1. Installation

The package is built and installed as a normal autotools project (i.e., use configure then make amd make install). The following is a list of dependencies, where relevant arguments for configure is shown in parenthesis. Futher below are specific instructions on how to install these dependencies.

  • This documentation requires Sphinx, preferably in the newest development version (--enable-doc-checks, --disable-doc-checks).
  • libMØD:
    • A C++ compiler with reasonable C++14 support is needed. GCC 5.1 or later should work.
    • Boost dev, 1.59 or >= 1.61 (--with-boost=<path>).
    • (optional) Open Babel dev, >= 2.3.2 (--with-OpenBabel=yes|no|<path>).
  • PyMØD (--enable-pymod, --disable-pymod):
    • Python 3 dev
    • Boost.Python built with Python 3
    • (Optional) IPython 3
  • PostMØD (--enable-postmod, --disable-postmod):
    • pdflatex available in the PATH, with not too old packages (Tex Live 2012 or newer should work).
    • pdf2svg available in the PATH
    • dot and neato from Graphviz available in the PATH. They must additionally be able to load SVG files and output as both SVG and PDF files (all via cairo). That is, in the output of dot -P the following edges must exist:
      • cairo_device_svg -> output_svg
      • cairo_device_pdf -> output_pdf
      • rsvg_loadimage_svg -> render_cairo

1.1. Ubuntu

Install the following packages.

  • (>= Ubuntu 16.10) Boost: libboost-regex-dev libboost-system-dev.
  • (>= Ubuntu 16.10) Boost.Python: python3-dev libboost-python-dev.
  • (< Ubuntu 16.10) Boost, Boost.Python: python3-dev, and then see Boost and Boost.Python with Python 3.
  • (>= Ubuntu 14.04) Open Babel: libopenbabel-dev.
  • (< Ubuntu 14.04) Open Babel: install from source.
  • pdflatex: texlive-full (less can do it, will be refined in the future).
  • pdf2svg: pdf2svg.
  • Graphviz: The Ubuntu package unfortunately does not include the plugin for converting SVG to PDF via rsvg and cairo. librsvg2-dev libpango1.0-dev, and see Graphviz.

1.2. Fedora

Install the following packages.

  • (>= Fedora 24) Boost: boost-devel boost-regex boost-system.
  • (>= Fedora 24) Boost.Python: python3-devel boost-python3-devel.
  • (< Fedora 24) Boost, Boost.Python: python3-devel, and then see Boost and Boost.Python with Python 3.
  • Open Babel: openbabel-devel.
  • pdflatex: texlive-scheme-full (less can do it, will be refined in the future).
  • pdf2svg: pdf2svg.
  • Graphviz: graphviz.

1.3. Boost and Boost.Python with Python 3

A package with the sources of Boost can be downloaded from http://boost.org.

1.3.1. Basic Installation

Boost uses a custom build system which may be difficult to use. A procedure for compiling and installing Boost with Python 3 for Boost.Python is the following.

  1. ./bootstrap.sh --with-python=python3 (optionally give --prefix=some/path to specify a non-standard installation path.
  2. ./b2 (optionally give -j N (similar to GNU Make) to compile with multiple threads)
  3. ./b2 install (optionally give --prefix=some/path to specify a non-standard installation path (if not done earlier).

After bootstrap.sh has been run, the file project-config.jam has been created, which can be edited to customise installation path and a lot of other things. All edits should be done before running b2.

1.3.2. Non-standard Python Installation

Passing --with-python=python3 to bootstrap.sh should work. This adds a line similar to “using python : 3.3 ;” to project-config.jam. After compilation (running b2) the file stage/lib/libboost_python3.so should exist. If not, it did not detect Python 3 properly.

If Python is installed in a non-standard location, add the a line similar to “using python : 3.3 : python3 : /path/to/python/3/installtion/include ;” to project-config.jam, where the last path is the path to the include-folder of the Python-installation.

1.3.3. Custom GCC Version

Before running b2 create the file user-config.jam in the root of the home dir (see here for the full documentation). Put a line similar to “using gcc : : /path/to/g++-4.8” in the file.

1.4. Graphviz

A package with the sources of Graphviz can be downloaded from http://graphviz.org. Make sure that the status output in the end of configure includes pangocairo:    Yes and rsvg:          Yes.