[SciPy-user] cephes : gfortran

Johann Cohen-Tanugi cohen@slac.stanford....
Thu Apr 24 16:07:23 CDT 2008


hi Robert,
thanks for your help!
Here is the full build log (I cant find anything wrong related to 
cephes, but there are many things which look weird) :
[cohen@jarrett scipy-svn]$ python setup.py  build --fcompiler=gnu95
Warning: No configuration returned, assuming unavailable.
mkl_info:
  libraries mkl,vml,guide not found in /usr/local/lib
  libraries mkl,vml,guide not found in /usr/lib
  NOT AVAILABLE

fftw3_info:
  libraries fftw3 not found in /usr/local/lib
  FOUND:
    libraries = ['fftw3']
    library_dirs = ['/usr/lib']
    define_macros = [('SCIPY_FFTW3_H', None)]
    include_dirs = ['/usr/include']

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

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 -O2 -g -pipe 
-Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector 
--param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic 
-fasynchronous-unwind-tables -D_GNU_SOURCE -fPIC -fPIC

compile options: '-c'
gcc: _configtest.c
gcc -pthread _configtest.o -L/usr/local/atlas/lib -lptf77blas -lptcblas 
-latlas -llapack -lptf77blas -lptcblas -latlas -o _configtest
ATLAS version 3.8.0 built by cohen on Sun Mar 30 22:47:43 CEST 2008:
   UNAME    : Linux jarrett 2.6.24.3-50.fc8 #1 SMP Thu Mar 20 14:47:10 
EDT 2008 i686 i686 i386 GNU/Linux
   INSTFLG  : -1 0 -a 1
   ARCHDEFS : -DATL_OS_Linux -DATL_ARCH_Core2Duo -DATL_CPUMHZ=1801 
-DATL_SSE3 -DATL_SSE2 -DATL_SSE1 -DATL_GAS_x8632
   F2CDEFS  : -DAdd_ -DF77_INTEGER=int -DStringSunStyle
   CACHEEDGE: 2097152
   F77      : gfortran, version GNU Fortran (GCC) 4.1.2 20070925 (Red 
Hat 4.1.2-33)
   F77FLAGS : -O -fPIC -m32
   SMC      : gcc, version gcc (GCC) 4.1.2 20070925 (Red Hat 4.1.2-33)
   SMCFLAGS : -fomit-frame-pointer -mfpmath=sse -msse3 -O2 -fPIC -m32
   SKC      : gcc, version gcc (GCC) 4.1.2 20070925 (Red Hat 4.1.2-33)
   SKCFLAGS : -fomit-frame-pointer -mfpmath=sse -msse3 -O2 -fPIC -m32
success!
removing: _configtest.c _configtest.o _configtest
  FOUND:
    libraries = ['ptf77blas', 'ptcblas', 'atlas', 'lapack', 'ptf77blas', 
'ptcblas', 'atlas']
    library_dirs = ['/usr/local/atlas/lib']
    language = c
    define_macros = [('ATLAS_INFO', '"\\"3.8.0\\""')]
    include_dirs = ['/usr/local/atlas/include']

ATLAS version 3.8.0
lapack_opt_info:
lapack_mkl_info:
  NOT AVAILABLE

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

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 -O2 -g -pipe 
-Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector 
--param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic 
-fasynchronous-unwind-tables -D_GNU_SOURCE -fPIC -fPIC

compile options: '-c'
gcc: _configtest.c
gcc -pthread _configtest.o -L/usr/local/atlas/lib -llapack -lptf77blas 
-lptcblas -latlas -llapack -lptf77blas -lptcblas -latlas -o _configtest
ATLAS version 3.8.0 built by cohen on Sun Mar 30 22:47:43 CEST 2008:
   UNAME    : Linux jarrett 2.6.24.3-50.fc8 #1 SMP Thu Mar 20 14:47:10 
EDT 2008 i686 i686 i386 GNU/Linux
   INSTFLG  : -1 0 -a 1
   ARCHDEFS : -DATL_OS_Linux -DATL_ARCH_Core2Duo -DATL_CPUMHZ=1801 
-DATL_SSE3 -DATL_SSE2 -DATL_SSE1 -DATL_GAS_x8632
   F2CDEFS  : -DAdd_ -DF77_INTEGER=int -DStringSunStyle
   CACHEEDGE: 2097152
   F77      : gfortran, version GNU Fortran (GCC) 4.1.2 20070925 (Red 
Hat 4.1.2-33)
   F77FLAGS : -O -fPIC -m32
   SMC      : gcc, version gcc (GCC) 4.1.2 20070925 (Red Hat 4.1.2-33)
   SMCFLAGS : -fomit-frame-pointer -mfpmath=sse -msse3 -O2 -fPIC -m32
   SKC      : gcc, version gcc (GCC) 4.1.2 20070925 (Red Hat 4.1.2-33)
   SKCFLAGS : -fomit-frame-pointer -mfpmath=sse -msse3 -O2 -fPIC -m32
success!
removing: _configtest.c _configtest.o _configtest
  FOUND:
    libraries = ['lapack', 'ptf77blas', 'ptcblas', 'atlas', 'lapack', 
'ptf77blas', 'ptcblas', 'atlas']
    library_dirs = ['/usr/local/atlas/lib']
    language = f77
    define_macros = [('ATLAS_INFO', '"\\"3.8.0\\""')]
    include_dirs = ['/usr/local/atlas/include']

ATLAS version 3.8.0
ATLAS version 3.8.0
umfpack_info:
amd_info:
  libraries amd not found in /usr/local/lib
  FOUND:
    libraries = ['amd']
    library_dirs = ['/usr/lib']

  FOUND:
    libraries = ['umfpack', 'amd']
    library_dirs = ['/data1/sources/MATHSTUFF/UMFPACK/Lib/', '/usr/lib']
    swig_opts = ['-I/data1/sources/MATHSTUFF/UMFPACK/Include']
    define_macros = [('SCIPY_UMFPACK_H', None)]
    include_dirs = ['/data1/sources/MATHSTUFF/UMFPACK/Include']

running build
running scons
customize UnixCCompiler
Found executable /usr/lib/ccache/gcc
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 UnixCCompiler
customize UnixCCompiler using scons
running config_cc
unifing config_cc, config, build_clib, build_ext, build commands 
--compiler options
running config_fc
unifing config_fc, config, build_clib, build_ext, build commands 
--fcompiler options
running build_src
building py_modules sources
building library "dfftpack" sources
building library "linpack_lite" sources
building library "mach" sources
building library "quadpack" sources
building library "odepack" sources
building library "fitpack" sources
building library "odrpack" sources
building library "minpack" sources
building library "rootfind" sources
building library "superlu_src" sources
building library "arpack" sources
building library "c_misc" sources
building library "cephes" sources
building library "mach" sources
building library "toms" sources
building library "amos" sources
building library "cdf" sources
building library "specfun" sources
building library "statlib" sources
building extension "scipy.cluster._vq" sources
building extension "scipy.cluster._hierarchy_wrap" sources
building extension "scipy.fftpack._fftpack" sources
f2py options: []
  adding 'build/src.linux-i686-2.5/fortranobject.c' to sources.
  adding 'build/src.linux-i686-2.5' to include_dirs.
building extension "scipy.fftpack.convolve" sources
f2py options: []
  adding 'build/src.linux-i686-2.5/fortranobject.c' to sources.
  adding 'build/src.linux-i686-2.5' to include_dirs.
building extension "scipy.integrate._quadpack" sources
building extension "scipy.integrate._odepack" sources
building extension "scipy.integrate.vode" sources
f2py options: []
  adding 'build/src.linux-i686-2.5/fortranobject.c' to sources.
  adding 'build/src.linux-i686-2.5' to include_dirs.
building extension "scipy.interpolate._fitpack" sources
building extension "scipy.interpolate.dfitpack" sources
f2py options: []
  adding 'build/src.linux-i686-2.5/fortranobject.c' to sources.
  adding 'build/src.linux-i686-2.5' to include_dirs.
  adding 
'build/src.linux-i686-2.5/scipy/interpolate/dfitpack-f2pywrappers.f' to 
sources.
building extension "scipy.io.numpyio" sources
building extension "scipy.lib.blas.fblas" sources
f2py options: ['skip:', ':']
  adding 'build/src.linux-i686-2.5/fortranobject.c' to sources.
  adding 'build/src.linux-i686-2.5' to include_dirs.
  adding 
'build/src.linux-i686-2.5/build/src.linux-i686-2.5/scipy/lib/blas/fblas-f2pywrappers.f' 
to sources.
building extension "scipy.lib.blas.cblas" sources
  adding 'scipy/lib/blas/cblas.pyf.src' to sources.
f2py options: ['skip:', ':']
  adding 'build/src.linux-i686-2.5/fortranobject.c' to sources.
  adding 'build/src.linux-i686-2.5' to include_dirs.
building extension "scipy.lib.lapack.flapack" sources
f2py options: ['skip:', ':']
  adding 'build/src.linux-i686-2.5/fortranobject.c' to sources.
  adding 'build/src.linux-i686-2.5' to include_dirs.
building extension "scipy.lib.lapack.clapack" sources
  adding 'scipy/lib/lapack/clapack.pyf.src' to sources.
f2py options: ['skip:', ':']
  adding 'build/src.linux-i686-2.5/fortranobject.c' to sources.
  adding 'build/src.linux-i686-2.5' to include_dirs.
building extension "scipy.lib.lapack.calc_lwork" sources
f2py options: []
  adding 'build/src.linux-i686-2.5/fortranobject.c' to sources.
  adding 'build/src.linux-i686-2.5' to include_dirs.
building extension "scipy.lib.lapack.atlas_version" sources
building extension "scipy.linalg.fblas" sources
  adding 'build/src.linux-i686-2.5/scipy/linalg/fblas.pyf' to sources.
f2py options: []
  adding 'build/src.linux-i686-2.5/fortranobject.c' to sources.
  adding 'build/src.linux-i686-2.5' to include_dirs.
  adding 
'build/src.linux-i686-2.5/build/src.linux-i686-2.5/scipy/linalg/fblas-f2pywrappers.f' 
to sources.
building extension "scipy.linalg.cblas" sources
  adding 'build/src.linux-i686-2.5/scipy/linalg/cblas.pyf' to sources.
f2py options: []
  adding 'build/src.linux-i686-2.5/fortranobject.c' to sources.
  adding 'build/src.linux-i686-2.5' to include_dirs.
building extension "scipy.linalg.flapack" sources
  adding 'build/src.linux-i686-2.5/scipy/linalg/flapack.pyf' to sources.
f2py options: []
  adding 'build/src.linux-i686-2.5/fortranobject.c' to sources.
  adding 'build/src.linux-i686-2.5' to include_dirs.
  adding 
'build/src.linux-i686-2.5/build/src.linux-i686-2.5/scipy/linalg/flapack-f2pywrappers.f' 
to sources.
building extension "scipy.linalg.clapack" sources
  adding 'build/src.linux-i686-2.5/scipy/linalg/clapack.pyf' to sources.
f2py options: []
  adding 'build/src.linux-i686-2.5/fortranobject.c' to sources.
  adding 'build/src.linux-i686-2.5' to include_dirs.
building extension "scipy.linalg._flinalg" sources
f2py options: []
  adding 'build/src.linux-i686-2.5/fortranobject.c' to sources.
  adding 'build/src.linux-i686-2.5' to include_dirs.
building extension "scipy.linalg.calc_lwork" sources
f2py options: []
  adding 'build/src.linux-i686-2.5/fortranobject.c' to sources.
  adding 'build/src.linux-i686-2.5' to include_dirs.
building extension "scipy.linalg.atlas_version" sources
building extension "scipy.odr.__odrpack" sources
building extension "scipy.optimize._minpack" sources
building extension "scipy.optimize._zeros" sources
building extension "scipy.optimize._lbfgsb" sources
f2py options: []
  adding 'build/src.linux-i686-2.5/fortranobject.c' to sources.
  adding 'build/src.linux-i686-2.5' to include_dirs.
building extension "scipy.optimize.moduleTNC" sources
building extension "scipy.optimize._cobyla" sources
f2py options: []
  adding 'build/src.linux-i686-2.5/fortranobject.c' to sources.
  adding 'build/src.linux-i686-2.5' to include_dirs.
building extension "scipy.optimize.minpack2" sources
f2py options: []
  adding 'build/src.linux-i686-2.5/fortranobject.c' to sources.
  adding 'build/src.linux-i686-2.5' to include_dirs.
building extension "scipy.optimize._slsqp" sources
f2py options: []
  adding 'build/src.linux-i686-2.5/fortranobject.c' to sources.
  adding 'build/src.linux-i686-2.5' to include_dirs.
building extension "scipy.signal.sigtools" sources
building extension "scipy.signal.spline" sources
building extension "scipy.sparse.linalg.isolve._iterative" sources
f2py options: []
  adding 'build/src.linux-i686-2.5/fortranobject.c' to sources.
  adding 'build/src.linux-i686-2.5' to include_dirs.
building extension "scipy.sparse.linalg.dsolve._zsuperlu" sources
building extension "scipy.sparse.linalg.dsolve._dsuperlu" sources
building extension "scipy.sparse.linalg.dsolve._csuperlu" sources
building extension "scipy.sparse.linalg.dsolve._ssuperlu" sources
building extension "scipy.sparse.linalg.dsolve.umfpack.__umfpack" sources
  adding 'scipy/sparse/linalg/dsolve/umfpack/umfpack.i' to sources.
building extension "scipy.sparse.linalg.eigen.arpack._arpack" sources
f2py options: []
  adding 'build/src.linux-i686-2.5/fortranobject.c' to sources.
  adding 'build/src.linux-i686-2.5' to include_dirs.
  adding 
'build/src.linux-i686-2.5/build/src.linux-i686-2.5/scipy/sparse/linalg/eigen/arpack/_arpack-f2pywrappers.f' 
to sources.
building extension "scipy.sparse.sparsetools._csr" sources
building extension "scipy.sparse.sparsetools._csc" sources
building extension "scipy.sparse.sparsetools._coo" sources
building extension "scipy.sparse.sparsetools._bsr" sources
building extension "scipy.sparse.sparsetools._dia" sources
building extension "scipy.special._cephes" sources
building extension "scipy.special.specfun" sources
f2py options: ['--no-wrap-functions']
  adding 'build/src.linux-i686-2.5/fortranobject.c' to sources.
  adding 'build/src.linux-i686-2.5' to include_dirs.
building extension "scipy.stats.statlib" sources
f2py options: ['--no-wrap-functions']
  adding 'build/src.linux-i686-2.5/fortranobject.c' to sources.
  adding 'build/src.linux-i686-2.5' to include_dirs.
building extension "scipy.stats.futil" sources
f2py options: []
  adding 'build/src.linux-i686-2.5/fortranobject.c' to sources.
  adding 'build/src.linux-i686-2.5' to include_dirs.
building extension "scipy.stats.mvn" sources
f2py options: []
  adding 'build/src.linux-i686-2.5/fortranobject.c' to sources.
  adding 'build/src.linux-i686-2.5' to include_dirs.
  adding 'build/src.linux-i686-2.5/scipy/stats/mvn-f2pywrappers.f' to 
sources.
building extension "scipy.ndimage._nd_image" sources
building extension "scipy.ndimage._segment" sources
building extension "scipy.ndimage._register" sources
building extension "scipy.stsci.convolve._correlate" sources
building extension "scipy.stsci.convolve._lineshape" sources
building extension "scipy.stsci.image._combine" sources
building data_files sources
running build_py
copying scipy/__svn_version__.py -> build/lib.linux-i686-2.5/scipy
copying build/src.linux-i686-2.5/scipy/__config__.py -> 
build/lib.linux-i686-2.5/scipy
running build_clib
customize UnixCCompiler
customize UnixCCompiler using build_clib
customize Gnu95FCompiler
Found executable /usr/bin/gfortran
customize Gnu95FCompiler using build_clib
running build_ext
customize UnixCCompiler
customize UnixCCompiler using build_ext
library 'mach' defined more than once, overwriting build_info
{'sources': ['scipy/integrate/mach/r1mach.f', 
'scipy/integrate/mach/d1mach.f', 'scipy/integrate/mach/xerror.f', 
'scipy/integrate/mach/i1mach.f'], 'config_fc': {'noopt': 
('scipy/integrate/setup.pyc', 1)}, 'source_languages': ['f77']}...
with
{'sources': ['scipy/special/mach/r1mach.f', 
'scipy/special/mach/d1mach.f', 'scipy/special/mach/xerror.f', 
'scipy/special/mach/i1mach.f'], 'config_fc': {'noopt': 
('scipy/special/setup.pyc', 1)}, 'source_languages': ['f77']}...
resetting extension 'scipy.integrate._odepack' language from 'c' to 'f77'.
resetting extension 'scipy.integrate.vode' language from 'c' to 'f77'.
resetting extension 'scipy.lib.blas.fblas' language from 'c' to 'f77'.
resetting extension 'scipy.odr.__odrpack' language from 'c' to 'f77'.
extending extension 'scipy.sparse.linalg.dsolve._zsuperlu' 
defined_macros with [('USE_VENDOR_BLAS', 1)]
extending extension 'scipy.sparse.linalg.dsolve._dsuperlu' 
defined_macros with [('USE_VENDOR_BLAS', 1)]
extending extension 'scipy.sparse.linalg.dsolve._csuperlu' 
defined_macros with [('USE_VENDOR_BLAS', 1)]
extending extension 'scipy.sparse.linalg.dsolve._ssuperlu' 
defined_macros with [('USE_VENDOR_BLAS', 1)]
customize UnixCCompiler
customize UnixCCompiler using build_ext
customize Gnu95FCompiler
customize Gnu95FCompiler using build_ext

best,
Johann



Robert Kern wrote:
> On Thu, Apr 24, 2008 at 8:29 AM, Johann Cohen-Tanugi
> <cohen@slac.stanford.edu> wrote:
>   
>> hello again,
>>  I also have a problem  between cephes and gfortran :
>>  In [4]: from scipy import *
>>  ---------------------------------------------------------------------------
>>  ImportError                               Traceback (most recent call last)
>>
>>  /home/cohen/<ipython console> in <module>()
>>
>>  /usr/lib/python2.5/site-packages/scipy/special/__init__.py in <module>()
>>       6 #from special_version import special_version as __version__
>>       7
>>  ----> 8 from basic import *
>>       9 import specfun
>>      10 import orthogonal
>>
>>  /usr/lib/python2.5/site-packages/scipy/special/basic.py in <module>()
>>       6
>>       7 from numpy import *
>>  ----> 8 from _cephes import *
>>       9 import types
>>      10 import specfun
>>
>>  ImportError: /usr/lib/python2.5/site-packages/scipy/special/_cephes.so:
>>  undefined symbol: _gfortran_st_write_done
>>
>>  I rebuilt with --fcompiler=gfortran to make sure, but I still get this....
>>     
>
> It's --fcompiler=gnu95 . Presumably, the Fortran runtime libraries
> didn't get linked in. Please post the full build log.
>
>   


More information about the SciPy-user mailing list