GNU/Linux systems

The instructions to build Slicer for GNU/Linux systems are slightly different depending on the linux distribution and the specific configuration of the system. In the following sections you can find instructions that will work for some of the most common linux distributions in their standard configuration. If you are using a different distribution you can use these instructions to adapt the process to your system. You can also ask questions related to the building process in the Slicer forum.

Pre-requisites

First, you need to install the tools that will be used for fetching the source code of slicer, generating the project files and build the project.

• Git and Subversion for fetching the code and version control.

• GNU Compiler Collection (GCC) for code compilation.

• CMake for configuration/generation of the project.

  • (Optional) CMake curses gui to configure the project from the command line.

  • (Optional) CMake Qt gui to configure the project through a GUI.

• GNU Make

• GNU Patch

In addition, Slicer requires a set of support libraries that are not includes as part of the superbuild:

• Qt5 with the components listed below. Qt version 5.15.2 is recommended, other Qt versions are not tested and may cause build errors or may cause problems when running the application.

  • Multimedia

  • UiTools

  • XMLPatterns

  • SVG

  • WebEngine

  • Script

  • X11Extras

  • Private

• libXt

Debian 11 Stable (Bullseye) and Testing (Bookworm)

Install the development tools and the support libraries:

sudo apt update && sudo apt install git subversion build-essential cmake cmake-curses-gui cmake-qt-gui \
  qtmultimedia5-dev qttools5-dev libqt5xmlpatterns5-dev libqt5svg5-dev qtwebengine5-dev qtscript5-dev \
  qtbase5-private-dev libqt5x11extras5-dev libxt-dev libssl-dev

Ubuntu 21.10 (Impish Indri)

Install the development tools and the support libraries:

sudo apt update && sudo apt install git subversion build-essential cmake cmake-curses-gui cmake-qt-gui \
  qtmultimedia5-dev qttools5-dev libqt5xmlpatterns5-dev libqt5svg5-dev qtwebengine5-dev qtscript5-dev \
  qtbase5-private-dev libqt5x11extras5-dev libxt-dev libssl-dev

Ubuntu 20.04 (Focal Fossa)

Note

Warning Since the default Qt5 packages available on Ubuntu 20.04 correspond to version 5.12.8 and version 5.15.2 is used to build and test the packages available for download. Compiling Slicer against version 5.12.8 may not succeed, and if it does, the compiled Slicer application may behave differently.

To use Qt 5.15.2, we recommend you download and install following these instructions

Install the development tools and the support libraries:

sudo apt update && sudo apt install git subversion build-essential cmake cmake-curses-gui cmake-qt-gui \
  qt5-default qtmultimedia5-dev qttools5-dev libqt5xmlpatterns5-dev libqt5svg5-dev qtwebengine5-dev qtscript5-dev \
  qtbase5-private-dev libqt5x11extras5-dev libxt-dev

ArchLinux

Note

Warning ArchLinux uses a rolling-release package distribution approach. This means that the versions of the packages will change over time and the following instructions might not be actual. Last time tested: 2022-03-08.

Install the development tools and the support libraries:

sudo pacman -S git make patch subversion gcc cmake \
  qt5-base qt5-multimedia qt5-tools qt5-xmlpatterns qt5-svg qt5-webengine qt5-script qt5-x11extras libxt

CentOS 7

Note

Slicer built on CentOS 7 will be available for many Linux distributions and releases

Install Qt and CMake as described in Any Distribution section.

Since by default CentOS 7 comes with gcc 4.8.5 only having experimental support for C++14, the following allows to install and activate the devtoolset-11 providing gcc 11.2.1 supporting C++20:

sudo yum install centos-release-scl
sudo yum install devtoolset-11-gcc*
scl enable devtoolset-11 bash         # activation is needed for every terminal session

Install pre-requisites:

sudo yum install patch mesa-libGL-devel libuuid-devel

Any Distribution

This section describes how to install Qt as distributed by The QT Company, which can be used for any GNU/Linux distribution.

Note

Warning

This process requires an account in qt.io

Download the Qt linux online installer and make it executable:

 curl -LO http://download.qt.io/official_releases/online_installers/qt-unified-linux-x64-online.run
 chmod +x qt-unified-linux-x64-online.run

You can run the installer and follow the instructions in the GUI. Keep in mind that the components needed by 3D Slicer are: qt.qt5.5152.gcc_64, qt.qt5.5152.qtscript qt.qt5.5152.qtscript.gcc_64, qt.qt5.5152.qtwebengine and qt.qt5.5152.qtwebengine.gcc_64.

Alternatively, you can request the installation of the components with the following command (you will be prompted for license agreements and permissions):

export QT_ACCOUNT_LOGIN=<set your qt.io account email here>
export QT_ACCOUNT_PASSWORD=<set your password here>
./qt-unified-linux-x64-online.run \
  install \
    qt.qt5.5152.gcc_64 \
    qt.qt5.5152.qtscript \
    qt.qt5.5152.qtscript.gcc_64 \
    qt.qt5.5152.qtwebengine \
    qt.qt5.5152.qtwebengine.gcc_64 \
  --root /opt/qt \
  --email $QT_ACCOUNT_LOGIN \
  --pw $QT_ACCOUNT_PASSWORD

Note

Warning

When configuring the Slicer build project, the CMake variable Qt5_DIR need to be set using the full path to the Qt5 installation directory ending with 5.15.2/gcc_64/lib/cmake/Qt5. For example, assuming you installed Qt in /opt/qt, you may use cmake -DCMAKE_BUILD_TYPE:STRING=Release -DQt5_DIR:PATH=/opt/qt/5.15.2/gcc_64/lib/cmake/Qt5 ../Slicer.

Checkout Slicer source files

The recommended way to obtain the source code of SLicer is cloning the repository using git:

git clone https://github.com/Slicer/Slicer.git

This will create a Slicer directory containing the source code of Slicer. Hereafter we will call this directory the source directory.

Note

Warning

It is highly recommended to avoid the use of the space character in the name of the source directory or any of its parent directories.

After obtaining the source code, we need to set up the development environment:

cd Slicer
./Utilities/SetupForDevelopment.sh
cd ..

Configure and generate the Slicer build project files

Slicer is highly configurable and multi-platform. To support this, Slicer needs a configuration of the build parameters before the build process takes place. In this configuration stage, it is possible to adjust variables that change the nature and behavior of its components. For instance, the type of build (Debug or Release mode), whether to use system-installed libraries, let the build process fetch and compile own libraries, or enable/disable some of the software components and functionalities of Slicer.

The following folders will be used in the instructions below:

Folder	Path
source	~/Slicer
build	~/Slicer-SuperBuild-Debug
inner-build	~/Slicer-SuperBuild-Debug/Slicer-build

To obtain a default configuration of the Slicer build project, create the build folder and use cmake:

mkdir Slicer-SuperBuild-Debug
cd Slicer-SuperBuild-Debug
cmake ../Slicer

It is possible to change variables with cmake. In the following example we change the built type (Debug as default) to Release:

cmake -DCMAKE_BUILD_TYPE:STRING=Release ../Slicer

Tip – Interfaces to change 3D Slicer configuration variables

Instead of cmake, one can use ccmake, which provides a text-based interface or cmake-gui, which provides a graphical user interface. These applications will also provide a list of variables that can be changed.

Tip – Speed up 3D Slicer build with ccache

ccache is a compiler cache that can speed up subsequent build of 3D Slicer. This can be useful if 3D Slicer is built often and there are no large divergences between subsequent builds. This requires ccache installed on the system (e.g., sudo apt install ccache).

The first time ccache is used, the compilation time can marginally increased as it includes the first caching. After the first build, subsequent build times will decrease significantly.

ccache is not detected as a valid compiler by the 3D Slicer building process. You can generate local symbolic links to disguise the use of ccache as valid compilers:

ln -s /usr/bin/ccache ~/.local/bin/c++
ln -s /usr/bin/ccache ~/.local/bin/cc

Then, the Slicer build can be configured to use these compilers:

cmake \
  -DCMAKE_BUILD_TYPE:STRING=Release \
  -DCMAKE_CXX_COMPILER:STRING=$HOME/.local/bin/c++ \
  -DCMAKE_C_COMPILER:STRING=$HOME/.local/bin/cc \
  ../Slicer

Build Slicer

Once the Slicer build project files have been generated, the Slicer project can be built by running this command in the build folder

make

Tip – Parallel build

Building Slicer will generally take long time, particularly on the first build or upon code/configuration changes. To help speeding up the process one can use make -j<N>, where <N> is the number of parallel builds. As a rule of thumb, many uses the number of CPU threads + 1 as the number of parallel builds.

Warning

Increasing the number of parallel builds generally increases the memory required for the build process. In the event that the required memory exceeds the available memory, the process will either fail or start using swap memory, which will make in practice the system to freeze.

Tip – Error detection during parallel build

Using parallel builds makes finding compilation errors difficult due to the fact that all parallel build processes use the same screen output, as opposed to sequential builds, where the compilation process will stop at the error. A common technique to have parallel builds and easily find errors is launch a parallel build followed by a sequential build. For the parallel build, it is advised to run make -j<N> -k to have the parallel build keep going as far as possible before doing the sequential build with make.

Run Slicer

After the building process has successfully completed, the executable file to run Slicer will be located in the inner-build folder.

The application can be launched by these commands:

cd Slicer-build
./Slicer`

Test Slicer

After building, run the tests in the inner-build folder.

Type the following (you can replace 4 by the number of processor cores in the computer):

ctest -j4

Package Slicer

Start a terminal and type the following in the inner-build folder:

make package

Common errors

See list of issues common to all operating systems on Common errors page.