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

[Craig Plaisance]

Thanks for the reply Andy.  I tried your suggestion and it still doesn't 
work.  The problem is actually in the numpy installation itself and has 
nothing to do with scipy - "import numpy" gives the same error.  When I 
run ldd on lapack_lite.so it still requires libmkl_intel_thread.so even 
though I compiled with lmkl_sequential. I'm used to compiling with make 
and don't really understand this python based compiling too well




On 10/19/2012 11:07 AM, Andy Ray Terrel wrote:
> 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 at 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 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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