To build BioDynaMo from source execute the following commands:

Note

If you are a user please follow the installation instructions in our User Guide.


git clone https://github.com/BioDynaMo/biodynamo.git
cd biodynamo

# Install the prerequisites
./prerequisites.sh all

# Create the build directory
mkdir build
cd build

# Build BioDynaMo
cmake ..
make

# (Optional) Installs the libraries
make install

The script prerequisites.sh is used to install all the dependencies needed by BioDynaMo. You will need to run it once before actually calling cmake. It will choose the specific dependencies depending on the used operating system. Run ./prerequisites.sh --help to see how to use it.

Note

On macOS the prerequisites script will use `brew` to install the needed packages. If you do not have `brew` on your system, do yourself a favour and install it. Please have a look to the prerequisites page for more details.

Rebuilding BioDynaMo

If you make developments in the BioDynaMo code you will typically create a new branch and recompile after making your code changes:

cd biodynamo
git pull
git checkout -b <new-branch>

[edit the files]

# clean the previous build but keep the third party libraries, typically ROOT and ParaView
cd build
ninja cleanbuild

# Build BioDynaMo
cmake -G Ninja -DCMAKE_BUILD_TYPE=Debug ..
ninja

When developing ninja is preferred as it is slightly faster than make.

Also we advice you to put the following lines in your .bashrc or .zshrc file on Linux platforms where we use pyenv to manage the different python versions:

export PATH="$HOME/.pyenv/bin:$PATH"
eval "$(pyenv init -)"

Once finished, we hope that you want to contribute your code changes back to the BioDynaMo project. For more on how to contribute see the page on Contributing your code.

CentOS 7

In case of CentOS 7, you will need to run the following commands before actually calling cmake. This is because CentOS do not provide by default the correct C++ compilers and the correct python interpreter. Moerover, we will need to load the OpenMPI module. You will need to run these instructions only before building BioDynaMo. You will not need them in order to run the program.

export MESA_GL_VERSION_OVERRIDE=3.3
. scl_source enable devtoolset-8

. /etc/profile.d/modules.sh
module load mpi

CMake Build Options

Our CMake build script uses a few options to influence the build process. They can be set as follows:

cmake -Doption=value ..

The value for binary options is on or off. If you change the value of these switches, you might have to delete CMakeCache.txt beforehand.

Option Default Value Description
test on build the test executables; precondition for e.g. valgrind and coverage
dict on build ROOT dictionaries. These are compulsory to use backups. Turning them off reduces compilation time.
paraview on Enable visualization using ParaView. Visualization cannot be used if this switch is turned off.
cuda off enable CUDA code generation for GPU acceleration
opencl off enable OpenCL code generation for GPU acceleration
valgrind on enable memory leak checks
coverage off creates a make target to generate a html report indicating which parts of the code are tested by automatic tests
jemalloc off use jemalloc for memory allocations
tcmalloc off use tcmalloc for memory allocations
website off enable website generation (make website<-live> target (see below for more information))

Further CMake command line parameters

Option Description
CMAKE_CXX_FLAGS specify additional compiler flags - e.g. "-mavx"
CMAKE_BUILD_TYPE specify the build type. Possible values are Debug, Release, RelWithDebInfo, MinSizeRel

Build Targets

Target Description
run-unit-tests executes all BioDynaMo unit tests
run-valgrind executes BioDynaMo valgrind tests
run-check executes both unit and valgrind tests
run-demos executes all demos and integration tests
clean will clean all targets, also the external projects
cleanbuild will clean everything in the build directory, except for third_party (useful for avoiding downloading third party software)
bdmclean will only clean the biodynamo and runBiodynamoTests* targets
testbdmclean will only clean the runBiodynamoTests* target
doc will generate the API, user and developer documentation in directory build/doc.
coverage will execute the test target and generate a coverage report in build/coverage. Make sure that kcov are installed and configure cmake with cmake -Dcoverage=on ..
coverage-build same as make coverage, but builds it in a separate directory (build/coverage). Since building the coverage report requires different compiler flags, building it in a separate directory keeps the current build directory in good order.

The following targets are only available if clang-format, clang-tidy and git are installed.

Build targets indicated with * always come in three different flavors.

  • no-suffix: executes the target on source files that changed compared to origin/master -- e.g. make check-format
  • -staged: executes the target on source files that have been staged -- e.g. make check-format-staged
  • -all: executes the target on all source files in the project -- e.g. make check-format-all
Target Description
check-format* run clang-format on selected files. Fails if any file needs to be reformatted
show-format* run clang-format on selected files and display differences
format* run clang-format on selected files and update them in-place
check-tidy* run clang-tidy on selected files. Fails if errors are found
show-tidy* run clang-tidy on selected files and display errors.
tidy* run clang-tidy on selected files and attempt to fix any warning automatically
check-cpplint* run cpplint on selected files. Fails if errors are found and displays them.
check-submission will build, run all tests, check formatting, code style, and generate documentation and coverage report
fix-submission will attempt to fix the reported issues using clang-format and clang-tidy. Failing build, tests, compiler warnings, issues from cpplint and warnings from doxygen must be fixed manually. Also some clang-tidy issues cannot be resolved automatically
Target Description
website will generate the static files used for biodynamo.org
website-live starts a local web server so you can immediately view the website in the browser. The website is automatically reloaded if you change a source file.

Advanced Build Options

Use a Custom Compiler

If you need to user a custom compilers (instead of the one automatically detected by BioDynaMo) you will need to set the variables: CXX for the C++ compiler and CC for the C compiler. Please not that your custom compiler must support the C++14 standard and must be compatible with OpenMP. The complete procedure will become:

git clone https://github.com/BioDynaMo/biodynamo.git
cd biodynamo

# Let's say I want to use a custom version of clang
export CXX=/opt/local/bin/clang++-mp-8.0
export C=/opt/local/bin/clang++-mp-8.0

./install.sh

Use a Specific ROOT / ParaView Installation

When you want to inform BioDynaMo of a specific installation of ROOT and /or ParaView on your system, you will need to perform the following instructions prior to installation.

git clone https://github.com/BioDynaMo/biodynamo.git
cd biodynamo

# For ROOT
source <root_installation_dir>/bin/thisroot.sh

# For ParaView
export ParaView_DIR=<paraview_installation_dir>/lib/cmake/paraview-5.8
export Qt5_DIR=<qt5_installation_dir>/lib/cmake/Qt5

./install.sh

Note

If you specify ParaView_DIR, then you will need to provide also the Qt5_DIR variable. This is because ParaView implicitly relies on the Qt5 installation.


Speed Up Installation Tests with a Local BioDynaMo-LFS Copy

The installation scripts fetch large precompiled dependencies like ROOT or ParaView from biodynamo's large file storage (LFS). To enable faster builds you can download the whole LFS and tell BioDynaMo to access the local version instead. This is done with the environmental flag BDM_LOCAL_LFS. Use an absolute path to the directory that contains the local copy.

export BDM_LOCAL_LFS=/path/to/local/lfs

If you want to download the files from remote LFS again execute:

unset BDM_LOCAL_LFS

Warning

At the moment there is no check if the local copy is in synch with remote. You have to ensure that yourself!