[SciPy-User] installation error: undefined symbol: omp_in_parallel

Andy Ray Terrel andy.terrel@gmail....
Fri Oct 19 10:07:40 CDT 2012


Hey Craig,

You might try using the mkl without OpenMP threading.  My guess from
just looking at the error is that the compiler isn't getting passed
the right omp flags.  Looking at:

http://software.intel.com/sites/products/mkl/

The link line should be:

-lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lpthread -lm

-- Andy

On Thu, Oct 18, 2012 at 11:30 PM, Craig Plaisance <cpp6f@virginia.edu> wrote:
> Hi, I'm having a problem getting scipy installed with linking to mkl 11.1.
> Here is the output and the mkl section from site.cfg.  I've played quite a
> bit with the mkl_libs variable in site.cfg and googled it to death with no
> success.  Any help is much appreciated!  Thanks
>
> Craig
>
>
> [root@atlas scipy-0.11.0]# python setup.py config --compiler=intelem
> --fcompiler=intelem
> Traceback (most recent call last):
>   File "setup.py", line 208, in <module>
>     setup_package()
>   File "setup.py", line 145, in setup_package
>     from numpy.distutils.core import setup
>   File "/usr/local/lib/python2.7/site-packages/numpy/__init__.py", line 137,
> in <module>
>     import add_newdocs
>   File "/usr/local/lib/python2.7/site-packages/numpy/add_newdocs.py", line
> 9, in <module>
>     from numpy.lib import add_newdoc
>   File "/usr/local/lib/python2.7/site-packages/numpy/lib/__init__.py", line
> 13, in <module>
>     from polynomial import *
>   File "/usr/local/lib/python2.7/site-packages/numpy/lib/polynomial.py",
> line 17, in <module>
>     from numpy.linalg import eigvals, lstsq
>   File "/usr/local/lib/python2.7/site-packages/numpy/linalg/__init__.py",
> line 48, in <module>
>     from linalg import *
>   File "/usr/local/lib/python2.7/site-packages/numpy/linalg/linalg.py", line
> 23, in <module>
>     from numpy.linalg import lapack_lite
> ImportError:
> /share/apps/intel/Compiler/11.1/046/mkl/lib/em64t/libmkl_intel_thread.so:
> undefined symbol: omp_in_parallel
>
>
> Here is the mkl section of site.cfg
>
> [mkl]
> library_dirs = /share/apps/intel/Compiler/11.1/046/mkl/lib/em64t
> include_dirs =
> /share/apps/intel/Compiler/11.1/046/mkl/include:/share/apps/intel/Compiler/11.1/046/include
> lapack_libs = mkl_lapack
> mkl_libs = mkl_def,mkl_intel_lp64,mkl_intel_thread,mkl_core,guide,iomp5
>
>
>
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