[Numpy-discussion] linalg.svd not working?

Muhammad Alkarouri malkarouri@yahoo.co...
Tue May 5 09:36:22 CDT 2009


Hi everyone,

I have installed numpy 1.3.0 on Python 2.5.1 in an x86_64 machine, and it hangs when I do a numpy.test(verbose=10) on
test_pinv (test_defmatrix.TestProperties) ...
which I believe hangs on a call to numpy.linalg.svd. Can you please help me with this problem?

The installation and configuration is probably a bit non-standard, so I am including the output of python -m numpy.distutils.system_info below. In particular, all the installation was done using CC='gcc -m32' to enforce 32 bit executables, as Python is a 32 bit executable here.

Regards,

Muhammad Alkarouri


lapack_info:
  libraries lapack not found in /GWD/appbase/common/lib
  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 /GWD/appbase/common/lib
  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 lapack_atlas not found in /users/d88/ma856388/lib
__main__.atlas_threads_info
Setting PTATLAS=ATLAS
Setting PTATLAS=ATLAS
  FOUND:
    libraries = ['lapack', 'ptf77blas', 'ptcblas', 'atlas']
    library_dirs = ['/users/d88/ma856388/lib']
    language = f77

customize GnuFCompiler
Found executable /usr/bin/g77
gnu: no Fortran 90 compiler found
gnu: no Fortran 90 compiler found
customize GnuFCompiler
gnu: no Fortran 90 compiler found
gnu: no Fortran 90 compiler found
customize GnuFCompiler using config
compiling '_configtest.c':

/* This file is generated from numpy/distutils/system_info.py */
void ATL_buildinfo(void);
int main(void) {
  ATL_buildinfo();
  return 0;
}
C compiler: gcc -m32 -fno-strict-aliasing -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -fPIC

compile options: '-c'
gcc: _configtest.c
gcc -m32 _configtest.o -m32 -fPIC -L/users/d88/ma856388/lib -llapack -lptf77blas -lptcblas -latlas -o _configtest
ATLAS version 3.8.3 built by ma856388 on Fri May  1 14:56:25 BST 2009:
   UNAME    : Linux stvwolx028 2.6.9-22.ELsmp #1 SMP Mon Sep 19 18:00:54 EDT 2005 x86_64 x86_64 x86_64 GNU/Linux
   INSTFLG  : -1 0 -a 1
   ARCHDEFS : -DATL_OS_Linux -DATL_ARCH_P4E -DATL_CPUMHZ=3200 -DATL_SSE3 -DATL_SSE2 -DATL_SSE1 -DATL_GAS_x8632
   F2CDEFS  : -DAdd__ -DF77_INTEGER=int -DStringSunStyle
   CACHEEDGE: 8388608
   F77      : g77, version GNU Fortran (GCC) 3.4.4 20050721 (Red Hat 3.4.4-2)
   F77FLAGS : -fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4 -fPIC -m32 -fPIC -m32
   SMC      : gcc, version gcc (GCC) 3.4.4 20050721 (Red Hat 3.4.4-2)
   SMCFLAGS : -fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4 -fPIC -m32
   SKC      : gcc, version gcc (GCC) 3.4.4 20050721 (Red Hat 3.4.4-2)
   SKCFLAGS : -fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4 -fPIC -m32
success!
removing: _configtest.c _configtest.o _configtest
  FOUND:
    libraries = ['lapack', 'ptf77blas', 'ptcblas', 'atlas']
    library_dirs = ['/users/d88/ma856388/lib']
    language = f77
    define_macros = [('ATLAS_INFO', '"\\"3.8.3\\""')]

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/d88/ma856388/lib
  libraries lapack_atlas not found in /users/d88/ma856388/lib
  libraries lapack_atlas,f77blas,cblas,atlas not found in /GWD/appbase/common/lib
  libraries lapack_atlas not found in /GWD/appbase/common/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/sse2
  libraries lapack_atlas not found in /usr/lib/sse2
  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 /GWD/appbase/common/lib
  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 /users/d88/ma856388/lib
  libraries lapack_atlas not found in /users/d88/ma856388/lib
  libraries lapack_atlas,ptf77blas,ptcblas,atlas not found in /GWD/appbase/common/lib
  libraries lapack_atlas not found in /GWD/appbase/common/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/sse2
  libraries lapack_atlas not found in /usr/lib/sse2
  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:
  FOUND:
    libraries = ['X11']
    library_dirs = ['/usr/X11R6/lib']

blas_info:
  libraries blas not found in /GWD/appbase/common/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 /GWD/appbase/common/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 /GWD/appbase/common/lib
  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 = ['/users/d88/ma856388/lib/python/numpy/f2py/src/fortranobject.c']
    include_dirs = ['/users/d88/ma856388/lib/python/numpy/f2py/src']

gdk_pixbuf_xlib_2_info:
  FOUND:
    libraries = ['gdk_pixbuf_xlib-2.0', 'gdk_pixbuf-2.0', 'm', 'gobject-2.0', 'gmodule-2.0', 'dl', 'glib-2.0']
    extra_link_args = ['-Wl,--export-dynamic']
    define_macros = [('GDK_PIXBUF_XLIB_2_INFO', '"\\"2.4.13\\""'), ('GDK_PIXBUF_XLIB_VERSION_2_4_13', None)]
    include_dirs = ['/usr/include/gtk-2.0', '/usr/include/glib-2.0', '/usr/lib64/glib-2.0/include']

dfftw_threads_info:
  libraries drfftw_threads,dfftw_threads not found in /GWD/appbase/common/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:
  FOUND:
    libraries = ['f77blas', 'cblas', 'atlas']
    library_dirs = ['/users/d88/ma856388/lib']
    language = c

fftw3_info:
  libraries fftw3 not found in /GWD/appbase/common/lib
  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 /GWD/appbase/common/lib
  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
Setting PTATLAS=ATLAS
Setting PTATLAS=ATLAS
  FOUND:
    libraries = ['ptf77blas', 'ptcblas', 'atlas']
    library_dirs = ['/users/d88/ma856388/lib']
    language = c

customize GnuFCompiler
gnu: no Fortran 90 compiler found
gnu: no Fortran 90 compiler found
customize GnuFCompiler
gnu: no Fortran 90 compiler found
gnu: no Fortran 90 compiler found
customize GnuFCompiler using config
compiling '_configtest.c':

/* This file is generated from numpy/distutils/system_info.py */
void ATL_buildinfo(void);
int main(void) {
  ATL_buildinfo();
  return 0;
}
C compiler: gcc -m32 -fno-strict-aliasing -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -fPIC

compile options: '-c'
gcc: _configtest.c
gcc -m32 _configtest.o -m32 -fPIC -L/users/d88/ma856388/lib -lptf77blas -lptcblas -latlas -o _configtest
ATLAS version 3.8.3 built by ma856388 on Fri May  1 14:56:25 BST 2009:
   UNAME    : Linux stvwolx028 2.6.9-22.ELsmp #1 SMP Mon Sep 19 18:00:54 EDT 2005 x86_64 x86_64 x86_64 GNU/Linux
   INSTFLG  : -1 0 -a 1
   ARCHDEFS : -DATL_OS_Linux -DATL_ARCH_P4E -DATL_CPUMHZ=3200 -DATL_SSE3 -DATL_SSE2 -DATL_SSE1 -DATL_GAS_x8632
   F2CDEFS  : -DAdd__ -DF77_INTEGER=int -DStringSunStyle
   CACHEEDGE: 8388608
   F77      : g77, version GNU Fortran (GCC) 3.4.4 20050721 (Red Hat 3.4.4-2)
   F77FLAGS : -fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4 -fPIC -m32 -fPIC -m32
   SMC      : gcc, version gcc (GCC) 3.4.4 20050721 (Red Hat 3.4.4-2)
   SMCFLAGS : -fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4 -fPIC -m32
   SKC      : gcc, version gcc (GCC) 3.4.4 20050721 (Red Hat 3.4.4-2)
   SKCFLAGS : -fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4 -fPIC -m32
success!
removing: _configtest.c _configtest.o _configtest
  FOUND:
    libraries = ['ptf77blas', 'ptcblas', 'atlas']
    library_dirs = ['/users/d88/ma856388/lib']
    language = c
    define_macros = [('ATLAS_INFO', '"\\"3.8.3\\""')]

sfftw_info:
  libraries srfftw,sfftw not found in /GWD/appbase/common/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:
  FOUND:
    libraries = ['Xft', 'X11', 'freetype', 'Xrender', 'fontconfig']
    library_dirs = ['/usr/X11R6/lib64']
    define_macros = [('XFT_INFO', '"\\"2.1.2.2\\""'), ('XFT_VERSION_2_1_2_2', None)]
    include_dirs = ['/usr/X11R6/include', '/usr/include/freetype2', '/usr/include/freetype2/config']

fft_opt_info:
fftw2_info:
  libraries rfftw,fftw not found in /GWD/appbase/common/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 /GWD/appbase/common/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:
  FOUND:
    libraries = ['gdk-x11-2.0', 'gdk_pixbuf-2.0', 'm', 'pangoxft-1.0', 'pangox-1.0', 'pango-1.0', 'gobject-2.0', 'gmodule-2.0', 'dl', 'glib-2.0']
    extra_link_args = ['-Wl,--export-dynamic']
    define_macros = [('GDK_X11_2_INFO', '"\\"2.4.13\\""'), ('GDK_X11_VERSION_2_4_13', None), ('XTHREADS', None), ('_REENTRANT', None), ('XUSE_MTSAFE_API', None)]
    include_dirs = ['/usr/include/gtk-2.0', '/usr/lib64/gtk-2.0/include', '/usr/X11R6/include', '/usr/include/pango-1.0', '/usr/include/freetype2', '/usr/include/freetype2/config', '/usr/include/glib-2.0', '/usr/lib64/glib-2.0/include']

agg2_info:
  NOT AVAILABLE

numarray_info:
  NOT AVAILABLE

blas_src_info:
  NOT AVAILABLE

fftw_threads_info:
  libraries rfftw_threads,fftw_threads not found in /GWD/appbase/common/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:
  FOUND:
    define_macros = [('NUMERIC_VERSION', '"\\"23.8\\""'), ('NUMERIC', None)]

gdk_info:
  FOUND:
    libraries = ['gdk', 'Xi', 'Xext', 'X11', 'm', 'glib']
    library_dirs = ['/usr/X11R6/lib64']
    define_macros = [('GDK_INFO', '"\\"1.2.10\\""'), ('GDK_VERSION_1_2_10', None)]
    include_dirs = ['/usr/include/gtk-1.2', '/usr/X11R6/include', '/usr/include/glib-1.2', '/usr/lib64/glib/include']

gtkp_x11_2_info:
  FOUND:
    libraries = ['gtk-x11-2.0', 'gdk-x11-2.0', 'atk-1.0', 'gdk_pixbuf-2.0', 'm', 'pangoxft-1.0', 'pangox-1.0', 'pango-1.0', 'gobject-2.0', 'gmodule-2.0', 'dl', 'glib-2.0']
    extra_link_args = ['-Wl,--export-dynamic']
    define_macros = [('GTKP_X11_2_INFO', '"\\"2.4.13\\""'), ('GTK_X11_VERSION_2_4_13', None), ('XTHREADS', None), ('_REENTRANT', None), ('XUSE_MTSAFE_API', None)]
    include_dirs = ['/usr/include/gtk-2.0', '/usr/lib64/gtk-2.0/include', '/usr/X11R6/include', '/usr/include/atk-1.0', '/usr/include/pango-1.0', '/usr/include/freetype2', '/usr/include/freetype2/config', '/usr/include/glib-2.0', '/usr/lib64/glib-2.0/include']

sfftw_threads_info:
  libraries srfftw_threads,sfftw_threads not found in /GWD/appbase/common/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:
  FOUND:
    libraries = ['freetype', 'z']
    define_macros = [('FREETYPE2_INFO', '"\\"9.7.3\\""'), ('FREETYPE2_VERSION_9_7_3', None)]
    include_dirs = ['/usr/include/freetype2']

gdk_2_info:
  FOUND:
    libraries = ['gdk-x11-2.0', 'gdk_pixbuf-2.0', 'm', 'pangoxft-1.0', 'pangox-1.0', 'pango-1.0', 'gobject-2.0', 'gmodule-2.0', 'dl', 'glib-2.0']
    extra_link_args = ['-Wl,--export-dynamic']
    define_macros = [('GDK_2_INFO', '"\\"2.4.13\\""'), ('GDK_VERSION_2_4_13', None), ('XTHREADS', None), ('_REENTRANT', None), ('XUSE_MTSAFE_API', None)]
    include_dirs = ['/usr/include/gtk-2.0', '/usr/lib64/gtk-2.0/include', '/usr/X11R6/include', '/usr/include/pango-1.0', '/usr/include/freetype2', '/usr/include/freetype2/config', '/usr/include/glib-2.0', '/usr/lib64/glib-2.0/include']

lapack_src_info:
  NOT AVAILABLE

gtkp_2_info:
  FOUND:
    libraries = ['gtk-x11-2.0', 'gdk-x11-2.0', 'atk-1.0', 'gdk_pixbuf-2.0', 'm', 'pangoxft-1.0', 'pangox-1.0', 'pango-1.0', 'gobject-2.0', 'gmodule-2.0', 'dl', 'glib-2.0']
    extra_link_args = ['-Wl,--export-dynamic']
    define_macros = [('GTKP_2_INFO', '"\\"2.4.13\\""'), ('GTK_VERSION_2_4_13', None), ('XTHREADS', None), ('_REENTRANT', None), ('XUSE_MTSAFE_API', None)]
    include_dirs = ['/usr/include/gtk-2.0', '/usr/lib64/gtk-2.0/include', '/usr/X11R6/include', '/usr/include/atk-1.0', '/usr/include/pango-1.0', '/usr/include/freetype2', '/usr/include/freetype2/config', '/usr/include/glib-2.0', '/usr/lib64/glib-2.0/include']

gdk_pixbuf_2_info:
  FOUND:
    libraries = ['gdk_pixbuf-2.0', 'm', 'gobject-2.0', 'gmodule-2.0', 'dl', 'glib-2.0']
    extra_link_args = ['-Wl,--export-dynamic']
    define_macros = [('GDK_PIXBUF_2_INFO', '"\\"2.4.13\\""'), ('GDK_PIXBUF_VERSION_2_4_13', None)]
    include_dirs = ['/usr/include/gtk-2.0', '/usr/include/glib-2.0', '/usr/lib64/glib-2.0/include']

amd_info:
  libraries amd not found in /GWD/appbase/common/lib
  libraries amd not found in /usr/local/lib
  libraries amd not found in /usr/lib
  NOT AVAILABLE

atlas_info:
  libraries lapack_atlas not found in /users/d88/ma856388/lib
__main__.atlas_info
  FOUND:
    libraries = ['lapack', 'f77blas', 'cblas', 'atlas']
    library_dirs = ['/users/d88/ma856388/lib']
    language = f77

Numeric_info:
  FOUND:
    define_macros = [('NUMERIC_VERSION', '"\\"23.8\\""'), ('NUMERIC', None)]

numerix_info:
numpy_info:
  FOUND:
    define_macros = [('NUMPY_VERSION', '"\\"1.3.0\\""'), ('NUMPY', None)]

  FOUND:
    define_macros = [('NUMPY_VERSION', '"\\"1.3.0\\""'), ('NUMPY', None)]






      


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