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Installing OpenStructure From Source

Note

This document describes how to install OpenStructure from source. If you are mainly insterested in using OpenStructure and are not planning to modify the code of OpenStructure itself, please use one of the binaries available for download.

Brief Overview

Compiling OpenStructure consists of several steps that are described below in more detail. In essence, these steps are:

  • Installing the Dependencies
  • Checking out the source code from SVN
  • Configuring the build with cmake
  • Compiling an Linking

Installing the Dependencies

OpenStructure uses a bunch of OpenSource libraries. If you haven’t already installed them, please install them now! Where appropriate the minimally required version is given in parantheses.

When you enable support for image processing, you will need:

  • FFTW3. By default, OpenStructure is compiled with single precision and thus also requires FFTW to be compiled with single precision. Most platforms offer this as a second package. If you are compiling manually, use the –enable-single option.
  • libtiff

If you would like to use the graphical user interface, also install:

In case you are compiling under Windows you have to install Visualstudio 2008. to compile the dependecies and OpenStructure. We recommend to compile the dependecies manually. Enter the directories where the dependencies are located in Tools->Options->Projects and Solutions->VC++ directories. Choose ‘bin’ directories to enter program paths to cmake, qmake and python, ‘lib’ directories to point to the location(s) of your dependencies.

Checking out the Source

You can checkout the source from SVN. The repository is located at

https://dng.biozentrum.unibas.ch/svn/openstructure/trunk

If you are using the commandline client, type in your shell

svn co https://dng.biozentrum.unibas.ch/svn/openstructure/trunk

On Windows, we recommend to install a graphical frontend for svn, for example tortoisesvn.

Configuring

OpenStructure uses CMake for compiling and building the project. The next required step is to configure the build environment using cmake. You can do that by invoking cmake in the project directory.

cmake . <options>

There are two kinds of options: Options that let you control the building behaviour, enabling and disabling the compilation of certain modules and options that let you tell CMake where to find the dependencies. All of them are passed to CMake with via -D<opt>=<value>.

On Windows, use Tools -> VisualStudio commandline prompt from within VisualStudio)

Flag to choose build generator

CMake supports different build generators. On UNIX, that is MacOS X and Linux, the default build generator is Makefiles, but it is also possible to use other programs. For a list of supported build generators on your platform, start cmake without parameters.

On Windows you have to explicitly set the buil generator to “Visual Studio 9 2008”:

cmake -G"Visual Studio 9 2008"

Flags to Control the Dependencies

By default, CMake searches the standard directories for dependencies. However, on some systems, this might not be enough. Here is a short description of how CMake figures out what dependencies to take and how you can influence it.

  • Boost is mainly controlled via the BOOST_ROOT option. If boost wasn’t found, it should be set to the prefix of the boost installation.
  • QT_QMAKE_EXECUTABLE defines the exact Qt installation to take. It should be set to the full path to qmake.
  • PYTHON_ROOT is the Python equivalent of BOOST_ROOT. It should be set to the prefix path containing the python binary, headers and libraries.
  • SYS_ROOT controls the general prefix for searching libraries and headers. By default, it is set to /.

Build Options

  • ENABLE_UI controls whether to build the graphical user interface module. By default it is set to true.
  • ENABLE_IMG controls whether to build the image processing module. This will enable support for density maps, and general image processing in 1, 2 an 3 dimensions. By default it is set to true.
  • ENABLE_GFX controls whether to build the graphics module. By default, this is set to true. If set to none, this implies ENABLE_UI=NO.
  • Shader support is controlled with USE_SHADER. By default, no shaders are used.
  • If OPTIMIZE is set to 1, an optimized version of OpenStructure is built.

Example Configurations

Ubuntu 10.04 Lucid/Lynx

All the dependencies can be installed from the package manager and are thus located in standard locations. cmake will automatically find them without the need to pass any additional parameters. The only exception is -DOPTIMIZE, which will tell cmake to build an optimized (-O3 -DNDEBUG) version of OpenStructure.

cmake . -DOPTIMIZE=1

MacOS X with MacPorts and optimization turned on

MacPorts installs all the software under /opt/local. Thus we have to tell cmake where to find Boost, Python and Qt.

cmake . -DBOOST_ROOT=/opt/local -DPYTHON_ROOT=/opt/local \
      -DSYS_ROOT=/opt/local -DQT_QMAKE_EXECUTABLE=/opt/local/bin/qmake \
      -DOPTIMIZE=1

Building the Project

Type make. If you are using a multi-core machine, you can use the -j flag to run multiple jobs at once.

On Windows run ‘Build OpenStructure’ from the build menu.

What’s next?

On Linux and MacOS X, you can start dng from the command-line. The binaries are all located in stage/bin:

stage/bin/dng

or, to start the command-line interpreter:

stage/bin/ost

If you repeatedly use OpenStructure, it is recommended to add /path/to/dng/stage/bin to your path.

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