Installing¶

Using Conda¶

For macOS and Linux x86-64, precompiled binary packages are available via (mini)conda:

conda config --add channels conda-forge
conda install faunus

In addition to the faunus executable, this installs a set of examples in share/faunus, as well as python bindings. To update an existing installation, use

faunus --version      # show version string
conda search faunus   # show (new) revisions
conda upgrade faunus

Starting from version 2.1, we adhere to semantic versioning.

Building from source code¶

Faunus is continuously tested on macOS/Linux, but should compile on most unix operating systems and possibly under Cygwin (Windows).

Requirements¶

CMake 3.16+
C/C++17 compiler (Clang 5+, GCC 7+, etc.)
Python 3.6+ with the following packages:
- jinja2, ruamel_yaml or yaml

The following are optional:

jsonschema (for validating input - highly recommended)
pandoc (for building manual)
pypandoc (for building manual)
BeautifulSoup4 (for building manual)
Message Passing Interface (MPI)

macOS tip: Apple’s developer tools, Xcode, include clang; CMake can be installed with an Installer package from Kitware, or using Homebrew, or (mini)conda

Compiling¶

Download the latest release or the developer branch and build using cmake:

cd faunus
cmake . [OPTIONS]
make faunus
make usagetips # requires `pandoc`, `pypandoc`, `BeautifulSoup4`

Use make help to see all build targets.

The following options are available:

CMake Option	Description
`-DENABLE_MPI=OFF`	Enable MPI
`-DENABLE_OPENMP=ON`	Enable OpenMP support
`-DENABLE_TESTS=ON`	Enable unittesting
`-DENABLE_PYTHON=OFF`	Build python bindings (experimental)
`-DENABLE_FREESASA=ON`	Enable SASA routines (external download)
`-DENABLE_TBB=OFF`	Build with Intel Threading Building Blocks (experimental)
`-DENABLE_PCG=OFF`	Use PCG random number generator instead of C++'s Mersenne Twister
`-DBUILD_STATIC=OFF`	Build statically linked binaries
`-DCMAKE_BUILD_TYPE=Release`	Alternatives: `Debug` or `RelWithDebInfo`
`-DCMAKE_CXX_FLAGS_RELEASE="..."`	Compiler options for Release mode
`-DCMAKE_CXX_FLAGS_DEBUG="..."`	Compiler options for Debug mode
`-DCMAKE_INSTALL_PREFIX:PATH="..."`	Install location (default: `/usr/local`)
`-DPYTHON_EXECUTABLE="..."`	Full path to Python executable
`-DPYTHON_INCLUDE_DIR="..."`	Full path to python headers
`-DPYTHON_LIBRARY="..."`	Full path to python library, i.e. libpythonX.dylib/so

Compiling the Manual¶

Pandoc is required to build the HTML manual:

make manual_html

In addition to pandoc, a TeX Live installation containing XeLaTeX is required to build the PDF manual. The manual is supposed to be typeset with EB Garamond, Garamond Math and Fira Code fonts thus they have to be available in your system. Alternatively, you can tweak the font options in the header.md file.

make manual

Python libraries in odd locations¶

Should there be multiple compilers or python distributions, be specific:

CC=/opt/bin/clang CXX=/opt/bin/clang++ cmake . \
  -DPYTHON_EXECUTABLE=/opt/bin/python3 \
  -DPYTHON_INCLUDE_DIR=/opt/include/python3.6 \
  -DPYTHON_LIBRARY=/opt/lib/libpython3.6.dylib

For solving python issues on macOS, the linked python library can be probed and, if needed, renamed:

otool -L pyfaunus.so
install_name_tool -change libpython3.6.dylib \
  $HOME/miniconda/lib/libpython3.6.dylib pyfaunus.so

Resetting the build system¶

To change the compiler or for another reason reset the build system, do:

make clean
rm -fR CMakeCache.txt CMakeFiles _deps

Intel Threading Building Blocks¶

If ENABLE_TBB=on, TBB may be used for threaded simulations which may or may not be advantageous, depending on the system. By default, an unspecified and possibly dated version of TBB will be downloaded and build. Alternatively you can use an existing installation via TBB_DIR:

cmake -DENABLE_TBB=on -DTBB_DIR={tbb-root}/lib/cmake/TBB

where {tbb-root} is the installation directory of TBB, e.g. /usr/local.

Development¶

The development of Faunus is done mainly in Jetbrain’s CLion (free academic license) but any other IDE or merely a text editor can be used. We recommend to use tools that respect the provided .clang-format which will ease merging changes into the codebase, see below.

Code Style¶

If you plan to contribute to Faunus it is recommended to activate the pre-commit hook for automatic styling of all changes:

cd faunus
./scripts/git-pre-commit-format install

This requires clang-format which may also be directly used in IDEs such as CLion. In the top-level directory of Faunus you will find the style configuration file .clang-format

Also, adhere to the following naming conventions:

Style	Elements
`CamelCase`	classes, namespaces
`camelBack`	functions
`snake_case`	variables

Creating a conda package (development usage)¶

The basic steps for creating a conda package is outlined below, albeit details depend on the build environment. See also the .travis.yml configuration file in the main repository.

conda config --add channels conda-forge
conda install conda-build anaconda-client
cd scripts/
conda-build .
anaconda login
anaconda upload -u USER ... # see output from build step

Instead of uploading to anaconda.org, install a local copy directly after the build step above:

conda install -c USER faunus --use-local