[SciPy-user] scipy build problem, linux centos4 (fwd)

Gary Strangman strang at nmr.mgh.harvard.edu
Wed Oct 11 20:28:17 CDT 2006


Hi,

I appear to have a compile problem similar to those reported by OS/X 
users, but this is on a Linux CentOS4 platform and I've been unable to 
find a solution in the list archives. The tail end of my "python setup.py 
install" command is shown below, followed by a the items requested by the 
scipy.org FAQ. I didn't have trouble compiling on my FedoraCore2 box but 
was forced to upgrade by my sysadmins (grrrr) and now I've hit a brick 
wall. It was (at least originally) an out-of-the-box installation attempt.

Any suggestions/help would be most appreciated.

Gary

build/temp.linux-i686-2.4/build/src.linux-i686-2.4/fortranobject.o(.text+0x1abf):build/src.linux-i686-2.4/fortranobject.c:267: 
undefined reference to `PyExc_AttributeError'
build/temp.linux-i686-2.4/build/src.linux-i686-2.4/fortranobject.o(.text+0x1ac6):build/src.linux-i686-2.4/fortranobject.c:267: 
undefined reference to `PyErr_SetString'
build/temp.linux-i686-2.4/build/src.linux-i686-2.4/fortranobject.o(.text+0x1adf):build/src.linux-i686-2.4/fortranobject.c:218: 
undefined reference to `PyExc_AttributeError'
build/temp.linux-i686-2.4/build/src.linux-i686-2.4/fortranobject.o(.text+0x1ae7):build/src.linux-i686-2.4/fortranobject.c:218: 
undefined reference to `PyErr_SetString'
/usr/lib/gcc/i386-redhat-linux/3.4.5/libfrtbegin.a(frtbegin.o)(.text+0x35): In 
function `main':
: undefined reference to `MAIN__'
collect2: ld returned 1 exit status
error: Command "/usr/bin/g77 -L/usr/X11R6/lib 
build/temp.linux-i686-2.4/build/src.linux-i686-2.4/Lib/fftpack/_fftpackmodule.o 
build/temp.linux-i686-2.4/Lib/fftpack/src/zfft.o 
build/temp.linux-i686-2.4/Lib/fftpack/src/drfft.o 
build/temp.linux-i686-2.4/Lib/fftpack/src/zrfft.o 
build/temp.linux-i686-2.4/Lib/fftpack/src/zfftnd.o 
build/temp.linux-i686-2.4/build/src.linux-i686-2.4/fortranobject.o 
-L/usr/local/lib -Lbuild/temp.linux-i686-2.4 -ldfftpack -lfftw3 -lg2c -o 
build/lib.linux-i686-2.4/scipy/fftpack/_fftpack.so" failed with exit status 1
/space/nsg/8/users/scipy-0.5.1>

-------------------------------------------

Linux guppy 2.6.9-42.0.2.ELsmp #1 SMP Wed Aug 23 00:17:26 CDT 2006 i686 i686 
i386 GNU/Linux

sys.platform = linux2
sys.version = '2.4.3 (#1, Oct  6 2006, 15:32:21) \n[GCC 3.4.5 20051201 (Red Hat 
3.4.5-2)]'
numpy.__version__ = '1.0b5'

/space/nsg/8/users> python -c 'from numpy.f2py.diagnose import run; run()'
------
os.name='posix'
------
sys.platform='linux2'
------
sys.version:
2.4.3 (#1, Oct  6 2006, 15:32:21)
[GCC 3.4.5 20051201 (Red Hat 3.4.5-2)]
------
sys.prefix:
/space/nsg/8/users
------
sys.path=':/homes/3/strang/python:/space/nsg/8/users/numpy-1.0b5/numpy/lib:/space/nsg/8/users/include/python2.3:/space/nsg/8/users/lib/python2.3:/usr/include:/usr/lib:/space/nsg/8/users/lib/R/lib:/space/nsg/8/users/lib/python24.zip:/space/nsg/8/users/lib/python2.4:/space/nsg/8/users/lib/python2.4/plat-linux2:/space/nsg/8/users/lib/python2.4/lib-tk:/space/nsg/8/users/lib/python2.4/lib-dynload:/space/nsg/8/users/lib/python2.4/site-packages:/space/nsg/8/users/lib/python2.4/site-packages/Numeric:/space/nsg/8/users/lib/python2.4/site-packages/PIL'
------
Failed to import numarray: No module named numarray
Found Numeric version '24.2' in 
/space/nsg/8/users/lib/python2.4/site-packages/Numeric/Numeric.pyc
Found new numpy version '1.0b5' in 
/space/nsg/8/users/lib/python2.4/site-packages/numpy/__init__.pyc
Found f2py2e version '2_3118' in 
/space/nsg/8/users/lib/python2.4/site-packages/numpy/f2py/f2py2e.pyc
Found numpy.distutils version '0.4.0' in 
'/space/nsg/8/users/lib/python2.4/site-packages/numpy/distutils/__init__.pyc'
------
Importing numpy.distutils.fcompiler ... ok
------
Checking availability of supported Fortran compilers:
customize CompaqFCompiler
customize NoneFCompiler
customize AbsoftFCompiler
Could not locate executable ifort
Could not locate executable ifc
Could not locate executable ifort
Could not locate executable efort
Could not locate executable efc
Could not locate executable ifort
Could not locate executable efort
Could not locate executable efc
customize IntelFCompiler
Could not locate executable gfortran
Could not locate executable f95
customize GnuFCompiler
customize SunFCompiler
customize NAGFCompiler
customize VastFCompiler
customize GnuFCompiler
customize IbmFCompiler
customize Gnu95FCompiler
customize IntelVisualFCompiler
customize G95FCompiler
customize IntelItaniumFCompiler
customize PGroupFCompiler
customize LaheyFCompiler
customize CompaqVisualFCompiler
customize MipsFCompiler
customize HPUXFCompiler
customize IntelItaniumVisualFCompiler
customize IntelEM64TFCompiler
List of available Fortran compilers:
   --fcompiler=gnu  GNU Fortran Compiler (3.4.5)
List of unavailable Fortran compilers:
   --fcompiler=absoft   Absoft Corp Fortran Compiler
   --fcompiler=compaq   Compaq Fortran Compiler
   --fcompiler=compaqv  DIGITAL|Compaq Visual Fortran Compiler
   --fcompiler=g95      G95 Fortran Compiler
   --fcompiler=gnu95    GNU 95 Fortran Compiler
   --fcompiler=hpux     HP Fortran 90 Compiler
   --fcompiler=ibm      IBM XL Fortran Compiler
   --fcompiler=intel    Intel Fortran Compiler for 32-bit apps
   --fcompiler=intele   Intel Fortran Compiler for Itanium apps
   --fcompiler=intelem  Intel Fortran Compiler for EM64T-based apps
   --fcompiler=intelev  Intel Visual Fortran Compiler for Itanium apps
   --fcompiler=intelv   Intel Visual Fortran Compiler for 32-bit apps
   --fcompiler=lahey    Lahey/Fujitsu Fortran 95 Compiler
   --fcompiler=mips     MIPSpro Fortran Compiler
   --fcompiler=nag      NAGWare Fortran 95 Compiler
   --fcompiler=none     Fake Fortran compiler
   --fcompiler=pg       Portland Group Fortran Compiler
   --fcompiler=sun      Sun|Forte Fortran 95 Compiler
   --fcompiler=vast     Pacific-Sierra Research Fortran 90 Compiler
List of unimplemented Fortran compilers:
   --fcompiler=f  Fortran Company/NAG F Compiler
For compiler details, run 'config_fc --verbose' setup command.
------
Importing numpy.distutils.cpuinfo ... ok
------
CPU information: getNCPUs has_mmx has_sse has_sse2 is_32bit is_Intel is_XEON 
is_Xeon ------
/space/nsg/8/users> python -c 'from numpy import show_config as s;s()'
atlas_threads_info:
     libraries = ['lapack', 'lapack', 'blas']
     library_dirs = ['/usr/lib']
     language = c

blas_opt_info:
     libraries = ['lapack', 'blas']
     library_dirs = ['/usr/lib']
     define_macros = [('NO_ATLAS_INFO', 2)]
     language = c

atlas_blas_threads_info:
     libraries = ['lapack', 'blas']
     library_dirs = ['/usr/lib']
     language = c

lapack_opt_info:
     libraries = ['lapack', 'lapack', 'blas']
     library_dirs = ['/usr/lib']
     define_macros = [('NO_ATLAS_INFO', 2)]
     language = c

lapack_mkl_info:
   NOT AVAILABLE

blas_mkl_info:
   NOT AVAILABLE

mkl_info:
   NOT AVAILABLE




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