[SciPy-User] Unit Test Seg Fault on SciPy
Simon Michnowicz
simon.michnowicz at monash.edu
Fri Oct 18 01:38:07 EDT 2013
Dear Group
I just built Scipy with python 2.7.5 but the unit test produce an error
which I can not resolve
test_nonlin.TestJacobianDotSolve.test_broyden1 ... Segmentation fault
When I googled the error, one site implied that MKL should not be used.
http://mail.scipy.org/pipermail/scipy-dev/2011-September/016588.html
Your advice would be most appreciated. Is this still the case?
I used gcc (4.5.3) with the MKL (2013)
I found I had to set "LDFLAGS=-shared" for the linker to work correctly.
numpy.test() worked OK,
The following system information is provided for you below.
During the build, the system seemed to see all libraries
blas_opt_info:
blas_mkl_info:
FOUND:
libraries = ['mkl_rt', 'pthread']
library_dirs = ['/opt/sw/intel-2013.3/mkl/lib/intel64']
define_macros = [('SCIPY_MKL_H', None)]
include_dirs = ['/opt/sw/intel-2013.3/mkl/include']
FOUND:
libraries = ['mkl_rt', 'pthread']
library_dirs = ['/opt/sw/intel-2013.3/mkl/lib/intel64']
define_macros = [('SCIPY_MKL_H', None)]
include_dirs = ['/opt/sw/intel-2013.3/mkl/include']
lapack_opt_info:
lapack_mkl_info:
mkl_info:
FOUND:
libraries = ['mkl_rt', 'pthread']
library_dirs = ['/opt/sw/intel-2013.3/mkl/lib/intel64']
define_macros = [('SCIPY_MKL_H', None)]
include_dirs = ['/opt/sw/intel-2013.3/mkl/include']
FOUND:
libraries = ['mkl_rt', 'pthread']
library_dirs = ['/opt/sw/intel-2013.3/mkl/lib/intel64']
define_macros = [('SCIPY_MKL_H', None)]
include_dirs = ['/opt/sw/intel-2013.3/mkl/include']
FOUND:
libraries = ['mkl_rt', 'pthread']
library_dirs = ['/opt/sw/intel-2013.3/mkl/lib/intel64']
define_macros = [('SCIPY_MKL_H', None)]
include_dirs = ['/opt/sw/intel-2013.3/mkl/include']
regards
Simon Michnowicz
python -c 'from numpy.f2py.diagnose import run; run()'
------
os.name='posix'
------
sys.platform='linux2'
------
sys.version:
2.7.5 (default, Oct 16 2013, 18:02:53)
[GCC 4.5.3]
------
sys.prefix:
/opt/sw/python-2.7.5
------
sys.path=':/opt/sw/python-2.7.5/lib/python2.7/site-packages/setuptools-0.6c11-py2.7.egg:/opt/sw/python-2.7.5/lib/python2.7/site-packages/setuptools-0.6c11-py2.7.egg:/opt/sw/python-2.7.5/lib/python2.7/site-packages/Cython-0.19.2-py2.7-linux-x86_64.egg:/opt/sw/python-2.7.5/lib/python2.7/site-packages/python_dateutil-1.5-py2.7.egg:/opt/sw/python-2.7.5/lib/python2.7/site-packages/tornado-3.1.1-py2.7.egg:/opt/sw/python-2.7.5/lib/python2.7/site-packages/pyparsing-2.0.1-py2.7.egg:/opt/sw/python-2.7.5/lib/python2.7/site-packages/distribute-0.6.28-py2.7.egg:/opt/sw/python-2.7.5/lib/python2.7/site-packages/matplotlib-1.3.1-py2.7-linux-x86_64.egg:/opt/sw/python-2.7.5/lib/python2.7/site-packages:/opt/sw/python-2.7.5/lib/python27.zip:/opt/sw/python-2.7.5/lib/python2.7:/opt/sw/python-2.7.5/lib/python2.7/plat-linux2:/opt/sw/python-2.7.5/lib/python2.7/lib-tk:/opt/sw/python-2.7.5/lib/python2.7/lib-old:/opt/sw/python-2.7.5/lib/python2.7/lib-dynload:/nfs/home/hpcmerc/smichnow/.local/lib/python2.7/site-packages'
------
Found new numpy version '1.7.0' in
/opt/sw/python-2.7.5/lib/python2.7/site-packages/numpy/__init__.pyc
Found f2py2e version '2' in
/opt/sw/python-2.7.5/lib/python2.7/site-packages/numpy/f2py/f2py2e.pyc
Found numpy.distutils version '0.4.0' in
'/opt/sw/python-2.7.5/lib/python2.7/site-packages/numpy/distutils/__init__.pyc'
------
Importing numpy.distutils.fcompiler ... ok
------
Checking availability of supported Fortran compilers:
Gnu95FCompiler instance properties:
archiver = ['/nfs-tmp/sw/gcc-4.5.3/bin/gfortran', '-cr']
compile_switch = '-c'
compiler_f77 = ['/nfs-tmp/sw/gcc-4.5.3/bin/gfortran', '-Wall', '-ffixed
-form', '-fno-second-underscore', '-fPIC', '-O3', '-
funroll-loops']
compiler_f90 = ['/nfs-tmp/sw/gcc-4.5.3/bin/gfortran', '-Wall', '-fno-
second-underscore', '-fPIC', '-O3', '-funroll-loops']
compiler_fix = ['/nfs-tmp/sw/gcc-4.5.3/bin/gfortran', '-Wall', '-ffixed
-form', '-fno-second-underscore', '-Wall', '-fno-second-
underscore', '-fPIC', '-O3', '-funroll-loops']
libraries = ['gfortran']
library_dirs = []
linker_exe = ['/nfs-tmp/sw/gcc-4.5.3/bin/gfortran', '-Wall', '-
L/opt/sw/hdf5-1.8.7-gcc-4.5.3/lib',
'-L/opt/sw/zlib-1.2.5-
gcc-4.5.3/lib', '-lz', '-L/opt/sw/mpc-0.9/lib', '-
L/opt/sw/mpfr-2.4.2/lib', '-L/opt/sw/gmp-4.3.2/lib']
linker_so = ['/nfs-tmp/sw/gcc-4.5.3/bin/gfortran', '-Wall', '-
L/opt/sw/hdf5-1.8.7-gcc-4.5.3/lib',
'-L/opt/sw/zlib-1.2.5-
gcc-4.5.3/lib', '-lz', '-L/opt/sw/mpc-0.9/lib', '-
L/opt/sw/mpfr-2.4.2/lib', '-L/opt/sw/gmp-4.3.2/lib']
object_switch = '-o '
ranlib = ['/nfs-tmp/sw/gcc-4.5.3/bin/gfortran']
version = LooseVersion ('4.5.3')
version_cmd = ['/nfs-tmp/sw/gcc-4.5.3/bin/gfortran', '--version']
GnuFCompiler instance properties:
archiver = ['/usr/bin/g77', '-cr']
compile_switch = '-c'
compiler_f77 = ['/usr/bin/g77', '-g', '-Wall', '-fno-second-
underscore', '-fPIC', '-O3', '-funroll-loops']
compiler_f90 = None
compiler_fix = None
libraries = ['g2c']
library_dirs = []
linker_exe = ['/usr/bin/g77', '-g', '-Wall', '-L/opt/sw/hdf5-1.8.7-
gcc-4.5.3/lib', '-L/opt/sw/zlib-1.2.5-gcc-4.5.3/lib', '-
lz', '-L/opt/sw/mpc-0.9/lib',
'-L/opt/sw/mpfr-2.4.2/lib',
'-L/opt/sw/gmp-4.3.2/lib']
linker_so = ['/usr/bin/g77', '-g', '-Wall', '-L/opt/sw/hdf5-1.8.7-
gcc-4.5.3/lib', '-L/opt/sw/zlib-1.2.5-gcc-4.5.3/lib', '-
lz', '-L/opt/sw/mpc-0.9/lib',
'-L/opt/sw/mpfr-2.4.2/lib',
'-L/opt/sw/gmp-4.3.2/lib']
object_switch = '-o '
ranlib = ['/usr/bin/g77']
version = LooseVersion ('3.4.6')
version_cmd = ['/usr/bin/g77', '--version']
Fortran compilers found:
--fcompiler=gnu GNU Fortran 77 compiler (3.4.6)
--fcompiler=gnu95 GNU Fortran 95 compiler (4.5.3)
Compilers available for this platform, but not found:
--fcompiler=absoft Absoft Corp Fortran Compiler
--fcompiler=compaq Compaq Fortran Compiler
--fcompiler=g95 G95 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 64-bit apps
--fcompiler=lahey Lahey/Fujitsu Fortran 95 Compiler
--fcompiler=nag NAGWare Fortran 95 Compiler
--fcompiler=pathf95 PathScale Fortran Compiler
--fcompiler=pg Portland Group Fortran Compiler
--fcompiler=vast Pacific-Sierra Research Fortran 90 Compiler
Compilers not available on this platform:
--fcompiler=hpux HP Fortran 90 Compiler
--fcompiler=ibm IBM XL Fortran Compiler
--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=mips MIPSpro Fortran Compiler
--fcompiler=none Fake Fortran compiler
--fcompiler=sun Sun or Forte Fortran 95 Compiler
For compiler details, run 'config_fc --verbose' setup command.
------
Importing numpy.distutils.cpuinfo ... ok
------
CPU information: CPUInfoBase__get_nbits getNCPUs has_3dnow has_3dnowext
has_mmx has_sse has_sse2 has_sse3 is_64bit is_AMD is_Opteron ------
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