.. _build_linux:

Build for Linux
===============

Prerequisites
-------------

-  CMake (>= 3.12.0)
-  GCC >= 5.0 or Clang >= 3.4
-  Optional: MATLAB R2009a or greater
-  Optional: Git

Assumed directory structure:

.. raw:: html

   <pre>
   &lt;ROOT&gt;
      |-libs
      |   |- sundials
      |   |- hdf5
      |   |- superlu
      |   |- suitesparse
      |-code
      |-cadet
      |-build
   </pre>

Note that the version numbers of the files and packages below are
subject to change and will not always reflect the most recent version.

Build dependencies
------------------

HDF5
~~~~

You can either build HDF5 yourself or rely on the packages provided by
your Linux distribution.

Obtain HDF5 from your distribution: \* Install the development package
of your distribution (e.g., ``libhdf5-dev`` for Ubuntu and Debian,
``hdf5-devel`` OpenSUSE) \* Additional postfixes or prefixes in the
library names (e.g., Debian uses ``libhdf5_serial.*`` instead of
``libhdf5.*``) can cause troubles when CMake is trying to find HDF5. If
this is the case, you can circumvent this by using symlinks
``ln -s libhdf5_serial.* libhdf5.*``. However, this can later cause
troubles because other packages might contain this file.

Build HDF5 yourself: \* Download CMake-enabled source from
https://www.hdfgroup.org/downloads/hdf5/source-code/ \* Unzip and make
sure that the directory path does not contain blank spaces \* Open a
terminal and change to the unzipped directory \* Execute
``ctest -S HDF5config.cmake,BUILD_GENERATOR=Unix,INSTALLDIR="<ROOT>/Libs/hdf5" -C Release -V``
\* Extract the created ``HDF5-1.10.0-patch1-Linux.tar.gz`` file to
``<ROOT>/Libs/hdf5`` such that you have ``<ROOT>/Libs/hdf5/lib``

SUNDIALS
~~~~~~~~

-  Download SUNDIALS source from
   http://computation.llnl.gov/projects/sundials/sundials-software
   (version <= 3.2.1)
-  Unzip
-  Open a terminal and change to the parent directory of the unzipped
   directory
-  Create a new folder ``sundialsbuild`` and change to it
-  Execute
   ``cmake -DCMAKE_INSTALL_PREFIX="<ROOT>/Libs/sundials" -DEXAMPLES_ENABLE=OFF -DOPENMP_ENABLE=ON -DBUILD_SHARED_LIBS=OFF -DCMAKE_C_FLAGS=-fPIC ../sundials-3.2.1/``
-  Execute ``make install``
-  Delete the folder ``sundialsbuild`` (e.g., execute
   ``rm -rf sundialsbuild`` in the parent directory of
   ``sundialsbuild``)

LAPACK
~~~~~~

You can either use a LAPACK implementation provided by your distribution
or install the freely available `Intel
MKL <https://software.intel.com/sites/campaigns/nest/>`__ which is very
fast and probably faster than your distribution’s implementation.

Obtain LAPACK from your distribution: \* Install the packages (LAPACK
and BLAS) of your distribution (e.g., ``liblapack3``, ``liblapack-dev``,
``libblas3``, ``libblas-dev`` for Ubuntu and Debian). Note that some
packages only provide reference (i.e., slow) implementations and others
(e.g., ATLAS, GOTO) perform much faster.

SuperLU
~~~~~~~

-  Download SuperLU source from https://github.com/xiaoyeli/superlu
-  Unzip
-  Open a terminal and change to the parent directory of the unzipped
   directory
-  Create a new folder ``superlubuild`` and change to it
-  Execute
   ``cmake -DCMAKE_INSTALL_PREFIX="<ROOT>/Libs/superlu" -Denable_complex=OFF -Denable_complex16=OFF -Denable_blaslib=OFF -DCMAKE_C_FLAGS=-fPIC -DCMAKE_BUILD_TYPE=Release ../SuperLU_5.2.1/``
-  Execute ``make install``
-  Delete the folder ``superlubuild`` (e.g., execute
   ``rm -rf superlubuild`` in the parent directory of ``superlubuild``)

UMFPACK
~~~~~~~

-  Download SuiteSparse source from
   http://faculty.cse.tamu.edu/davis/suitesparse.html
-  Unzip
-  Open a terminal and change to the unzipped directory
-  Execute
   ``make install INSTALL="<ROOT>/Libs/suitesparse" CHOLMOD_CONFIG=-DNPARTITION``
   or
   ``make install INSTALL="<ROOT>/Libs/suitesparse" CHOLMOD_CONFIG=-DNPARTITION AUTOCC=no CC=<COMPILER> CXX=<C++COMPILER>``
   if you want to manually select the compiler

Build CADET
-----------

-  Download release of CADET or checkout from git

-  Place the source in ``<ROOT>/code`` and create the directory
   ``<ROOT>/build``

-  Open a terminal and change to ``<ROOT>/build``

-  If you have built HDF5 yourself, execute
   ``export HDF5_ROOT=<ROOT>/Libs/hdf5``

-  Execute ``export SUNDIALS_ROOT=<ROOT>/Libs/sundials``

-  Execute ``export SUPERLU_ROOT=<ROOT>/Libs/superlu``

-  Execute ``export UMFPACK_ROOT=<ROOT>/Libs/suitesparse``

-  If using MKL, execute ``export MKLROOT=/opt/intel/mkl``

-  Using standard LAPACK: Execute
   ``cmake -DCMAKE_INSTALL_PREFIX="<ROOT>/cadet" ../code/``

   Using MKL (sequential): Execute
   ``cmake -DCMAKE_INSTALL_PREFIX="<ROOT>/cadet" -DBLA_VENDOR=Intel10_64lp_seq ../code/``

   Using MKL (parallel): Execute
   ``cmake -DCMAKE_INSTALL_PREFIX="<ROOT>/cadet" -DBLA_VENDOR=Intel10_64lp ../code/``

-  If CMake was not able to locate MATLAB, execute
   ``export MATLAB_ROOT=/path/to/my/MATLAB/R2016a`` and try to run CMake
   again

-  Execute ``make``

-  Execute ``make install``