Dear List,
I installed numpy and scipy from svn source as of yesterday (30 of
april), however get an segmentation fault in the scipy.test()..
Running unit tests for scipy
NumPy version 1.4.1
NumPy is installed in /usr/local/lib/python2.6/dist-packages/numpy
SciPy version 0.8.0.dev6362
SciPy is installed in /usr/local/lib/python2.6/dist-packages/scipy
Python version 2.6.2 (release26-maint, Apr 19 2009, 01:58:18) [GCC
4.3.3]
nose version 0.10.4
......
..saxpy:n=3
....scopy:n=4
..scopy:n=3
.............sscal:n=4
....sswap:n=4
..sswap:n=3
.....zaxpy:n=4
..zaxpy:n=3
....zcopy:n=4
..zcopy:n=3
.............zscal:n=4
....zswap:n=4
..zswap:n=3
.......Result may be inaccurate, approximate err = 6.98199990784e-09
...Result may be inaccurate, approximate err = 1.25504040833e-10
.....................................................................................................................
......................................................................................................................
.........................................................................................................................
........................................................................................................................
..............ESSSSSSSSSSS.......Segmentation fault
Anyone can shed some light ?
python -c 'import os,sys;print os.name,sys.platform'
posix linux2
uname -a
Linux hirubu 2.6.28-18-generic #60-Ubuntu SMP Fri Mar 12
04:26:47 UTC
2010 x86_64 GNU/Linux
hannes@hirubu:~$ gcc -v
Using built-in specs.
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Ubuntu
4.3.3-5ubuntu4'
--with-bugurl=file:///usr/share/doc/gcc-4.3/README.Bugs
--enable-languages=c,c++,fortran,objc,obj-c++ --prefix=/usr
--enable-shared --with-system-zlib --libexecdir=/usr/lib
--without-included-gettext --enable-threads=posix --enable-nls
--with-gxx-include-dir=/usr/include/c++/4.3
--program-suffix=-4.3
--enable-clocale=gnu --enable-libstdcxx-debug --enable-objc-gc
--enable-mpfr --with-tune=generic --enable-checking=release
--build=x86_64-linux-gnu --host=x86_64-linux-gnu
--target=x86_64-linux-gnu
Thread model: posix
gcc version 4.3.3 (Ubuntu 4.3.3-5ubuntu4)
hannes@hirubu:~$ g77 --version
bash: g77: command not found
hannes@hirubu:~$
python -c 'import sys;print sys.version'
2.6.2 (release26-maint, Apr 19 2009, 01:58:18)
[GCC 4.3.3]
for point 5
cd scipy/Lib/linalg
python setup_atlas_version.py build_ext --inplace --force
python -c 'import atlas_version'
i cant give any information as the scipy dir does not contain
any
directory lib
for
python /usr/lib/python2.6/site-packages/numpy/distutils/system_info.py
lapack_info:
libraries lapack not found in /usr/local/lib
FOUND:
libraries = ['lapack']
library_dirs = ['/usr/lib']
language = f77
lapack_opt_info:
lapack_mkl_info:
mkl_info:
libraries mkl,vml,guide not found in /usr/local/lib
libraries mkl,vml,guide not found in /usr/lib
NOT AVAILABLE
NOT AVAILABLE
atlas_threads_info:
Setting PTATLAS=ATLAS
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/atlas
libraries lapack_atlas not found in /usr/lib/atlas
libraries ptf77blas,ptcblas,atlas not found in /usr/lib
__main__.atlas_threads_info
NOT AVAILABLE
atlas_info:
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/atlas
libraries lapack_atlas not found in /usr/lib/atlas
__main__.atlas_info
FOUND:
libraries = ['lapack', 'f77blas', 'cblas', 'atlas']
library_dirs = ['/usr/lib']
language = f77
include_dirs = ['/usr/include']
/usr/local/lib/python2.6/dist-packages/numpy/distutils/command/config.py:394: DeprecationWarning:
+++++++++++++++++++++++++++++++++++++++++++++++++
Usage of get_output is deprecated: please do not
use it anymore, and avoid configuration checks
involving running executable on the target machine.
+++++++++++++++++++++++++++++++++++++++++++++++++
DeprecationWarning)
customize GnuFCompiler
Could not locate executable g77
Found executable /usr/bin/f77
gnu: no Fortran 90 compiler found
gnu: no Fortran 90 compiler found
customize IntelFCompiler
Could not locate executable ifort
Could not locate executable ifc
customize LaheyFCompiler
Could not locate executable lf95
customize PGroupFCompiler
Could not locate executable pgf90
Could not locate executable pgf77
customize AbsoftFCompiler
Could not locate executable f90
absoft: no Fortran 90 compiler found
absoft: no Fortran 90 compiler found
absoft: no Fortran 90 compiler found
absoft: no Fortran 90 compiler found
absoft: no Fortran 90 compiler found
absoft: no Fortran 90 compiler found
customize NAGFCompiler
Found executable /usr/bin/f95
customize VastFCompiler
customize GnuFCompiler
gnu: no Fortran 90 compiler found
gnu: no Fortran 90 compiler found
customize CompaqFCompiler
Could not locate executable fort
customize IntelItaniumFCompiler
Could not locate executable efort
Could not locate executable efc
customize IntelEM64TFCompiler
customize Gnu95FCompiler
Found executable /usr/bin/gfortran
customize Gnu95FCompiler
customize Gnu95FCompiler using config
FOUND:
libraries = ['lapack', 'f77blas', 'cblas', 'atlas']
library_dirs = ['/usr/lib']
language = f77
define_macros = [('ATLAS_INFO', '"\\"?.?.?\\""')]
include_dirs = ['/usr/include']
wx_info:
Found executable /usr/bin/wx-config
FOUND:
libraries = ['wx_baseu_xml-2.8', 'wx_baseu_net-2.8',
'wx_baseu-2.8']
extra_link_args = ['-pthread', '-Wl,-Bsymbolic-functions']
define_macros = [('WX_INFO', '"\\"2.8.9\\""'),
('WX_VERSION_2_8_9', None), ('WX_RELEASE_2_8', None),
('_FILE_OFFSET_BITS', '64'), ('_LARGE_FILES', None),
('wxUSE_GUI', '0')]
extra_compile_args = ['-pthread']
include_dirs =
['/usr/lib/wx/include/base-unicode-release-2.8',
'/usr/include/wx-2.8']
lapack_atlas_info:
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/atlas
libraries lapack_atlas not found in /usr/lib/atlas
__main__.lapack_atlas_info
FOUND:
libraries = ['lapack', 'lapack_atlas', 'f77blas', 'cblas',
'atlas']
library_dirs = ['/usr/lib']
language = f77
include_dirs = ['/usr/include']
umfpack_info:
libraries umfpack not found in /usr/local/lib
libraries umfpack not found in /usr/lib
NOT AVAILABLE
_pkg_config_info:
Found executable /usr/bin/pkg-config
NOT AVAILABLE
lapack_atlas_threads_info:
Setting PTATLAS=ATLAS
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/atlas
libraries lapack_atlas not found in /usr/lib/atlas
libraries lapack_atlas,ptf77blas,ptcblas,atlas not found
in /usr/lib
__main__.lapack_atlas_threads_info
NOT AVAILABLE
x11_info:
libraries X11 not found in /usr/local/lib
FOUND:
libraries = ['X11']
library_dirs = ['/usr/lib']
include_dirs = ['/usr/include']
blas_info:
libraries blas not found in /usr/local/lib
FOUND:
libraries = ['blas']
library_dirs = ['/usr/lib']
language = f77
fftw_info:
libraries fftw3 not found in /usr/local/lib
libraries fftw3 not found in /usr/lib
fftw3 not found
libraries rfftw,fftw not found in /usr/local/lib
libraries rfftw,fftw not found in /usr/lib
fftw2 not found
NOT AVAILABLE
f2py_info:
FOUND:
sources =
['/usr/local/lib/python2.6/dist-packages/numpy/f2py/src/fortranobject.c']
include_dirs =
['/usr/local/lib/python2.6/dist-packages/numpy/f2py/src']
gdk_pixbuf_xlib_2_info:
NOT AVAILABLE
dfftw_threads_info:
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 /usr/local/lib
libraries f77blas,cblas,atlas not found in /usr/lib/atlas
FOUND:
libraries = ['f77blas', 'cblas', 'atlas']
library_dirs = ['/usr/lib']
language = c
include_dirs = ['/usr/include']
fftw3_info:
libraries fftw3 not found in /usr/local/lib
libraries fftw3 not found in /usr/lib
fftw3 not found
NOT AVAILABLE
blas_opt_info:
blas_mkl_info:
libraries mkl,vml,guide not found in /usr/local/lib
libraries mkl,vml,guide not found in /usr/lib
NOT AVAILABLE
atlas_blas_threads_info:
Setting PTATLAS=ATLAS
libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib
libraries ptf77blas,ptcblas,atlas not found in /usr/lib/atlas
libraries ptf77blas,ptcblas,atlas not found in /usr/lib
NOT AVAILABLE
customize GnuFCompiler
gnu: no Fortran 90 compiler found
gnu: no Fortran 90 compiler found
customize IntelFCompiler
customize LaheyFCompiler
customize PGroupFCompiler
customize AbsoftFCompiler
absoft: no Fortran 90 compiler found
absoft: no Fortran 90 compiler found
absoft: no Fortran 90 compiler found
absoft: no Fortran 90 compiler found
absoft: no Fortran 90 compiler found
absoft: no Fortran 90 compiler found
customize NAGFCompiler
customize VastFCompiler
customize GnuFCompiler
gnu: no Fortran 90 compiler found
gnu: no Fortran 90 compiler found
customize CompaqFCompiler
customize IntelItaniumFCompiler
customize IntelEM64TFCompiler
customize Gnu95FCompiler
customize Gnu95FCompiler
customize Gnu95FCompiler using config
FOUND:
libraries = ['f77blas', 'cblas', 'atlas']
library_dirs = ['/usr/lib']
language = c
define_macros = [('ATLAS_INFO', '"\\"?.?.?\\""')]
include_dirs = ['/usr/include']
sfftw_info:
libraries srfftw,sfftw not found in /usr/local/lib
libraries srfftw,sfftw not found in /usr/lib
sfftw not found
NOT AVAILABLE
xft_info:
FOUND:
libraries = ['Xft']
define_macros = [('XFT_INFO', '"\\"2.1.13\\""'),
('XFT_VERSION_2_1_13', None)]
include_dirs = ['/usr/include/freetype2']
fft_opt_info:
fftw2_info:
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 /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 /usr/local/lib
libraries rfftw_threads,fftw_threads not found in /usr/lib
fftw threads not found
NOT AVAILABLE
_numpy_info:
FOUND:
define_macros = [('NUMERIC_VERSION', '"\\"24.2\\""'),
('NUMERIC', None)]
gdk_info:
NOT AVAILABLE
gtkp_x11_2_info:
NOT AVAILABLE
sfftw_threads_info:
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:
FOUND:
libraries = ['freetype']
define_macros = [('FREETYPE2_INFO', '"\\"9.20.3\\""'),
('FREETYPE2_VERSION_9_20_3', None)]
include_dirs = ['/usr/include/freetype2']
gdk_2_info:
NOT AVAILABLE
lapack_src_info:
NOT AVAILABLE
gtkp_2_info:
NOT AVAILABLE
gdk_pixbuf_2_info:
NOT AVAILABLE
amd_info:
libraries amd not found in /usr/local/lib
libraries amd not found in /usr/lib
NOT AVAILABLE
Numeric_info:
FOUND:
define_macros = [('NUMERIC_VERSION', '"\\"24.2\\""'),
('NUMERIC', None)]
numerix_info:
numpy_info:
FOUND:
define_macros = [('NUMPY_VERSION', '"\\"1.4.1\\""'),
('NUMPY', None)]
FOUND:
define_macros = [('NUMPY_VERSION', '"\\"1.4.1\\""'),
('NUMPY', None)]