[SciPy-Dev] Mountain Lion Scipy-dev build fails
Aaron Andalman
nerduno.list at gmail.com
Wed Aug 8 16:32:03 EDT 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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