[SciPy-User] how to fix this error from scipy

Zhibin Dai zhibin_dai@ynao.ac...
Tue Sep 18 11:14:34 CDT 2012


Dear sir,

I have installed numpy and scipy successfully. And the test of numpy has been passed.

But, I got an error when testing scipy. The details of error have been attached as follow:

-------------------------------------
sh-3.2# python
Python 2.7.1 (r271:86832, Jul 31 2011, 19:30:53) 
[GCC 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2335.15.00)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import scipy
>>> scipy.test('full')
Running unit tests for scipy
NumPy version 1.6.2
NumPy is installed in /Library/Python/2.7/site-packages/numpy-1.6.2-py2.7-macosx-10.7-intel.egg/numpy
SciPy version 0.10.1
SciPy is installed in /Library/Python/2.7/site-packages/scipy-0.10.1-py2.7-macosx-10.7-intel.egg/scipy
Python version 2.7.1 (r271:86832, Jul 31 2011, 19:30:53) [GCC 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2335.15.00)]
nose version 1.2.1
...................................................................................................................................................................................F.python(16154) malloc: *** error for object 0x7fe9125e7fa8: incorrect checksum for freed object - object was probably modified after being freed.
*** set a breakpoint in malloc_error_break to debug
Abort trap: 6
-------------------------------------


I also generate the following information in one command:

-------------------------------------
sh-3.2# python -c 'from numpy.f2py.diagnose import run; run()'
------
os.name='posix'
------
sys.platform='darwin'
------
sys.version:
2.7.1 (r271:86832, Jul 31 2011, 19:30:53) 
[GCC 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2335.15.00)]
------
sys.prefix:
/System/Library/Frameworks/Python.framework/Versions/2.7
------
sys.path=':/Library/Python/2.7/site-packages/pip-1.2.1-py2.7.egg:/Library/Python/2.7/site-packages/nose-1.2.1-py2.7.egg:/Library/Python/2.7/site-packages/numpy-1.6.2-py2.7-macosx-10.7-intel.egg:/Library/Python/2.7/site-packages/scipy-0.10.1-py2.7-macosx-10.7-intel.egg:/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python27.zip:/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7:/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-darwin:/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-mac:/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-mac/lib-scriptpackages:/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python:/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-tk:/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-old:/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload:/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/PyObjC:/Library/Python/2.7/site-packages'
------
Found new numpy version '1.6.2' in /Library/Python/2.7/site-packages/numpy-1.6.2-py2.7-macosx-10.7-intel.egg/numpy/__init__.pyc
Found f2py2e version '2' in /Library/Python/2.7/site-packages/numpy-1.6.2-py2.7-macosx-10.7-intel.egg/numpy/f2py/f2py2e.pyc
Found numpy.distutils version '0.4.0' in '/Library/Python/2.7/site-packages/numpy-1.6.2-py2.7-macosx-10.7-intel.egg/numpy/distutils/__init__.pyc'
------
Importing numpy.distutils.fcompiler ... ok
------
Checking availability of supported Fortran compilers:
Gnu95FCompiler instance properties:
  archiver        = ['/usr/local/bin/gfortran', '-cr']
  compile_switch  = '-c'
  compiler_f77    = ['/usr/local/bin/gfortran', '-Wall', '-ffixed-form', '-
                    fno-second-underscore', '-arch', 'i686', '-arch',
                    'x86_64', '-fPIC', '-O3', '-funroll-loops']
  compiler_f90    = ['/usr/local/bin/gfortran', '-Wall', '-fno-second-
                    underscore', '-arch', 'i686', '-arch', 'x86_64', '-fPIC',
                    '-O3', '-funroll-loops']
  compiler_fix    = ['/usr/local/bin/gfortran', '-Wall', '-ffixed-form', '-
                    fno-second-underscore', '-Wall', '-fno-second-underscore',
                    '-arch', 'i686', '-arch', 'x86_64', '-fPIC', '-O3', '-
                    funroll-loops']
  libraries       = ['gfortran']
  library_dirs    = []
  linker_exe      = ['/usr/local/bin/gfortran', '-Wall', '-Wall']
  linker_so       = ['/usr/local/bin/gfortran', '-Wall', '-arch', 'i686', '-
                    arch', 'x86_64', '-Wall', '-undefined', 'dynamic_lookup',
                    '-bundle']
  object_switch   = '-o '
  ranlib          = ['/usr/local/bin/gfortran']
  version         = LooseVersion ('4.2.3')
  version_cmd     = ['/usr/local/bin/gfortran', '--version']
Fortran compilers found:
  --fcompiler=gnu95  GNU Fortran 95 compiler (4.2.3)
Compilers available for this platform, but not found:
  --fcompiler=absoft  Absoft Corp Fortran Compiler
  --fcompiler=g95     G95 Fortran Compiler
  --fcompiler=gnu     GNU Fortran 77 compiler
  --fcompiler=ibm     IBM XL Fortran Compiler
  --fcompiler=intel   Intel Fortran Compiler for 32-bit apps
  --fcompiler=nag     NAGWare Fortran 95 Compiler
  --fcompiler=pg      Portland Group Fortran Compiler
Compilers not available on this platform:
  --fcompiler=compaq    Compaq Fortran Compiler
  --fcompiler=hpux      HP Fortran 90 Compiler
  --fcompiler=intele    Intel Fortran Compiler for Itanium apps
  --fcompiler=intelem   Intel Fortran Compiler for 64-bit apps
  --fcompiler=intelev   Intel Visual Fortran Compiler for Itanium apps
  --fcompiler=intelv    Intel Visual Fortran Compiler for 32-bit apps
  --fcompiler=intelvem  Intel Visual Fortran Compiler for 64-bit apps
  --fcompiler=lahey     Lahey/Fujitsu Fortran 95 Compiler
  --fcompiler=mips      MIPSpro Fortran Compiler
  --fcompiler=none      Fake Fortran compiler
  --fcompiler=pathf95   PathScale Fortran Compiler
  --fcompiler=sun       Sun or Forte Fortran 95 Compiler
  --fcompiler=vast      Pacific-Sierra Research Fortran 90 Compiler
For compiler details, run 'config_fc --verbose' setup command.
------
Importing numpy.distutils.cpuinfo ... ok
------
CPU information: CPUInfoBase__get_nbits getNCPUs is_64bit is_i386 ------
-------------------------------------

Could you have any idea for my error?

Thanks in advance and looking forward to your reply.



With best regards,
Zhibin Dai

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