[SciPy-User] Install fail on Mac 10.6.2 in fftpack._fftpack
Adam Ginsburg
adam.ginsburg at colorado.edu
Mon Feb 15 17:22:42 EST 2010
Hi, I'm trying to get scipy running on my new Snow Leopard system. I
was able to get scipy built successfully yesterday, but not so much
today. I'd appreciate any assistance in getting scipy installed.
I built fftw with the following setup:
./configure CC="gcc -arch i386 -arch x86_64" CXX="g++ -arch i386 -arch
x86_64" CPP="gcc -E" CXXCPP="g++ -E"
make
sudo make install
I've also tried multiple variations of architection for fftw (e.g. not
using -arch i386 and passing no compiler flags). I built UMFTPACK
following the instructions on: http://blog.hyperjeff.net/?p=160
I get the following error:
building 'scipy.fftpack._fftpack' extension
compiling C sources
C compiler: gcc-4.2 -DNDEBUG -g -O3 -arch i386 -arch x86_64
creating build/temp.macosx-10.6-intel-2.6/build
creating build/temp.macosx-10.6-intel-2.6/build/src.macosx-10.6-intel-2.6
creating build/temp.macosx-10.6-intel-2.6/build/src.macosx-10.6-intel-2.6/scipy
creating build/temp.macosx-10.6-intel-2.6/build/src.macosx-10.6-intel-2.6/scipy/fftpack
creating build/temp.macosx-10.6-intel-2.6/build/src.macosx-10.6-intel-2.6/scipy/fftpack/src
compile options: '-Iscipy/fftpack/src
-Ibuild/src.macosx-10.6-intel-2.6
-I/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/numpy/core/include
-I/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6
-c'
gcc-4.2: build/src.macosx-10.6-intel-2.6/scipy/fftpack/src/dct.c
gcc-4.2: build/src.macosx-10.6-intel-2.6/scipy/fftpack/_fftpackmodule.c
gcc-4.2: scipy/fftpack/src/drfft.c
gcc-4.2: scipy/fftpack/src/zfft.c
gcc-4.2: scipy/fftpack/src/zrfft.c
gcc-4.2: scipy/fftpack/src/zfftnd.c
gcc-4.2: build/src.macosx-10.6-intel-2.6/fortranobject.c
/usr/local/bin/gfortran -Wall -lgfortran -arch x86_64
build/temp.macosx-10.6-intel-2.6/build/src.macosx-10.6-intel-2.6/scipy/fftpack/_fftpackmodule.o
build/temp.macosx-10.6-intel-2.6/scipy/fftpack/src/zfft.o
build/temp.macosx-10.6-intel-2.6/scipy/fftpack/src/drfft.o
build/temp.macosx-10.6-intel-2.6/scipy/fftpack/src/zrfft.o
build/temp.macosx-10.6-intel-2.6/scipy/fftpack/src/zfftnd.o
build/temp.macosx-10.6-intel-2.6/build/src.macosx-10.6-intel-2.6/scipy/fftpack/src/dct.o
build/temp.macosx-10.6-intel-2.6/build/src.macosx-10.6-intel-2.6/fortranobject.o
-L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3/x86_64
-Lbuild/temp.macosx-10.6-intel-2.6 -ldfftpack -lfftpack -lgfortran -o
build/lib.macosx-10.6-intel-2.6/scipy/fftpack/_fftpack.so
Undefined symbols:
"_Py_BuildValue", referenced from:
_f2py_rout__fftpack_destroy_dct1_cache in _fftpackmodule.o
(...cut for brevity...)
"_PyErr_Print", referenced from:
_init_fftpack in _fftpackmodule.o
_F2PyDict_SetItemString in fortranobject.o
ld: symbol(s) not found
collect2: ld returned 1 exit status
error: Command "/usr/local/bin/gfortran -Wall -lgfortran -arch x86_64
build/temp.macosx-10.6-intel-2.6/build/src.macosx-10.6-intel-2.6/scipy/fftpack/_fftpackmodule.o
build/temp.macosx-10.6-intel-2.6/scipy/fftpack/src/zfft.o
build/temp.macosx-10.6-intel-2.6/scipy/fftpack/src/drfft.o
build/temp.macosx-10.6-intel-2.6/scipy/fftpack/src/zrfft.o
build/temp.macosx-10.6-intel-2.6/scipy/fftpack/src/zfftnd.o
build/temp.macosx-10.6-intel-2.6/build/src.macosx-10.6-intel-2.6/scipy/fftpack/src/dct.o
build/temp.macosx-10.6-intel-2.6/build/src.macosx-10.6-intel-2.6/fortranobject.o
-L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3/x86_64
-Lbuild/temp.macosx-10.6-intel-2.6 -ldfftpack -lfftpack -lgfortran -o
build/lib.macosx-10.6-intel-2.6/scipy/fftpack/_fftpack.so" failed with
exit status 1
My numpy setup information:
$ python -c 'from numpy.f2py.diagnose import run; run()'
------
os.name='posix'
------
sys.platform='darwin'
------
sys.version:
2.6.4 (r264:75706, Feb 1 2010, 13:22:43)
[GCC 4.2.1 (Apple Inc. build 5646) (dot 1)]
------
sys.prefix:
/Library/Frameworks/Python.framework/Versions/2.6
------
sys.path=':/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/distribute-0.6.10-py2.6.egg:/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/pip-0.6.3-py2.6.egg:/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/readline-2.6.4-py2.6-macosx-10.6-intel.egg:/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/pytz-2010b-py2.6.egg:/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/h5py-1.2.0-py2.6-macosx-10.6-intel.egg:/Users/adam/Downloads/yt-i386/src/yt-trunk-svn:/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/pyregion-0.1c-py2.6-macosx-10.6-intel.egg:/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/pyparsing-1.5.2-py2.6.egg:/Users/adam/Downloads/gildas-exe-jul09a/pc-darwin-g95/python:/Library/Frameworks/Python.framework/Versions/2.6/lib/python26.zip:/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6:/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/plat-darwin:/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/plat-mac:/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/plat-mac/lib-scriptpackages:/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/lib-tk:/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/lib-old:/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/lib-dynload:/Users/adam/.local/lib/python2.6/site-packages:/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages'
------
Failed to import Numeric: No module named Numeric
Failed to import numarray: No module named numarray
Found new numpy version '1.4.0rc2' in
/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/numpy/__init__.pyc
Found f2py2e version '2_8112' in
/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/numpy/f2py/f2py2e.pyc
Found numpy.distutils version '0.4.0' in
'/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/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', 'ppc', '-arch', 'i686', '
-arch', 'x86_64', '-fPIC', '-O3', '-funroll-loops']
compiler_f90 = ['/usr/local/bin/gfortran', '-Wall', '-fno-second-
underscore', '-arch', 'ppc', '-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', 'ppc', '-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', 'ppc', '-
arch', 'i686', '-arch', 'x86_64', '-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']
G95FCompiler instance properties:
archiver = None
compile_switch = '-c'
compiler_f77 = ['/usr/local/bin/g95', '-ffixed-form', '-fno-second-
underscore', '-O']
compiler_f90 = ['/usr/local/bin/g95', '-fno-second-underscore', '-O']
compiler_fix = ['/usr/local/bin/g95', '-ffixed-form', '-fno-second-
underscore', '-O']
libraries = []
library_dirs = []
linker_exe = None
linker_so = ['/usr/local/bin/g95', '-shared', '-shared']
object_switch = '-o '
ranlib = None
version = LooseVersion ('0.92')
version_cmd = ['/usr/local/bin/g95', '--version']
Fortran compilers found:
--fcompiler=g95 G95 Fortran Compiler (0.92)
--fcompiler=gnu95 GNU Fortran 95 compiler (4.2.3)
Compilers available for this platform, but not found:
--fcompiler=absoft Absoft Corp 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_64bit is_i386 ------
Thanks,
--
Adam Ginsburg
Graduate Student
Center for Astrophysics and Space Astronomy
University of Colorado at Boulder
http://casa.colorado.edu/~ginsbura/
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