[SciPy-User] Compiling scipy.sparse.sparsetools extension throws g++ internal error

Diederik van Liere dvanliere@gmail....
Tue Mar 9 19:04:18 CST 2010


As a follow up to the problem I had yesterday with the GCC compiler, I have
circumvented that by temporarily disabling the sparse module but now I am
running into the following import error:

ImportError: /usr/local/lib/python2.6/site-packages/scipy/linalg/clapack.so:
undefined symbol: clapack_sgesv

This error has been reported before and I have read those threads and
attempted their suggestions to fix it by I have not been lucky so far.
Below is the output of numpy/dist-utils/system_info.py
Hopefully this will give some pointers why I am having issues:

lapack_info:
  FOUND:
    libraries = ['lapack']
    library_dirs = ['/usr/local/atlas/lib/']
    language = f77

lapack_opt_info:
lapack_mkl_info:
mkl_info:
  libraries mkl,vml,guide not found in /usr/local/atlas/lib/
  NOT AVAILABLE

  NOT AVAILABLE

atlas_threads_info:
Setting PTATLAS=ATLAS
  libraries lapack_atlas not found in /usr/local/atlas/lib/
__main__.atlas_threads_info
Setting PTATLAS=ATLAS
Setting PTATLAS=ATLAS
  FOUND:
    libraries = ['lapack', 'ptf77blas', 'ptcblas', 'atlas']
    library_dirs = ['/usr/local/atlas/lib/']
    language = f77
    include_dirs = ['/usr/local/atlas/include']

customize GnuFCompiler
Could not locate executable g77
Could not locate executable f77
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
customize NAGFCompiler
Could not locate executable f95
customize VastFCompiler
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/local/bin/gfortran
customize Gnu95FCompiler
customize Gnu95FCompiler 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 -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall
-Wstrict-prototypes -fPIC

compile options: '-c'
gcc: _configtest.c
gcc -pthread _configtest.o -L/usr/local/atlas/lib/ -llapack -lptf77blas
-lptcblas -latlas -o _configtest
ATLAS version 3.8.3 built by root on Tue Mar  9 13:52:29 CST 2010:
   UNAME    : Linux vps.network-labs.org 2.6.18-028stab064.7-ent #1 SMP Thu
Aug 20 22:25:02 MSD 2009 i686 i686 i386 GNU/Linux
   INSTFLG  : -1 0 -a 1
   ARCHDEFS : -DATL_OS_Linux -DATL_ARCH_Corei7 -DATL_CPUMHZ=2133 -DATL_SSE3
-DATL_SSE2 -DATL_SSE1 -DATL_GAS_x8632
   F2CDEFS  : -DAdd_ -DF77_INTEGER=int -DStringSunStyle
   CACHEEDGE: 786432
   F77      : gfortran, version GNU Fortran 95 (GCC) 4.1.2
   F77FLAGS : -O -fPIC -m32
   SMC      : gcc, version gcc (GCC) 4.1.2
   SMCFLAGS : -fomit-frame-pointer -mfpmath=sse -msse3 -O2
-fno-schedule-insns2 -fPIC -m32
   SKC      : gcc, version gcc (GCC) 4.1.2
   SKCFLAGS : -fomit-frame-pointer -mfpmath=sse -msse3 -O2
-fno-schedule-insns2 -fPIC -m32
success!
removing: _configtest.c _configtest.o _configtest
  FOUND:
    libraries = ['lapack', 'ptf77blas', 'ptcblas', 'atlas']
    library_dirs = ['/usr/local/atlas/lib/']
    language = f77
    define_macros = [('ATLAS_INFO', '"\\"3.8.3\\""')]
    include_dirs = ['/usr/local/atlas/include']

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
/usr/local/atlas/lib/
  libraries lapack_atlas not found in /usr/local/atlas/lib/
__main__.lapack_atlas_info
  NOT AVAILABLE

umfpack_info:
  libraries umfpack not found in /usr/local/atlas/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/atlas/lib/
  libraries lapack_atlas not found in /usr/local/atlas/lib/
__main__.lapack_atlas_threads_info
  NOT AVAILABLE

x11_info:
  libraries X11 not found in /usr/local/atlas/lib/
  NOT AVAILABLE

blas_info:
  libraries blas not found in /usr/local/atlas/lib/
  NOT AVAILABLE

fftw_info:
  libraries fftw3 not found in /usr/local/atlas/lib/
  fftw3 not found
  libraries rfftw,fftw not found in /usr/local/atlas/lib/
  fftw2 not found
  NOT AVAILABLE

f2py_info:
  FOUND:
    sources =
['/usr/local/lib/python2.6/site-packages/numpy/f2py/src/fortranobject.c']
    include_dirs = ['/usr/local/lib/python2.6/site-packages/numpy/f2py/src']

gdk_pixbuf_xlib_2_info:
  NOT AVAILABLE

dfftw_threads_info:
  libraries drfftw_threads,dfftw_threads not found in /usr/local/atlas/lib/
  dfftw threads not found
  NOT AVAILABLE

atlas_blas_info:
  FOUND:
    libraries = ['f77blas', 'cblas', 'atlas']
    library_dirs = ['/usr/local/atlas/lib/']
    language = c
    include_dirs = ['/usr/local/atlas/include']

fftw3_info:
  libraries fftw3 not found in /usr/local/atlas/lib/
  fftw3 not found
  NOT AVAILABLE

blas_opt_info:
blas_mkl_info:
  libraries mkl,vml,guide not found in /usr/local/atlas/lib/
  NOT AVAILABLE

atlas_blas_threads_info:
Setting PTATLAS=ATLAS
Setting PTATLAS=ATLAS
Setting PTATLAS=ATLAS
  FOUND:
    libraries = ['ptf77blas', 'ptcblas', 'atlas']
    library_dirs = ['/usr/local/atlas/lib/']
    language = c
    include_dirs = ['/usr/local/atlas/include']

customize GnuFCompiler
customize IntelFCompiler
customize LaheyFCompiler
customize PGroupFCompiler
customize AbsoftFCompiler
customize NAGFCompiler
customize VastFCompiler
customize CompaqFCompiler
customize IntelItaniumFCompiler
customize IntelEM64TFCompiler
customize Gnu95FCompiler
customize Gnu95FCompiler
customize Gnu95FCompiler 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 -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall
-Wstrict-prototypes -fPIC

compile options: '-c'
gcc: _configtest.c
gcc -pthread _configtest.o -L/usr/local/atlas/lib/ -lptf77blas -lptcblas
-latlas -o _configtest
ATLAS version 3.8.3 built by root on Tue Mar  9 13:52:29 CST 2010:
   UNAME    : Linux vps.network-labs.org 2.6.18-028stab064.7-ent #1 SMP Thu
Aug 20 22:25:02 MSD 2009 i686 i686 i386 GNU/Linux
   INSTFLG  : -1 0 -a 1
   ARCHDEFS : -DATL_OS_Linux -DATL_ARCH_Corei7 -DATL_CPUMHZ=2133 -DATL_SSE3
-DATL_SSE2 -DATL_SSE1 -DATL_GAS_x8632
   F2CDEFS  : -DAdd_ -DF77_INTEGER=int -DStringSunStyle
   CACHEEDGE: 786432
   F77      : gfortran, version GNU Fortran 95 (GCC) 4.1.2
   F77FLAGS : -O -fPIC -m32
   SMC      : gcc, version gcc (GCC) 4.1.2
   SMCFLAGS : -fomit-frame-pointer -mfpmath=sse -msse3 -O2
-fno-schedule-insns2 -fPIC -m32
   SKC      : gcc, version gcc (GCC) 4.1.2
   SKCFLAGS : -fomit-frame-pointer -mfpmath=sse -msse3 -O2
-fno-schedule-insns2 -fPIC -m32
success!
removing: _configtest.c _configtest.o _configtest
  FOUND:
    libraries = ['ptf77blas', 'ptcblas', 'atlas']
    library_dirs = ['/usr/local/atlas/lib/']
    language = c
    define_macros = [('ATLAS_INFO', '"\\"3.8.3\\""')]
    include_dirs = ['/usr/local/atlas/include']

sfftw_info:
  libraries srfftw,sfftw not found in /usr/local/atlas/lib/
  sfftw not found
  NOT AVAILABLE

xft_info:
  NOT AVAILABLE

fft_opt_info:
fftw2_info:
  libraries rfftw,fftw not found in /usr/local/atlas/lib/
  fftw2 not found
  NOT AVAILABLE

dfftw_info:
  libraries drfftw,dfftw not found in /usr/local/atlas/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/atlas/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 /usr/local/atlas/lib/
  sfftw threads not found
  NOT AVAILABLE

boost_python_info:
  NOT AVAILABLE

freetype2_info:
  FOUND:
    libraries = ['freetype']
    define_macros = [('FREETYPE2_INFO', '"\\"9.10.3\\""'),
('FREETYPE2_VERSION_9_10_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/atlas/lib/
  NOT AVAILABLE

atlas_info:
  libraries lapack_atlas not found in /usr/local/atlas/lib/
__main__.atlas_info
  FOUND:
    libraries = ['lapack', 'f77blas', 'cblas', 'atlas']
    library_dirs = ['/usr/local/atlas/lib/']
    language = f77
    include_dirs = ['/usr/local/atlas/include']

Numeric_info:
  NOT AVAILABLE

numerix_info:
numpy_info:
  FOUND:
    define_macros = [('NUMPY_VERSION', '"\\"2.0.0.dev8291\\""'), ('NUMPY',
None)]

  FOUND:
    define_macros = [('NUMPY_VERSION', '"\\"2.0.0.dev8291\\""'), ('NUMPY',
None)]


Thanks so much for your help!
best regards,
Diederik
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