SciPy

Building From Source on Linux

Generic instructions

To build NumPy/SciPy from source, get the source package, unpack it, and:

python setup.py install --user   # installs to your home directory

or

python setup.py build
python setup.py install --prefix=$HOME/local

Before building, you will also need to install packages that NumPy and SciPy depend on

  • BLAS and LAPACK libraries (optional but strongly recommended for NumPy, required for SciPy): typically ATLAS + OpenBLAS, or MKL.

  • C and Fortran compilers (typically gcc and gfortran).

  • Python header files (typically a package named python-dev or python-devel)

  • Unless you are building from released source packages, the Cython compiler is necessary (typically in a package named cython). For building recent SciPy, it is possible that you need Cython in a newer version than is available in your distribution.

Typically, you will want to install all of the above from packages supplied by your Linux distribution, as building them yourself is complicated. If you need to use specific BLAS/LAPACK libraries, you can do

export BLAS=/path/to/libblas.so
export LAPACK=/path/to/liblapack.so
export ATLAS=/path/to/libatlas.so
python setup.py ............

If you don’t want to any LAPACK, just do “export LAPACK=”.

You will find below additional installation instructions and advice for many major Linux distributions.

Specific instructions

Debian / Ubuntu

To build from source the following packages are needed:

sudo apt-get install gcc gfortran python-dev libopenblas-dev liblapack-dev cython

To customize which BLAS is used, you can setup a site.cfg file. See the site.cfg.example file in the numpy source for the options you can set.

Note that Debian and Ubuntu package optimized BLAS libraries in a exchangeable way. You can install libraries such as ATLAS or OpenBLAS and change the default one used via the alternatives mechanism:

$ sudo apt-get install libopenblas-base libatlas3-base
$ update-alternatives --list libblas.so.3
/usr/lib/atlas-base/atlas/libblas.so.3
/usr/lib/libblas/libblas.so.3
/usr/lib/openblas-base/libopenblas.so.0

$ sudo update-alternatives --set libblas.so.3 /usr/lib/openblas-base/libopenblas.so.0

See /usr/share/doc/libatlas3-base/README.Debian for instructions on how to build optimized ATLAS packages for your specific CPU. The packaged OpenBLAS chooses the optimal code at runtime so it does not need recompiling unless the packaged version does not yet support the used CPU.

You can also use a library you built yourself by preloading it. This does not require administrator rights.

LD_PRELOAD=/path/to/libatlas.so.3 ./my-application

Fedora 26

To install scipy build requirements, you can do:

sudo dnf install gcc-gfortran python3-devel python2-devel openblas-devel lapack-devel Cython

Intel C compiler and MKL

Intel MKL 11.0 (updated Dec 2012)

Add the following lines to site.cfg in your top level NumPy directory to use Intel® MKL for Intel® 64 (or earlier known as em64t) architecture, considering the default installation path of Intel® MKL which is bundled with Intel® Composer XE SP1 version on Linux:

[mkl]
library_dirs = /opt/intel/composer_xe_2013/mkl/lib/intel64
include_dirs = /opt/intel/composer_xe_2013/mkl/include
mkl_libs = mkl_intel_lp64,mkl_intel_thread,mkl_core

If you are building NumPy for 32 bit, please add as the following

[mkl]
library_dirs = /opt/intel/composer_xe_2013/mkl/lib/ia32
include_dirs = /opt/intel/composer_xe_2013/mkl/include
mkl_libs = mkl_intel,mkl_intel_thread,mkl_core

Instead of the layered linking approach for the Intel® MKL as shown above, you may also use the dynamic interface lib mkl_rt.lib. So, for both the ia32 and intel64 architecture make the change as below

mkl_libs = mkl_rt

Modify cc_exe in numpy/numpy/distutils/intelccompiler.py to be something like:

cc_exe = 'icc -O2 -g -openmp -avx'

Here we use, default optimizations (-O2), OpenMP threading (-openmp) and Intel® AVX optimizations for Intel® Xeon E5 or E3 Series which are based on Intel® SandyBridge Architecture (-avx). Run icc –help for more information on processor-specific options.

Compile and install NumPy with the Intel compiler (on 64-bit platforms replace “intel” with “intelem”):

python setup.py config --compiler=intel build_clib --compiler=intel build_ext --compiler=intel install

Compile and install SciPy with the Intel compilers (on 64-bit platforms replace “intel” with “intelem”):

python setup.py config --compiler=intel --fcompiler=intel build_clib --compiler=intel --fcompiler=intel build_ext --compiler=intel --fcompiler=intel install

You’ll have to set LD_LIBRARY_PATH to Intel® MKL libraries (exact values will depend on your architecture, compiler and library versions) and OpenMP library for NumPy to work. If you build NumPy for Intel® 64 platforms:

$export LD_LIBRARY_PATH=/opt/intel/composer_xe_2013/mkl/lib/intel64: /opt/intel/composer_xe_2013/compiler/lib/intel64:$LD_LIBRARY_PATH

If you build NumPy for ia32 bit platforms:

$export LD_LIBRARY_PATH=/opt/intel/composer_xe_2013/mkl/lib/ia32: /opt/intel/composer_xe_2013/compiler/lib/ia32:$LD_LIBRARY_PATH

Fortran ABI mismatch

Some linear algebra libraries are built with G77 ABI and others with GFortran ABI and these two ABIs are incompatible. Therefore if you build scipy with gfortran and link to a linear algebra library like MKL which is built with G77 ABI then there’ll be an exception or a segfault. SciPy fixes this by using the CBLAS API for the few functions in the BLAS API that suffers from this issue.

Note that SciPy needs to know at build time, what needs to be done and the build system will automatically check whether linear algebra library is MKL and if so use the CBLAS API instead of the BLAS API. If autodetection fails or if the user wants to override this autodetection mechanism, setting the environment variable SCIPY_USE_G77_ABI_WRAPPER to 0 or 1 to disable or enable using CBLAS API.