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

Ralf Gommers ralf.gommers@gmail....
Thu Aug 9 02:28:47 CDT 2012


On Wed, Aug 8, 2012 at 10:32 PM, Aaron Andalman <nerduno.list@gmail.com>wrote:

> 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?
>

The -msse4 flag must have come from Python. Numpy.distutils should have
added -msse3 (-msse4 isn't present anywhere). Relevant code from
numpy/distutils/system_info.py:

       if sys.platform == 'darwin' and not os.environ.get('ATLAS', None):
             args = []
             link_args = []
             if get_platform()[-4:] == 'i386' or 'intel' in get_platform()
or \
                'i386' in platform.platform():
                 intel = 1
             else:
                 intel = 0
             if os.path.exists('/System/Library/Frameworks'
                               '/Accelerate.framework/'):
                 if intel:
                     args.extend(['-msse3'])
                 else:
                     args.extend(['-faltivec'])

Since you're using Homebrew, Python is likely also the Homebrew installed
one?

Ralf



> 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
>
>
>
>
>
> _______________________________________________
> SciPy-Dev mailing list
> SciPy-Dev@scipy.org
> http://mail.scipy.org/mailman/listinfo/scipy-dev
>
>
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