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

Craig Plaisance cpp6f@virginia....
Thu Oct 18 23:07:32 CDT 2012


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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