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Ziyuan
Beginner
457 Views

Cannot find BLAS on a machine with MKL when installing scipy via pip

I installed Intel MKL and other libraries for a customized numpy. Here is my `~/.numpy-site.cfg`:

    [DEFAULT]
    library_dirs = /usr/lib:/usr/local/lib
    include_dirs = /usr/include:/usr/local/include
    
    [mkl]
    library_dirs = /opt/intel/mkl/lib/intel64/
    include_dirs = /opt/intel/mkl/include/
    mkl_libs = mkl_intel_ilp64, mkl_intel_thread, mkl_core, mkl_rt
    lapack_libs =
    
    [amd]
    amd_libs = amd
    
    [umfpack]
    umfpack_libs = umfpack
    
    [djbfft]
    include_dirs = /usr/local/djbfft/include
    library_dirs = /usr/local/djbfft/lib

This configuration file seems OK during the installation of numpy. But when I was installing scipy via `pip3 install scipy`, it reported that

    numpy.distutils.system_info.BlasNotFoundError:
    
        Blas (http://www.netlib.org/blas/) libraries not found.
    
        Directories to search for the libraries can be specified in the
    
        numpy/distutils/site.cfg file (section [blas]) or by setting
    
        the BLAS environment variable.


In my mind MKL is an implementation of Blas so just mentioning MKL should be fine. I've tried

 1. `export LD_LIBRARY_PATH=/opt/intel/mkl/lib/intel64:$LD_LIBRARY_PATH‌​`
 2. `export BLAS=/opt/intel/mkl/lib/intel64`
 3. Copy the content in the `[mkl]` section and paste into the `[blas]` section in the file `~/.numpy-site.cfg`

But none of these works. So what is going wrong? Does scipy respect `~/.numpy-site.cfg`? Thank you.

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7 Replies
mecej4
Black Belt
457 Views

I don't have an answer specific to scipy, but when you port any configure/make scripts from Gcc/GFortran/Netlib BLAS/Lapack to Ifort/MKL, you may need to adapt the scripts in view of the fact that MKL includes BLAS as well as Lapack, so that it suffices to link against MKL. 

Ziyuan
Beginner
457 Views

mecej4 wrote:

I don't have an answer specific to scipy, but when you port any configure/make scripts from Gcc/GFortran/Netlib BLAS/Lapack to Ifort/MKL, you may need to adapt the scripts in view of the fact that MKL includes BLAS as well as Lapack, so that it suffices to link against MKL. 

Yes I think so too. Scipy does support MKL, and this is an example about how to write the ~/.numpy-site.cfg: https://github.com/numpy/numpy/blob/master/site.cfg.example

 

457 Views

Please refer this article on installing scipy/numpy with mkl

http://software.intel.com/en-us/articles/numpyscipy-with-intel-mkl

--Vipin

 

Ziyuan
Beginner
457 Views

Vipin Kumar E K (Intel) wrote:

Please refer this article on installing scipy/numpy with mkl

http://software.intel.com/en-us/articles/numpyscipy-with-intel-mkl

--Vipin

 

It's for installing from source, while I am asking about installing via pip.

457 Views

 

Can you modify your site.config for mkl_libs instead of

mkl_libs = mkl_intel_ilp64, mkl_intel_thread, mkl_core, mkl_rt

to

mkl_libs =  mkl_rt

mkl_rt is the runtime dynamic lib and you don't need to specify other libs from different layers.

Also, set the MKl env variables by running

 

$source /opt/intel/mkl/bin/mklvars.sh ?

Vipin

 

Ziyuan
Beginner
457 Views

Vipin Kumar E K (Intel) wrote:

 

Can you modify your site.config for mkl_libs instead of

mkl_libs = mkl_intel_ilp64, mkl_intel_thread, mkl_core, mkl_rt

to

mkl_libs =  mkl_rt

mkl_rt is the runtime dynamic lib and you don't need to specify other libs from different layers.

Also, set the MKl env variables by running

 

$source /opt/intel/mkl/bin/mklvars.sh ?

Vipin

 

Hi. It doesn't work either.

$ source /opt/intel/mkl/bin/mklvars.sh intel64 ilp64
$ echo $MKLROOT
/opt/intel/composer_xe_2013_sp1.2.144/mkl
$ sudo pip3 install scipy

will give the same error. Particularly, here are the messages about not finding the libs:

Installing collected packages: scipy
  Running setup.py install for scipy
    blas_opt_info:
    blas_mkl_info:
      libraries mkl,vml,guide not found in ['/usr/local/lib', '/usr/lib64', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
      NOT AVAILABLE
    
    openblas_info:
      libraries  not found in ['/usr/local/lib', '/usr/lib64', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
      NOT AVAILABLE
    
    atlas_blas_threads_info:
    Setting PTATLAS=ATLAS
      libraries ptf77blas,ptcblas,atlas not found in ['/usr/local/lib', '/usr/lib64', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
      NOT AVAILABLE
    
    atlas_blas_info:
      libraries f77blas,cblas,atlas not found in ['/usr/local/lib', '/usr/lib64', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
      NOT AVAILABLE
    
    blas_info:
      libraries blas not found in ['/usr/local/lib', '/usr/lib64', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
      NOT AVAILABLE
    
    blas_src_info:
      NOT AVAILABLE
    
    /usr/local/lib/python3.3/dist-packages/numpy/distutils/system_info.py:1521: UserWarning:
        Atlas (http://math-atlas.sourceforge.net/) libraries not found.
        Directories to search for the libraries can be specified in the
        numpy/distutils/site.cfg file (section [atlas]) or by setting
        the ATLAS environment variable.
      warnings.warn(AtlasNotFoundError.__doc__)
    /usr/local/lib/python3.3/dist-packages/numpy/distutils/system_info.py:1530: UserWarning:
        Blas (http://www.netlib.org/blas/) libraries not found.
        Directories to search for the libraries can be specified in the
        numpy/distutils/site.cfg file (section [blas]) or by setting
        the BLAS environment variable.
      warnings.warn(BlasNotFoundError.__doc__)
    /usr/local/lib/python3.3/dist-packages/numpy/distutils/system_info.py:1533: UserWarning:
        Blas (http://www.netlib.org/blas/) sources not found.
        Directories to search for the sources can be specified in the
        numpy/distutils/site.cfg file (section [blas_src]) or by setting
        the BLAS_SRC environment variable.

It seems that the MKL paths haven't gone into the environmental variables.

Ying_H_Intel
Employee
457 Views

Hi ziyuan, 

Could you please try the Root to install the scipy? 

I haven't investigated how pip3 works, but sudo can't inherit the environment setting from  source /opt/intel/mkl/bin/mklvars.sh intel64 ilp64

as we mentioned in 

https://software.intel.com/en-us/forums/topic/277619#comment-1794098. ;

Best Regards,

Ying