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The Open Chemistry project uses Git for version control, and CMake to direct the build process. The openchemistry repository contains git submodules with other actively developed projects such as Avogadro, MongoChem and MoleQueue. It will also automatically download source tarballs and build them for third party dependencies, with variables named USE_SYSTEM_LIBRARY to attempt to find and build against system versions.

This page goes through the steps of building the Open Chemistry projects using the openchemistry git repository. It is entirely possible to build each project individually without using the "superbuild" approach, but you will need to ensure all dependencies are built and can be found by the project. Once successfully built you will be left with several build directories which you can treat as normal build directories, developing and compiling from inside them largely ignoring the outer build tree. The Development page goes through the steps of developing and submitting patches for inclusion in the projects.

Cloning Repositories

You should clone the repositories from our source code hosting infrastructure, or the Github/Gitorious mirror. You should also track changes from here as the cloning/update process will be faster, and is always in sync with Gerrit. To clone the Open Chemistry repository that contains the other projects as submodules,

 git clone --recursive git://


In order to update the repository from the openchemistry module you can run,

 git pull
 git submodule update --init


The Open Chemistry projects have a number of prerequisites, and these vary by platform. On Windows Visual Studio 2017 is best supported. The superbuild will attempt to build a number of dependencies, on Linux you are likely best off installing these with your package manager, and on macOS the Home Brew package manager works well.

We should add a package listing for various Linux distributions, but as a guide you will need a C/C++ compiler that supports C++11, OpenGL, Qt 5.6+, CMake 3.3+ and Python installed.


It is recommended that you create a build tree outside of the source tree. Assuming you are in the directory where you cloned the repository the following commands will create a build tree, configure it and build.

 mkdir openchemistry-build
 cd openchemistry-build
 cmake ../openchemistry
 cmake --build . --config Release

You may wish to run cmake-gui in the build directory once it has been configured. You can build against system libraries to avoid building them (examples include Boost, Eigen, etc), and turn testing on globally (ENABLE_TESTS) if you would like to ensure all tests are configured and built for sub-projects. The --config argument to cmake --build is only used on the Windows platform with MSVC, and can be removed elsewhere.

Finding Qt, Windows Generators

We go to great care to use Qt5_DIR as the base for all Qt 5 modules, so setting the correct Qt5_DIR should result in a valid tree, you can also use CMAKE_PREFIX_PATH to point at the install prefix of Qt. When setting Qt5_DIR for Windows, using Qt 5.10.1 as an example, you should set the variable to 'C:/Qt/Qt5.10.1/5.10.1/msvc2017_64/lib/cmake/Qt5' (without the quotes). As you upgrade, you can usually just replace the version (that occurs twice), you must also be careful to match the CMake generator to the compiler and architecture on Windows, I recommend 'Visual Studio 15 2017 Win64', we no longer build/test 32 bit binaries on any platform.

Normal Development

You can also open the top-level CMakeLists.txt in Qt Creator, choose the build location, have that configure and build and then open the top-level CMakeLists.txt for each of the sub-projects. When setting the build location choose the openchemistry-build/avogadrolibs for Avogadro, openchemistry-build/molequeue for MoleQueue, etc. Once you have compiled the top-level, for normal day-to-day development you are free to ignore it and perform the majority of work in the project being developed.

Build Tree Layout

The build tree mirrors the source tree for most active projects. So avogadrolibs is in the same relative path in the source and build trees. For things such as Boost which are built from a source tarball they can be found only in the build tree, and are under thirdparty/boost-prefix, these projects are dependencies but are not expected to be edited in place.

There is a prefix directory in the base of the build tree. This acts as an install prefix for all projects, with the normal include, bin, share and lib directories. This can be used to inject an additional prefix in CMAKE_PREFIX_PATH to ensure projects build by the superbuild are found. It keeps the sub-projects relatively simple as they either find stuff in the prefix, or normal system paths.

Running Executables

It is recommended that you run the binaries from within the prefix directory in the build tree. The top-level targets (avogadroapp, molequeue, monogochem) all install to the prefix, if running make from within the individual build trees run make install to ensure you are using the latest version. On Linux and Windows running Avogadro 2 looks like,


There is an issue with the installed packages on Mac OS X only being partially fixed up. You can use make a package (see below), or run the app bundle from the appropriate build tree after setting DYLD_LIBRARY_PATH,

 export DYLD_LIBRARY_PATH=/Users/your-user/openchemistry-build/prefix/lib
 open /Users/your-user/openchemistry-build/avogadroapp/bin/

We will look into improving this situation soon.

Building Packages

The molequeue, mongochem and avogadroapps projects can build installers. In order to do this you must cd into the appropriate subdirectory and call make package. So to build the Avogadro 2 package,

 cd avogadroapp
 make package

You may need to run cmake-gui, toggle advanced variables and enable/disable packages you are interested in. They are prefixed by CPACK_, and can be toggled before calling make package. A binary installer will be created in the build directory.