info.py:538:
UserWarning: Specified path /usr/local/include/python2.7 is invalid.
  warnings.warn('Specified path %s is invalid.' % d)
/usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/Current/lib/python2.7/site-packages//numpy/distutils/system_info.py:538:
UserWarning: Specified path  is invalid.
  warnings.warn('Specified path %s is invalid.' % d)
  FOUND:
    define_macros = [('NUMPY_VERSION', '"\\"1.6.2\\""'), ('NUMPY', None)]
    include_dirs =
['/usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/include']

  FOUND:
    define_macros = [('NUMPY_VERSION', '"\\"1.6.2\\""'), ('NUMPY', None)]
    include_dirs =
['/usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/include']

lapack_mkl_info:
mkl_info:
  libraries mkl,vml,guide not found in
/Users/andalman/Documents/Code/_virtualenvs/main_projects/bin/../lib
  libraries mkl,vml,guide not found in /usr/local/lib
  libraries mkl,vml,guide not found in /usr/lib
  NOT AVAILABLE

  NOT AVAILABLE
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