You are reading the documentation for version 1.1 of OpenStructure. You may also want to read the documentation for: 1.2 1.3 1.4 1.5 1.6 1.7 1.7.1 1.8 1.9 1.10 1.11 2.0 2.1 2.2 devel

# 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 GIT
• Configuring the build with cmake

## 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.

## Getting the Source Code¶

OpenStructure uses git as the revision control system. The main repository can be browsed here. To get the source code, use git clone:

git clone https://git.scicore.unibas.ch/schwede/openstructure.git <directory-name>


The above command will clone OpenStructre into the directory called directory-name. If omitted, the directory will be called ost. Alternatively, you might consider getting one of the nightly source code snapshots from the downloads section.

Note

Some version of curl have have trouble with the certificate of the OpenStructure git server and fail to clone the repository. To work around this, disable the SSL certificate verification with the following command:

git config --global http.sslVerify false


## Picking the right branch¶

By default you are checking out the master branch. Master is, by definition a stable branch. It always points to the latest release. However, there are several other branches at your disposal. The main development is happening in the develop branch. It contains the newest features and bug fixes. However, we dont’t make any guarantees that the develop branch is bug free and doesn’t contain major bugs. After all, it’s in constant flux. If you are developing new features, start your feature branch off develop. Besides that, there are several smaller features branches that are used to group together commits for one specific features. To change to a specific branch, use

git checkout <branch-name>


## 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.
• 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.

To get the newest changes from the central git repository, enter

git pull


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