This page lists the prerequisite packages that need to be installed in order to build correctly BioDynaMo. BioDynaMo provides also an automated procedure to install all the needed libraries.

Ubuntu 18.04 and 20.04

Required Packages

  • wget: Retrieves files from the web
  • curl: Command line tool for transferring data with URL syntax
  • cmake: Set of tools for automate building, testing of software
  • make: Build automation tool
  • gcc: GNU C compiler
  • g++: GNU C++ compiler
  • libopenmpi-dev: Development files for OpenMPI (Open Source Message Passing Interface)
  • libomp5: OpenMP library
  • libomp-dev: Development files for OpenMP (API for multiprocessor programming)
  • libnuma-dev: Development files for NUMA (simple programming interface to the policy supported by the Linux kernel)
  • freeglut3-dev: Development files for GLUT (OpenGL Utility Toolkit)
  • libpthread-stubs0-dev: Development files for managing threads

Required package for custom Python installation with pyenv

  • libssl-dev: Secure Sockets Layer toolkit - development files
  • zlib1g-dev: Compression library - development
  • libbz2-dev: High-quality block-sorting file compressor library - development
  • libreadline-dev: GNU readline and history libraries, development files
  • libsqlite3-dev: SQLite 3 development files
  • xz-utils: XZ-format compression utilities
  • tk-dev: Toolkit for Tcl and X11 (default version) - development files
  • libffi-dev: Foreign Function Interface library (development files)
  • liblzma-dev: XZ-format compression library - development files
  • python-openssl: Python wrapper around the OpenSSL library

Optional Packages

  • valgrind: A suite of tools for debugging and profiling
  • clang-format: clang-based C++ style checker and formatter
  • clang-tidy: clang-based C++ “linter” tool
  • doxygen: Tool for generating documentation from annotated C++ sources
  • graphviz: Graph Visualization Software used optionally by Doxygen
  • kcov: Code coverage testing tool (only on Ubuntu 20.04)
  • libxml2-dev: Development files for the GNOME XML library
  • libgsl-dev: GNU Scientific Library (GSL) -- development package

Installation

Required Packages

sudo apt-get update
sudo apt-get install -y wget curl make gcc g++ \
libopenmpi-dev libomp5 libomp-dev libnuma-dev freeglut3-dev \
libpthread-stubs0-dev

curl -L -O https://github.com/Kitware/CMake/releases/download/v3.19.3/cmake-3.19.3-Linux-x86_64.sh
chmod +x cmake-3.19.3-Linux-x86_64.sh
sudo ./cmake-3.19.3-Linux-x86_64.sh --skip-license --prefix=/usr/local

We install pyenv as the Python Version Management tool to be able to switch to a supported Python environment for BioDynaMo. This will not interfere with your system's Python installation.

sudo apt-get install -y libssl-dev zlib1g-dev libbz2-dev libreadline-dev \
  libsqlite3-dev xz-utils tk-dev libffi-dev liblzma-dev python-openssl

curl https://pyenv.run | bash
export PATH="$HOME/.pyenv/bin:$PATH"
eval "$(pyenv init --path)"
eval "$(pyenv init -)"
PYTHON_CONFIGURE_OPTS="--enable-shared" pyenv install 3.9.1

Optional Packages

pyenv shell 3.9.1
python -m pip install nbformat jupyter metakernel jupyterlab
sudo apt-get install -y valgrind \
  clang-format clang-tidy \
  doxygen graphviz libxml2-dev libgsl-dev
# on Ubuntu 20.04
sudo apt-get install -y kcov

CentOS 7

Required Packages

  • epel-release: Provides a set of additional packages for Enterprise Linux
  • ius-release: Provides RPM packages for newer software versions for for Enterprise Linux distributions
  • wget: Retrieves files from the web
  • cmake: Set of tools for automate building, testing of software
  • libXt-devel: Basic library for developing X11
  • libXext-devel: Library which contains a handful of X11 extensions
  • devtoolset-8-gcc: Compiler suite for C and C++
  • numactl-devel: Development files for NUMA (simple programming interface to the policy supported by the Linux kernel)
  • freeglut-devel: Development files for GLUT (OpenGL Utility Toolkit)
  • openmpi3-devel: Development files for OpenMP (API for multiprocessor programming)

Required package for custom Python installation with pyenv

  • zlib-devel: Header files and libraries for Zlib development
  • bzip2: A file compression utility
  • bzip2-devel: Libraries and header files for apps which will use bzip2
  • readline-devel: Files needed to develop programs which use the readline library
  • sqlite: Library that implements an embeddable SQL database engine
  • sqlite-devel: Development tools for the sqlite3 embeddable SQL database engine
  • openssl-devel: Files for development of applications which will use OpenSSL
  • xz: LZMA compression utilities
  • xz-devel: Devel libraries & headers for liblzma
  • libffi-devel: Development files for libffi
  • findutils: The GNU versions of find utilities (find and xargs)

Optional Packages

  • llvm-toolset-7: software collection that provides software from the LLVM suite
  • llvm-toolset-7-clang-tools-extra: software collection that provides clang-format and clang-tidy
  • llvm-toolset-7-llvm-devel: LLVM developer libraries
  • llvm-toolset-7-llvm-static: LLVM static libraries
  • valgrind: A suite of tools for debugging and profiling
  • doxygen: Tool for generating documentation from annotated C++ sources
  • graphviz: Graph Visualization Software used optionally by Doxygen
  • libxml2-devel: Development files for the GNOME XML library
  • gsl-devel: GNU Scientific Library (GSL) -- development package
  • atlas-devel: Automatically Tuned Linear Algebra Software -- development package
  • blas-devel: The Basic Linear Algebra Subprograms library -- development package
  • lapack-devel: Numerical linear algebra package libraries -- development package

Installation

Required Packages

sudo yum update -y
sudo yum -y install centos-release-scl epel-release
sudo yum -y install https://centos7.iuscommunity.org/ius-release.rpm
sudo yum -y install wget libXt-devel libXext-devel \
  devtoolset-8-gcc* numactl-devel \
  openmpi3-devel freeglut-devel git

curl -L -O https://github.com/Kitware/CMake/releases/download/v3.19.3/cmake-3.19.3-Linux-x86_64.sh
chmod +x cmake-3.19.3-Linux-x86_64.sh
./cmake-3.19.3-Linux-x86_64.sh --skip-license --prefix=/usr/local

We install pyenv as the Python Version Management tool to be able to switch to a supported Python environment for BioDynaMo. This will not interfere with your system's Python installation.

sudo yum install -y @development zlib-devel bzip2 bzip2-devel readline-devel \
  sqlite sqlite-devel openssl-devel xz xz-devel libffi-devel findutils

curl https://pyenv.run | bash
export PATH="$HOME/.pyenv/bin:$PATH"
eval "$(pyenv init --path)"
eval "$(pyenv init -)"
PYTHON_CONFIGURE_OPTS="--enable-shared" pyenv install 3.9.1

Optional Packages

pyenv shell 3.9.1
python -m pip install nbformat jupyter metakernel jupyterlab
# SBML integration
sudo bash -c 'cat << EOF  > /etc/yum.repos.d/springdale-7-SCL.repo
[SCL-core]
name=Springdale SCL Base 7.6 - x86_64
mirrorlist=http://springdale.princeton.edu/data/springdale/SCL/7.6/x86_64/mirrorlist
#baseurl=http://springdale.princeton.edu/data/springdale/SCL/7.6/x86_64
gpgcheck=1
gpgkey=http://springdale.math.ias.edu/data/puias/7.6/x86_64/os/RPM-GPG-KEY-puias
EOF'
sudo yum update -y
sudo yum install -y doxygen graphviz valgrind freeglut-devel libxml2-devel
sudo yum install -y llvm-toolset-7 llvm-toolset-7-clang-tools-extra \
   llvm-toolset-7-llvm-devel llvm-toolset-7-llvm-static \
   gdl-devel atlas-devel blas-devel lapack-devel

macOS

Requirements to build on macOS are:

  • A 64-bit Intel CPU or Apple Silicon CPU
  • macOS Catalina (10.15) or higher
  • Xcode and the Command Line Tools (CLT) for Xcode: xcode-select --install
    (or from developer.apple.com/downloads)
  • An up to date Homebrew instalation (MacPorts and Fink are not supported)
  • A Bourne-compatible shell for installation (e.g. bash or zsh)

Required Packages

  • libomp: Development files for OpenMP (API for multiprocessor programming)
  • open-mpi: Development files for OpenMP (API for multiprocessor programming)
  • python@3.9: Python interpreter
  • wget: Retrieves files from the web
  • cmake: Set of tools for automate building, testing of software
  • ninja: Ninja is a small build system with a focus on speed
  • bash: Recent version of bash shell
  • tbb: Rich and complete approach to parallelism in C++ (needed by ROOT on Apple M1)

Optional Packages

  • doxygen: Tool for generating documentation from annotated C++ sources
  • graphviz: Graph Visualization Software used optionally by Doxygen
  • kcov: Code coverage testing tool
  • gsl: GNU Scientific Library (GSL) -- development package

Installation

Required Packages

brew update; brew upgrade
brew install libomp open-mpi python@3.9 wget cmake ninja bash tbb

Optional Packages

brew install doxygen graphviz kcov gsl
python3 -m pip install nbformat jupyter metakernel jupyterlab