You're reading an old version of this documentation. For the latest released version, please have a look at v5.0.1.

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:

<ROOT>
   |-libs
   |   |- sundials
   |   |- hdf5
   |   |- superlu
   |   |- suitesparse
   |-code
   |-cadet
   |-build

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 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

Before running cadet, make sure to

  • add <ROOT>/cadet/bin to your PATH, by executing export PATH=<ROOT>/cadet/bin:$PATH, and

  • add <ROOT>/cadet/lib to your LD_LIBRARY_PATH, by executing export LD_LIBRARY_PATH=<ROOT>/cadet/lib:$LD_LIBRARY_PATH.