[SciPy-user] scipy.test() from trunk segfaults

Scott Beardsley scott@cse.ucdavis....
Fri Feb 8 15:35:12 CST 2008


I'm having a problem building/testing scipy from the svn trunk. I built 
the ATLAS libraries from scratch (including the dynamic libs). All seems 
to go great with the numpy install (also the trunk). numpy tests all 
finish successfully. I've tried searching the archives and found a 
message about adding libg2c and libm but that didn't seem to work. As 
you can see from the log below scipy.test() segfaults:

$ python
Python 2.5.1 (r251:54863, Jul 17 2007, 16:59:41)
[GCC 3.4.6 20060404 (Red Hat 3.4.6-8)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
 >>> import numpy
 >>> print numpy.__version__
1.0.5.dev4775
 >> numpy.test()
Numpy is installed in 
/share/apps/python-2.5.1/lib/python2.5/site-packages/numpy
Numpy version 1.0.5.dev4775
Python version 2.5.1 (r251:54863, Jul 17 2007, 16:59:41) [GCC 3.4.6 
20060404 (Red Hat 3.4.6-8)]
   Found 10/10 tests for numpy.core.defmatrix
   Found 36/36 tests for numpy.core.ma
   Found 237/237 tests for numpy.core.multiarray
   Found 65/65 tests for numpy.core.numeric
   Found 31/31 tests for numpy.core.numerictypes
   Found 12/12 tests for numpy.core.records
   Found 6/6 tests for numpy.core.scalarmath
   Found 14/14 tests for numpy.core.umath
   Found 4/4 tests for numpy.ctypeslib
   Found 5/5 tests for numpy.distutils.misc_util
   Found 2/2 tests for numpy.fft.fftpack
   Found 3/3 tests for numpy.fft.helper
   Found 10/10 tests for numpy.lib.arraysetops
   Found 0/0 tests for numpy.lib.format
   Found 46/46 tests for numpy.lib.function_base
   Found 5/5 tests for numpy.lib.getlimits
   Found 4/4 tests for numpy.lib.index_tricks
   Found 3/3 tests for numpy.lib.polynomial
   Found 49/49 tests for numpy.lib.shape_base
   Found 15/15 tests for numpy.lib.twodim_base
   Found 43/43 tests for numpy.lib.type_check
   Found 1/1 tests for numpy.lib.ufunclike
   Found 40/40 tests for numpy.linalg
   Found 3/3 tests for numpy.random
   Found 0/0 tests for __main__
....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
----------------------------------------------------------------------
Ran 708 tests in 0.651s

OK
 >>> import scipy
 >>> print scipy.__version__
0.7.0.dev3905
 >>> scipy.test()
/share/apps/python-2.5.1/lib/python2.5/site-packages/scipy/linsolve/__init__.py:4: 
DeprecationWarning: scipy.linsolve has moved to scipy.splinalg.dsolve
   warn('scipy.linsolve has moved to scipy.splinalg.dsolve', 
DeprecationWarning)
.../share/apps/python-2.5.1/lib/python2.5/site-packages/scipy/cluster/vq.py:477: 
UserWarning: One of the clusters is empty. Re-run kmean with a different 
initialization.
   warnings.warn("One of the clusters is empty. "
exception raised as expected: One of the clusters is empty. Re-run kmean 
with a different initialization.
................................................Residual: 1.05006987327e-07
............../share/apps/python-2.5.1/lib/python2.5/site-packages/scipy/interpolate/fitpack2.py:458: 
UserWarning:
The coefficients of the spline returned have been computed as the
minimal norm least-squares solution of a (numerically) rank deficient
system (deficiency=7). If deficiency is large, the results may be
inaccurate. Deficiency may strongly depend on the value of eps.
   warnings.warn(message)
...........................................
Don't worry about a warning regarding the number of bytes read.
Warning: 1000000 bytes requested, 20 bytes read.
./share/apps/python-2.5.1/lib/python2.5/site-packages/numpy/lib/utils.py:111: 
DeprecationWarning: write_array is deprecated
   warnings.warn(str1, DeprecationWarning)
/share/apps/python-2.5.1/lib/python2.5/site-packages/numpy/lib/utils.py:111: 
DeprecationWarning: read_array is deprecated
   warnings.warn(str1, DeprecationWarning)
..................../share/apps/python-2.5.1/lib/python2.5/site-packages/numpy/lib/utils.py:111: 
DeprecationWarning: npfile is deprecated
   warnings.warn(str1, DeprecationWarning)
..............F..FF.........caxpy:n=4
..caxpy:n=3
....ccopy:n=4
..ccopy:n=3
.............cscal:n=4
....cswap:n=4
..cswap:n=3
.....daxpy:n=4
..daxpy:n=3
....dcopy:n=4
..dcopy:n=3
.............dscal:n=4
....dswap:n=4
..dswap:n=3
.....saxpy:n=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
..
****************************************************************
WARNING: clapack module is empty
-----------
See scipy/INSTALL.txt for troubleshooting.
Notes:
* If atlas library is not found by numpy/distutils/system_info.py,
   then scipy uses flapack instead of clapack.
****************************************************************

.........................FFFFFFFFFFFFFFFFFNO ATLAS INFO AVAILABLE
.........................................
****************************************************************
WARNING: cblas module is empty
-----------
See scipy/INSTALL.txt for troubleshooting.
Notes:
* If atlas library is not found by numpy/distutils/system_info.py,
   then scipy uses fblas instead of cblas.
****************************************************************

....F.Segmentation fault
$




When I run numpy/distutils/system_info.py it looks like it finds 
everything except I do get and "undefined reference" error from 
liblapack.so. See:




$ python 
/share/apps/python-2.5.1/lib/python2.5/site-packages/numpy/distutils/system_info.py
lapack_info:
   libraries lapack not found in /share/apps/fftw-3.2alpha3-test/lib
   FOUND:
     libraries = ['lapack']
     library_dirs = ['/share/apps/ATLAS-3.8.0/lib']
     language = f77

lapack_opt_info:
lapack_mkl_info:
mkl_info:
   libraries mkl,vml,guide not found in /share/apps/fftw-3.2alpha3-test/lib
   libraries mkl,vml,guide not found in /share/apps/ATLAS-3.8.0/lib
   libraries mkl,vml,guide not found in /share/apps/UMFPACK-5.2.0/lib
   libraries mkl,vml,guide not found in /share/apps/AMD-2.2.0/lib
   libraries mkl,vml,guide not found in 
/usr/lib/gcc/x86_64-redhat-linux/3.4.3
   NOT AVAILABLE

   NOT AVAILABLE

atlas_threads_info:
Setting PTATLAS=ATLAS
   libraries ptf77blas,ptcblas,atlas not found in 
/share/apps/fftw-3.2alpha3-test/lib
   libraries lapack_atlas not found in /share/apps/fftw-3.2alpha3-test/lib
   libraries lapack_atlas not found in /share/apps/ATLAS-3.8.0/lib
__main__.atlas_threads_info
Setting PTATLAS=ATLAS
Setting PTATLAS=ATLAS
   FOUND:
     libraries = ['lapack', 'ptf77blas', 'ptcblas', 'atlas']
     library_dirs = ['/share/apps/ATLAS-3.8.0/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 -pthread -fno-strict-aliasing -DNDEBUG -g -O3 -Wall 
-Wstrict-prototypes -fPIC

compile options: '-c'
gcc: _configtest.c
gcc -pthread _configtest.o -L/share/apps/ATLAS-3.8.0/lib -llapack 
-lptf77blas -lptcblas -latlas -o _configtest
/share/apps/ATLAS-3.8.0/lib/liblapack.so: undefined reference to `e_wsfe'
/share/apps/ATLAS-3.8.0/lib/liblapack.so: undefined reference to `z_abs'
/share/apps/ATLAS-3.8.0/lib/liblapack.so: undefined reference to `c_sqrt'
/share/apps/ATLAS-3.8.0/lib/liblapack.so: undefined reference to `z_exp'
/share/apps/ATLAS-3.8.0/lib/liblapack.so: undefined reference to `c_exp'
/share/apps/ATLAS-3.8.0/lib/liblapack.so: undefined reference to `do_fio'
/share/apps/ATLAS-3.8.0/lib/liblapack.so: undefined reference to `z_sqrt'
/share/apps/ATLAS-3.8.0/lib/liblapack.so: undefined reference to `s_cat'
/share/apps/ATLAS-3.8.0/lib/liblapack.so: undefined reference to `c_abs'
/share/apps/ATLAS-3.8.0/lib/liblapack.so: undefined reference to `s_wsfe'
collect2: ld returned 1 exit status
/share/apps/ATLAS-3.8.0/lib/liblapack.so: undefined reference to `e_wsfe'
/share/apps/ATLAS-3.8.0/lib/liblapack.so: undefined reference to `z_abs'
/share/apps/ATLAS-3.8.0/lib/liblapack.so: undefined reference to `c_sqrt'
/share/apps/ATLAS-3.8.0/lib/liblapack.so: undefined reference to `z_exp'
/share/apps/ATLAS-3.8.0/lib/liblapack.so: undefined reference to `c_exp'
/share/apps/ATLAS-3.8.0/lib/liblapack.so: undefined reference to `do_fio'
/share/apps/ATLAS-3.8.0/lib/liblapack.so: undefined reference to `z_sqrt'
/share/apps/ATLAS-3.8.0/lib/liblapack.so: undefined reference to `s_cat'
/share/apps/ATLAS-3.8.0/lib/liblapack.so: undefined reference to `c_abs'
/share/apps/ATLAS-3.8.0/lib/liblapack.so: undefined reference to `s_wsfe'
collect2: ld returned 1 exit status
failure.
removing: _configtest.c _configtest.o
Status: 255
Output:
   FOUND:
     libraries = ['lapack', 'ptf77blas', 'ptcblas', 'atlas']
     library_dirs = ['/share/apps/ATLAS-3.8.0/lib']
     language = f77
     define_macros = [('NO_ATLAS_INFO', 2)]

lapack_atlas_info:
   libraries lapack_atlas,f77blas,cblas,atlas not found in 
/share/apps/fftw-3.2alpha3-test/lib
   libraries lapack_atlas not found in /share/apps/fftw-3.2alpha3-test/lib
   libraries lapack_atlas,f77blas,cblas,atlas not found in 
/share/apps/ATLAS-3.8.0/lib
   libraries lapack_atlas not found in /share/apps/ATLAS-3.8.0/lib
   libraries lapack_atlas,f77blas,cblas,atlas not found in 
/share/apps/UMFPACK-5.2.0/lib
   libraries lapack_atlas not found in /share/apps/UMFPACK-5.2.0/lib
   libraries lapack_atlas,f77blas,cblas,atlas not found in 
/share/apps/AMD-2.2.0/lib
   libraries lapack_atlas not found in /share/apps/AMD-2.2.0/lib
   libraries lapack_atlas,f77blas,cblas,atlas not found in 
/usr/lib/gcc/x86_64-redhat-linux/3.4.3
   libraries lapack_atlas not found in 
/usr/lib/gcc/x86_64-redhat-linux/3.4.3
__main__.lapack_atlas_info
   NOT AVAILABLE

umfpack_info:
   libraries umfpack not found in /share/apps/fftw-3.2alpha3-test/lib
   libraries umfpack not found in /share/apps/ATLAS-3.8.0/lib
amd_info:
   libraries amd not found in /share/apps/fftw-3.2alpha3-test/lib
   libraries amd not found in /share/apps/ATLAS-3.8.0/lib
   libraries amd not found in /share/apps/UMFPACK-5.2.0/lib
   FOUND:
     libraries = ['amd']
     library_dirs = ['/share/apps/AMD-2.2.0/lib']
     swig_opts = ['-I/share/apps/AMD-2.2.0/include']
     define_macros = [('SCIPY_AMD_H', None)]
     include_dirs = ['/share/apps/AMD-2.2.0/include']

   FOUND:
     libraries = ['umfpack', 'amd']
     library_dirs = ['/share/apps/UMFPACK-5.2.0/lib', 
'/share/apps/AMD-2.2.0/lib']
     swig_opts = ['-I/share/apps/UMFPACK-5.2.0/include', 
'-I/share/apps/AMD-2.2.0/include']
     define_macros = [('SCIPY_UMFPACK_H', None), ('SCIPY_AMD_H', None)]
     include_dirs = ['/share/apps/UMFPACK-5.2.0/include', 
'/share/apps/AMD-2.2.0/include']

_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 
/share/apps/fftw-3.2alpha3-test/lib
   libraries lapack_atlas not found in /share/apps/fftw-3.2alpha3-test/lib
   libraries lapack_atlas,ptf77blas,ptcblas,atlas not found in 
/share/apps/ATLAS-3.8.0/lib
   libraries lapack_atlas not found in /share/apps/ATLAS-3.8.0/lib
   libraries lapack_atlas,ptf77blas,ptcblas,atlas not found in 
/share/apps/UMFPACK-5.2.0/lib
   libraries lapack_atlas not found in /share/apps/UMFPACK-5.2.0/lib
   libraries lapack_atlas,ptf77blas,ptcblas,atlas not found in 
/share/apps/AMD-2.2.0/lib
   libraries lapack_atlas not found in /share/apps/AMD-2.2.0/lib
   libraries lapack_atlas,ptf77blas,ptcblas,atlas not found in 
/usr/lib/gcc/x86_64-redhat-linux/3.4.3
   libraries lapack_atlas not found in 
/usr/lib/gcc/x86_64-redhat-linux/3.4.3
__main__.lapack_atlas_threads_info
   NOT AVAILABLE

x11_info:
   libraries X11 not found in /share/apps/fftw-3.2alpha3-test/lib
   libraries X11 not found in /share/apps/ATLAS-3.8.0/lib
   libraries X11 not found in /share/apps/UMFPACK-5.2.0/lib
   libraries X11 not found in /share/apps/AMD-2.2.0/lib
   libraries X11 not found in /usr/lib/gcc/x86_64-redhat-linux/3.4.3
   NOT AVAILABLE

blas_info:
   libraries blas not found in /share/apps/fftw-3.2alpha3-test/lib
   FOUND:
     libraries = ['blas']
     library_dirs = ['/share/apps/ATLAS-3.8.0/lib']
     language = f77

fftw_info:
   FOUND:
     libraries = ['fftw3', 'fftw3']
     library_dirs = ['/share/apps/fftw-3.2alpha3-test/lib']
     define_macros = [('SCIPY_FFTW3_H', None)]
     include_dirs = ['/share/apps/fftw-3.2alpha3-test/include']

f2py_info:
   FOUND:
     sources = 
['/share/apps/python-2.5.1/lib/python2.5/site-packages/numpy/f2py/src/fortranobject.c']
     include_dirs = 
['/share/apps/python-2.5.1/lib/python2.5/site-packages/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 
/share/apps/fftw-3.2alpha3-test/lib
   libraries drfftw_threads,dfftw_threads not found in 
/share/apps/ATLAS-3.8.0/lib
   libraries drfftw_threads,dfftw_threads not found in 
/share/apps/UMFPACK-5.2.0/lib
   libraries drfftw_threads,dfftw_threads not found in 
/share/apps/AMD-2.2.0/lib
   libraries drfftw_threads,dfftw_threads not found in 
/usr/lib/gcc/x86_64-redhat-linux/3.4.3
   dfftw threads not found
   NOT AVAILABLE

atlas_blas_info:
   libraries f77blas,cblas,atlas not found in 
/share/apps/fftw-3.2alpha3-test/lib
   FOUND:
     libraries = ['f77blas', 'cblas', 'atlas']
     library_dirs = ['/share/apps/ATLAS-3.8.0/lib']
     language = c

fftw3_info:
   FOUND:
     libraries = ['fftw3']
     library_dirs = ['/share/apps/fftw-3.2alpha3-test/lib']
     define_macros = [('SCIPY_FFTW3_H', None)]
     include_dirs = ['/share/apps/fftw-3.2alpha3-test/include']

blas_opt_info:
blas_mkl_info:
   libraries mkl,vml,guide not found in /share/apps/fftw-3.2alpha3-test/lib
   libraries mkl,vml,guide not found in /share/apps/ATLAS-3.8.0/lib
   libraries mkl,vml,guide not found in /share/apps/UMFPACK-5.2.0/lib
   libraries mkl,vml,guide not found in /share/apps/AMD-2.2.0/lib
   libraries mkl,vml,guide not found in 
/usr/lib/gcc/x86_64-redhat-linux/3.4.3
   NOT AVAILABLE

atlas_blas_threads_info:
Setting PTATLAS=ATLAS
   libraries ptf77blas,ptcblas,atlas not found in 
/share/apps/fftw-3.2alpha3-test/lib
Setting PTATLAS=ATLAS
Setting PTATLAS=ATLAS
   FOUND:
     libraries = ['ptf77blas', 'ptcblas', 'atlas']
     library_dirs = ['/share/apps/ATLAS-3.8.0/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 -pthread -fno-strict-aliasing -DNDEBUG -g -O3 -Wall 
-Wstrict-prototypes -fPIC

compile options: '-c'
gcc: _configtest.c
gcc -pthread _configtest.o -L/share/apps/ATLAS-3.8.0/lib -lptf77blas 
-lptcblas -latlas -o _configtest
ATLAS version 3.8.0 built by root on Thu Feb  7 16:08:30 PST 2008:
    UNAME    : Linux tribe.cse.ucdavis.edu 2.6.9-67.ELsmp #1 SMP Fri Nov 
16 12:49:06 EST 2007 x86_64 x86_64 x86_64 GNU/Linux
    INSTFLG  : -1 0 -a 1
    ARCHDEFS : -DATL_OS_Linux -DATL_ARCH_HAMMER -DATL_CPUMHZ=1808 
-DATL_SSE3 -DATL_SSE2 -DATL_SSE1 -DATL_3DNow -DATL_USE64BITS -DATL_GAS_x8664
    F2CDEFS  : -DAdd_ -DF77_INTEGER=int -DStringSunStyle
    CACHEEDGE: 0
    F77      : gfortran, version GNU Fortran 95 (GCC) 4.1.1 20070105 
(Red Hat 4.1.1-53)
    F77FLAGS : -fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4 
-fPIC -m64
    SMC      : gcc, version gcc (GCC) 3.4.6 20060404 (Red Hat 3.4.6-8)
    SMCFLAGS : -fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4 
-fPIC -m64
    SKC      : gcc, version gcc (GCC) 3.4.6 20060404 (Red Hat 3.4.6-8)
    SKCFLAGS : -fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4 
-fPIC -m64
success!
removing: _configtest.c _configtest.o _configtest
   FOUND:
     libraries = ['ptf77blas', 'ptcblas', 'atlas']
     library_dirs = ['/share/apps/ATLAS-3.8.0/lib']
     language = c
     define_macros = [('ATLAS_INFO', '"\\"3.8.0\\""')]

sfftw_info:
   libraries srfftw,sfftw not found in /share/apps/fftw-3.2alpha3-test/lib
   libraries srfftw,sfftw not found in /share/apps/ATLAS-3.8.0/lib
   libraries srfftw,sfftw not found in /share/apps/UMFPACK-5.2.0/lib
   libraries srfftw,sfftw not found in /share/apps/AMD-2.2.0/lib
   libraries srfftw,sfftw not found in 
/usr/lib/gcc/x86_64-redhat-linux/3.4.3
   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:
djbfft_info:
   NOT AVAILABLE

   FOUND:
     libraries = ['fftw3']
     library_dirs = ['/share/apps/fftw-3.2alpha3-test/lib']
     define_macros = [('SCIPY_FFTW3_H', None)]
     include_dirs = ['/share/apps/fftw-3.2alpha3-test/include']

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

fftw2_info:
   libraries rfftw,fftw not found in /share/apps/fftw-3.2alpha3-test/lib
   libraries rfftw,fftw not found in /share/apps/ATLAS-3.8.0/lib
   libraries rfftw,fftw not found in /share/apps/UMFPACK-5.2.0/lib
   libraries rfftw,fftw not found in /share/apps/AMD-2.2.0/lib
   libraries rfftw,fftw not found in /usr/lib/gcc/x86_64-redhat-linux/3.4.3
   fftw2 not found
   NOT AVAILABLE

fftw_threads_info:
   libraries rfftw_threads,fftw_threads not found in 
/share/apps/fftw-3.2alpha3-test/lib
   libraries rfftw_threads,fftw_threads not found in 
/share/apps/ATLAS-3.8.0/lib
   libraries rfftw_threads,fftw_threads not found in 
/share/apps/UMFPACK-5.2.0/lib
   libraries rfftw_threads,fftw_threads not found in 
/share/apps/AMD-2.2.0/lib
   libraries rfftw_threads,fftw_threads not found in 
/usr/lib/gcc/x86_64-redhat-linux/3.4.3
   fftw threads not found
   NOT AVAILABLE

_numpy_info:
   NOT AVAILABLE

wx_info:
Could not locate executable wx-config
File not found: None. Cannot determine wx info.
   NOT AVAILABLE

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 
/share/apps/fftw-3.2alpha3-test/lib
   libraries srfftw_threads,sfftw_threads not found in 
/share/apps/ATLAS-3.8.0/lib
   libraries srfftw_threads,sfftw_threads not found in 
/share/apps/UMFPACK-5.2.0/lib
   libraries srfftw_threads,sfftw_threads not found in 
/share/apps/AMD-2.2.0/lib
   libraries srfftw_threads,sfftw_threads not found in 
/usr/lib/gcc/x86_64-redhat-linux/3.4.3
   sfftw threads not found
   NOT AVAILABLE

boost_python_info:
   FOUND:
     libraries = [('boost_python_src', {'sources': 
['./boost_1_34_1/libs/python/src/long.cpp', 
'./boost_1_34_1/libs/python/src/errors.cpp...
...
...python/src/converter/registry.cpp'], 'include_dirs': 
['./boost_1_34_1', '/share/apps/python-2.5.1/include/python2.5']})]
     include_dirs = ['./boost_1_34_1']

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']

dfftw_info:
   libraries drfftw,dfftw not found in /share/apps/fftw-3.2alpha3-test/lib
   libraries drfftw,dfftw not found in /share/apps/ATLAS-3.8.0/lib
   libraries drfftw,dfftw not found in /share/apps/UMFPACK-5.2.0/lib
   libraries drfftw,dfftw not found in /share/apps/AMD-2.2.0/lib
   libraries drfftw,dfftw not found in 
/usr/lib/gcc/x86_64-redhat-linux/3.4.3
   dfftw not found
   NOT AVAILABLE

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']

atlas_info:
   libraries f77blas,cblas,atlas not found in 
/share/apps/fftw-3.2alpha3-test/lib
   libraries lapack_atlas not found in /share/apps/fftw-3.2alpha3-test/lib
   libraries lapack_atlas not found in /share/apps/ATLAS-3.8.0/lib
__main__.atlas_info
   FOUND:
     libraries = ['lapack', 'f77blas', 'cblas', 'atlas']
     library_dirs = ['/share/apps/ATLAS-3.8.0/lib']
     language = f77

Numeric_info:
   NOT AVAILABLE

numerix_info:
numpy_info:
   FOUND:
     define_macros = [('NUMPY_VERSION', '"\\"1.0.5.dev4775\\""'), 
('NUMPY', None)]

   FOUND:
     define_macros = [('NUMPY_VERSION', '"\\"1.0.5.dev4775\\""'), 
('NUMPY', None)]


Any ideas?

Here is my site.cfg:
[DEFAULT]
library_dirs = 
/share/apps/fftw-3.2alpha3-test/lib:/share/apps/ATLAS-3.8.0/lib:/share/apps/UMFPACK-5.2.0/lib:/share/apps/AMD-2.2.0/lib:/usr/lib/gcc/x86_64-redhat-linux/3.4.3
include_dirs = 
/share/apps/fftw-3.2alpha3-test/include:/share/apps/ATLAS-3.8.0/include:/share/apps/UMFPACK-5.2.0/include:/share/apps/AMD-2.2.0/include
[blas_opt]
libraries = g2c, m, ptf77blas, ptcblas, atlas
[lapack_opt]
libraries = g2c, m, lapack, ptf77blas, ptcblas, atlas
[amd]
amd_libs = amd
[umfpack]
umfpack_libs = umfpack
[fftw]
libraries = fftw3

Scott



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