[SciPy-User] installation error: undefined symbol: omp_in_parallel
Craig Plaisance
cpp6f at virginia.edu
Fri Oct 19 00:07:32 EDT 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 at 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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