I think the fix is to add the blas info to the setup.py.
have a look at sklearn/linear_model/setup.py
and see how get_blas_info is used,
and do the same for metrics/setup.py
If that solves the problem, please do a PR.
It's a bit odd because numpy is not linked against iomp5. What is that /
where does it come from?
On 07/11/2015 02:37 PM, Fulton, Ben wrote:
>>>> print(np.__config__.show())
> lapack_opt_info:
> libraries = ['mkl_lapack32', 'mkl_lapack64', 'mkl_intel_lp64',
> 'mkl_intel_thread', 'mkl_core', 'pthread']
> library_dirs =
> ['/N/soft/rhel6/intel/13.1.2/composer_xe_2013.4.183/mkl/lib/intel64/']
> define_macros = [('SCIPY_MKL_H', None)]
> include_dirs =
> ['/N/soft/rhel6/intel/13.1.2/composer_xe_2013.4.183/mkl/include']
> blas_opt_info:
> libraries = ['mkl_intel_lp64', 'mkl_intel_thread', 'mkl_core', 'pthread']
> library_dirs =
> ['/N/soft/rhel6/intel/13.1.2/composer_xe_2013.4.183/mkl/lib/intel64/']
> define_macros = [('SCIPY_MKL_H', None)]
> include_dirs =
> ['/N/soft/rhel6/intel/13.1.2/composer_xe_2013.4.183/mkl/include']
> openblas_info:
> NOT AVAILABLE
> lapack_mkl_info:
> libraries = ['mkl_lapack32', 'mkl_lapack64', 'mkl_intel_lp64',
> 'mkl_intel_thread', 'mkl_core', 'pthread']
> library_dirs =
> ['/N/soft/rhel6/intel/13.1.2/composer_xe_2013.4.183/mkl/lib/intel64/']
> define_macros = [('SCIPY_MKL_H', None)]
> include_dirs =
> ['/N/soft/rhel6/intel/13.1.2/composer_xe_2013.4.183/mkl/include']
> blas_mkl_info:
> libraries = ['mkl_intel_lp64', 'mkl_intel_thread', 'mkl_core', 'pthread']
> library_dirs =
> ['/N/soft/rhel6/intel/13.1.2/composer_xe_2013.4.183/mkl/lib/intel64/']
> define_macros = [('SCIPY_MKL_H', None)]
> include_dirs =
> ['/N/soft/rhel6/intel/13.1.2/composer_xe_2013.4.183/mkl/include']
> mkl_info:
> libraries = ['mkl_intel_lp64', 'mkl_intel_thread', 'mkl_core', 'pthread']
> library_dirs =
> ['/N/soft/rhel6/intel/13.1.2/composer_xe_2013.4.183/mkl/lib/intel64/']
> define_macros = [('SCIPY_MKL_H', None)]
> include_dirs =
> ['/N/soft/rhel6/intel/13.1.2/composer_xe_2013.4.183/mkl/include']
> None
>>>> print(get_blas_info())
> (['mkl_intel_lp64', 'mkl_intel_thread', 'mkl_core', 'pthread'],
> {'library_dirs':
> ['/N/soft/rhel6/intel/13.1.2/composer_xe_2013.4.183/mkl/lib/intel64/'],
> 'define_macros': [('SCIPY_MKL_H', None)], 'include_dirs':
> ['/N/soft/rhel6/intel/13.1.2/composer_xe_2013.4.183/mkl/include']})
>
> --
> Ben Fulton
> Research Technologies
> Scientific Applications and Performance Tuning
> Indiana University
> E-Mail: beful...@iu.edu
>
> -----Original Message-----
> From: Andreas Mueller [mailto:t3k...@gmail.com]
> Sent: Saturday, July 11, 2015 3:19 PM
> To: scikit-learn-general@lists.sourceforge.net
> Subject: Re: [Scikit-learn-general] Linking error with intel 13.1
>
> Can you do
>
> import numpy as np
> print(np.__config__.show())
>
> from sklearn._build_utils import get_blas_info
> print(get_blas_info)
>
>
> On 07/11/2015 12:44 PM, Fulton, Ben wrote:
>> I installed by downloading the latest tar file and "python setup.py
>> install". Yes, numpy also relies on the intel/13.1 libraries.
>>
>> --
>> Ben Fulton
>> Research Technologies
>> Scientific Applications and Performance Tuning Indiana University
>> E-Mail: beful...@iu.edu
>>
>> -----Original Message-----
>> From: Andreas Mueller [mailto:t3k...@gmail.com]
>> Sent: Saturday, July 11, 2015 1:12 PM
>> To: scikit-learn-general@lists.sourceforge.net
>> Subject: Re: [Scikit-learn-general] Linking error with intel 13.1
>>
>> Hi Ben.
>> How did you install?
>> I'm not sure if we can get the linker flags form numpy. Is your numpy also
>> installed with the intel compiler?
>>
>> Thanks,
>> Andy
>>
>> On 07/11/2015 11:45 AM, Fulton, Ben wrote:
>>> Hi,
>>>
>>> I tried to install sklearn on our cluster. It installed successfully, but
>>> when running we got this error:
>>>
>>> >from sklearn.metrics.cluster import normalized_mutual_info_score
>>> intel/13.1/composer_xe_2013.1.117/mkl/lib/intel64/libmkl_intel_thread.
>>> so: undefined symbol: __kmpc_reduce_nowait
>>>
>>> I add the following line to metrics/setup.py to fix it:
>>>
>>> extra_link_args=["-Lintel/13.1/composer_xe_2013.1.117/compiler/lib/in
>>> t
>>> el64/", "-liomp5"],
>>>
>>> But I suspect that there may be other places with the same issue. Can
>>> anyone suggest a more permanent fix?
>>>
>>>
>>> --
>>> Ben Fulton
>>> Research Technologies
>>> Scientific Applications and Performance Tuning Indiana University
>>> E-Mail: beful...@iu.edu
>>>
>>>
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