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Link ATLAS/MKL to an installed Numpy

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TL;DR how to link ATLAS/MKL to existing Numpy without rebuilding.

I have used Numpy to calculate with the large matrix and I found that it is very slow because Numpy only use 1 core to do calculation. After doing a lot of search I figure that my Numpy does not link to some optimized library like ATLAS/MKL. Here is my config of numpy:

>>>import numpy as np >>>np.__config__.show() blas_info:     libraries = ['blas']     library_dirs = ['/usr/lib']     language = f77 lapack_info:     libraries = ['lapack']     library_dirs = ['/usr/lib']     language = f77 atlas_threads_info:     NOT AVAILABLE blas_opt_info:     libraries = ['blas']     library_dirs = ['/usr/lib']     language = f77     define_macros = [('NO_ATLAS_INFO', 1)] atlas_blas_threads_info:   NOT AVAILABLE openblas_info:   NOT AVAILABLE lapack_opt_info:     libraries = ['lapack', 'blas']     library_dirs = ['/usr/lib']     language = f77     define_macros = [('NO_ATLAS_INFO', 1)] atlas_info:   NOT AVAILABLE lapack_mkl_info:   NOT AVAILABLE blas_mkl_info:   NOT AVAILABLE atlas_blas_info:   NOT AVAILABLE mkl_info:   NOT AVAILABLE 

For this reason, I want to link ATLAS/MKL to Numpy. However, my Numpy is installed from PIP so I don't want to install manually because I want to use the latest version. I have done some search but they are only for building from scratch. For this reason, my question are:

  • Are there any way to link ATLAS/MKL to Numpy without rebuilding again?
  • I have found that the config info is saved in _config_.py in the installed folder of Numpy. So will modifying it solve my problem? If yes, would you please show me how?
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tndoan Avatar asked Feb 10 '14 07:02

tndoan


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1 Answers

Assuming you're running some flavour of linux, here's one way you could do it:

  1. Find out what BLAS library numpy is currently linked against using ldd.

    • For versions of numpy older than v1.10:

      $ ldd /<path_to_site-packages>/numpy/core/_dotblas.so 

      For example, if I install numpy via apt-get, it links to

      ... libblas.so.3 => /usr/lib/libblas.so.3 (0x00007fed81de8000) ... 

      If _dotblas.so doesn't exist, this probably means that numpy failed to detect any BLAS libraries when it was originally installed, in which case it simply doesn't build any of the BLAS-dependent components. This often happens if you install numpy using pip without manually specifying a BLAS library (see below). I'm afraid you'll have no option but to rebuild numpy if you want to link against an external BLAS library.


    • For numpy v1.10 and newer:

      _dotblas.so has been removed from recent versions of numpy, but you should be able to check the dependencies of multiarray.so instead:

      $ ldd /<path_to_site-packages>/numpy/core/multiarray.so 
  2. Install ATLAS/MKL/OpenBLAS if you haven't already. By the way, I would definitely recommend OpenBLAS over ATLAS - take a look at this answer (although the benchmarking data is now probably a bit out of date).

  3. Use update-alternatives to create a symlink to the new BLAS library of your choice. For example, if you installed libopenblas.so into /opt/OpenBLAS/lib, you would do:

    $ sudo update-alternatives --install /usr/lib/libblas.so.3 \                                      libblas.so.3 \                                      /opt/OpenBLAS/lib/libopenblas.so \                                      50 

    You can have multiple symlinks configured for a single target library, allowing you to manually switch between multiple installed BLAS libraries.

    For example, when I call $ sudo update-alternatives --config libblas.so.3, I can choose between one of 3 libraries:

      Selection    Path                                    Priority   Status ------------------------------------------------------------   0            /opt/OpenBLAS/lib/libopenblas.so         40        auto mode   1            /opt/OpenBLAS/lib/libopenblas.so         40        manual mode   2            /usr/lib/atlas-base/atlas/libblas.so.3   35        manual mode * 3            /usr/lib/libblas/libblas.so.3            10        manual mode 

If you really want the "newest" version of numpy, you could also take a look at my answer on compiling numpy from source with OpenBLAS integration.

Installing numpy with BLAS support using pip

As @tndoan mentioned in the comments, it's possible to make pip respect a particular configuration for numpy by placing a config file in ~/.numpy-site.cfg - see this answer for more details.

My personal preference is to configure and build numpy by hand. It's not particularly difficult, and it gives you better control over numpy's configuration.

like image 151
ali_m Avatar answered Sep 19 '22 12:09

ali_m