python - Installing numpy-1.7.1 with MKL-10.3 using gcc-4.7.2 on linux -


i have been trying install numpy-1.7.1 mkl-10.3 on python-2.7.5 using gcc-4.7.2 on linux-2.6.18-308.24.1.el5 system few days now. have not long ago compiled r-3.0.1 mkl using same compiler.

i modified site.cfg file in numpy-1.7.1 follows:

[mkl] library_dirs = /sb/software/libraries/mkl/10.3/lib/intel64 include_dirs = /sb/software/libraries/mkl/10.3/include mkl_libs = mkl_rt lapack_libs =

when call python setup.py install, finds mkl libraries blas , lapack. until point, there no complaint or warning. breaks down once try numpy.

 $ python  python 2.7.5 (default, jul 31 2013, 16:54:43)  [gcc 4.7.2] on linux2  type "help", "copyright", "credits" or "license" more information.  >>> import numpy  >>> numpy.test('full')  running unit tests numpy  numpy version 1.7.1  numpy installed in /sb/project/mjd-574/ndejay/modules/python-2.7.5/lib/python2.7/site-packages/numpy  python version 2.7.5 (default, jul 31 2013, 16:54:43) [gcc 4.7.2]  nose version 1.3.0  .................python: symbol lookup error: /sb/software/libraries/mkl/10.3/lib/intel64/libmkl_intel_thread.so: undefined symbol: omp_get_num_procs

this appears known issue (link source) whereby libiomp5 not loaded libmkl_rt. when add path libiomp5 library_dirs variable in site.cfg, numpy fails detect all mkl libraries.

i have tried following force gcc use own openmp libraries/headers, no avail.

cflags='-fopenmp -lgomp' python setup.py install

i grateful sort of or advice on matter. not hesitate let me know have omitted critical information in thread.

edit: running on x86_64 platform.

adding path libiomp5 ld_modules_path environment. servers using use modules library manage server-wide applications , libraries. had used standalone mkl/10.3 module substituting ifort_icc/13.0 (which contains mkl) added icc-related paths ld_modules_path. using same site.cfg described above seems work , numpy runs test suite.

i don't know if elegant solution trick now.


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