[SciPy-User] Dynamic library loading problem

[John Rowe]

I have installed python3.3.2 and the latest numpy and scipy on linux
x86_64 using the Intel compilers and MKL following a few variants of the
advice on http://www.scipy.org/Installing_SciPy/Linux and
http://software.intel.com/en-us/articles/numpyscipy-with-intel-mkl.

However, although the installation goes fine the moment I try to use it
it fails, for example:

> python3 -c 'import scipy; scipy.test()'
Running unit tests for scipy
NumPy version 1.7.0
NumPy is installed
in /usr/local64/python3.3.2/lib/python3.3/site-packages/numpy
SciPy version 0.12.0
SciPy is installed
in /usr/local64/python3.3.2/lib/python3.3/site-packages/scipy
Python version 3.3.2 (default, May 22 2013, 15:10:00) [GCC Intel(R) C++
gcc 4.3 mode]
nose version 1.3.0
............................................................................

*** libmkl_mc3.so *** failed with
error : /opt/intel/intel-fc/x86_64/11.1.064/mkl/lib/em64t/libmkl_mc3.so:
undefined symbol: mkl_dft_commit_descriptor_s_c2c_md_omp
*** libmkl_def.so *** failed with
error : /opt/intel/intel-fc/x86_64/11.1.064/mkl/lib/em64t/libmkl_def.so:
undefined symbol: mkl_dft_commit_descriptor_s_c2c_md_omp
MKL FATAL ERROR: Cannot load neither libmkl_mc3.so nor libmkl_def.so

I get pretty much the same message with numpy.test() and if I try to run
the actual program, but with different libraries and missing symbols.

The missing symbols always appear to be ones that are found in the
specified mkl shared libraries, eg in this case:

> nm libmkl_intel_thread.so  | grep \
 mkl_dft_commit_descriptor_s_c2c_md_omp
00000000006181a0 T mkl_dft_commit_descriptor_s_c2c_md_omp

This makes me think it's a systemic issue with shared libraries rather
than me having just missed one out.

Any help would be hugely appreciated (scipy config follows).

Thanks

John


> python3 -c 'import scipy; scipy.show_config()'
blas_mkl_info:
    libraries = ['mkl_intel_lp64', 'mkl_intel_thread', 'mkl_core',
'mkl_mc', 'iomp5', 'pthread']
    define_macros = [('SCIPY_MKL_H', None)]
    library_dirs = ['/opt/intel/intel-fc/x86_64/11.1.064/mkl/lib/em64t',
'/opt/intel/intel-fc/x86_64/11.1.064/lib/intel64']
    include_dirs =
['/opt/intel/intel-fc/x86_64/11.1.064/mkl/include/em64t',
'/opt/intel/intel-fc/x86_64/11.1.064/include/intel64']
lapack_mkl_info:
    libraries = ['mkl_intel_lp64', 'mkl_intel_thread', 'mkl_core',
'mkl_mc', 'iomp5', 'pthread']
    define_macros = [('SCIPY_MKL_H', None)]
    library_dirs = ['/opt/intel/intel-fc/x86_64/11.1.064/mkl/lib/em64t',
'/opt/intel/intel-fc/x86_64/11.1.064/lib/intel64']
    include_dirs =
['/opt/intel/intel-fc/x86_64/11.1.064/mkl/include/em64t',
'/opt/intel/intel-fc/x86_64/11.1.064/include/intel64']
lapack_opt_info:
    libraries = ['mkl_intel_lp64', 'mkl_intel_thread', 'mkl_core',
'mkl_mc', 'iomp5', 'pthread']
    define_macros = [('SCIPY_MKL_H', None)]
    library_dirs = ['/opt/intel/intel-fc/x86_64/11.1.064/mkl/lib/em64t',
'/opt/intel/intel-fc/x86_64/11.1.064/lib/intel64']
    include_dirs =
['/opt/intel/intel-fc/x86_64/11.1.064/mkl/include/em64t',
'/opt/intel/intel-fc/x86_64/11.1.064/include/intel64']
umfpack_info:
  NOT AVAILABLE
mkl_info:
    libraries = ['mkl_intel_lp64', 'mkl_intel_thread', 'mkl_core',
'mkl_mc', 'iomp5', 'pthread']
    define_macros = [('SCIPY_MKL_H', None)]
    library_dirs = ['/opt/intel/intel-fc/x86_64/11.1.064/mkl/lib/em64t',
'/opt/intel/intel-fc/x86_64/11.1.064/lib/intel64']
    include_dirs =
['/opt/intel/intel-fc/x86_64/11.1.064/mkl/include/em64t',
'/opt/intel/intel-fc/x86_64/11.1.064/include/intel64']
blas_opt_info:
    libraries = ['mkl_intel_lp64', 'mkl_intel_thread', 'mkl_core',
'mkl_mc', 'iomp5', 'pthread']
    define_macros = [('SCIPY_MKL_H', None)]
    library_dirs = ['/opt/intel/intel-fc/x86_64/11.1.064/mkl/lib/em64t',
'/opt/intel/intel-fc/x86_64/11.1.064/lib/intel64']
    include_dirs =
['/opt/intel/intel-fc/x86_64/11.1.064/mkl/include/em64t',
'/opt/intel/intel-fc/x86_64/11.1.064/include/intel64']