# Installation¶

• Linux systems Yade can be installed from packages (pre-compiled binaries) or source code. The choice depends on what you need: if you don’t plan to modify Yade itself, package installation is easier. In the contrary case, you must download and install the source code.

## Packages¶

Stable packages

Since 2011, all Ubuntu (starting from 11.10, Oneiric) and Debian (starting from Wheezy) versions have Yade in their main repositories. There are only stable releases in place. To install Yade, run the following:

sudo apt-get install yade


After that you can normally start Yade using the command yade or yade-batch.

To check which version of Yade is included in your specific distribution, visit Ubuntu or Debian. The Debian-Backports repository is updated regularly to bring the newest Yade version to the users of stable Debians.

Daily packages

Pre-built packages updated more frequently than the stable versions are provided for all currently supported Debian and Ubuntu versions and available on yade-dem.org/packages .

These are “daily” versions of the packages which are being updated regularly and, hence, include all the newly added features.

Warning

yade-daily packages are currently out of date, this issue is being worked on. Yade can be installed from source code.

To install the daily-version you need to add the repository to your /etc/apt/sources.list, add the PGP-key AA915EEB as trusted and install yadedaily:

sudo bash -c 'echo "deb http://www.yade-dem.org/packages/ xenial/" >> /etc/apt/sources.list'
sudo apt-get update


Be sure to use the correct name of your Ubuntu/Debian distribution in the first line (xenial for Ubuntu 16.04 LTS, whereas stretch would be required for Debian 9, for instance). For the list of currently supported distributions, please visit yade-dem.org/packages.

After that you can normally start Yade using the command yadedaily or yadedaily-batch. yadedaily on older distributions can have some disabled features due to older library versions, shipped with particular distribution.

The Git-repository for packaging stuff is available on GitLab. Each branch corresponds to one distribution, e.g., xenial, stretch etc. The scripts for building all of this stuff are here. It uses “pbuilder” to build packages, so all packages are built in a clean environment.

If you do not need yadedaily-package anymore, just remove the corresponding line in /etc/apt/sources.list and the package itself:

sudo apt-get remove yadedaily


To remove our key from keyring, execute the following command:

sudo apt-key remove AA915EEB


Daily and stable Yade versions can coexist without any conflicts, i.e., you can use yade and yadedaily at the same time.

## Source code¶

Installation from source code is reasonable, when you want to add or modify constitutive laws, engines, functions etc. Installing the latest trunk version allows one to use newly added features, which are not yet available in packaged versions.

If you want to install from source, you can install either a release (numbered version, which is frozen) or the current development version (updated by the developers frequently). You should download the development version (called trunk) if you want to modify the source code, as you might encounter problems that will be fixed by the developers. Release versions will not be updated (except for updates due to critical and easy-to-fix bugs), but generally they are more stable than the trunk.

2. The development version (trunk) can be obtained from the code repository at GitLab.

We use GIT (the git command) for code management (install the git package on your system and create a GitLab account):

git clone git@gitlab.com:yade-dev/trunk.git


will download the whole code repository of the trunk. Check out Yade on GitLab for more details on how to collaborate using git.

Alternatively, a read-only checkout is possible via https without a GitLab account (easier if you don’t want to modify the trunk version):

git clone https://gitlab.com/yade-dev/trunk.git


For those behind a firewall, you can download the sources from our GitLab repository as compressed archive.

Release and trunk sources are compiled in exactly the same way.

### Prerequisites¶

Yade relies on a number of external software to run; they are checked before the compilation starts. Some of them are only optional. The last ones are only relevant for using the fluid coupling module (FlowEngine).

Most of the list above is very likely already packaged for your distribution. In case you are confronted with some errors concerning not available packages (e.g., package libmetis-dev is not available) it may be necessary to add yade external ppa from https://launchpad.net/~yade-users/+archive/external (see below) as well as http://www.yade-dem.org/packages (see the top of this page):

sudo add-apt-repository ppa:yade-users/external
sudo apt-get update


The following commands have to be executed in the command line of your corresponding distribution. Just copy&paste to the terminal. Note, to execute these commands you need root privileges.

• Ubuntu 18.04, 18.10, Debian 9, 10 and their derivatives:

sudo apt install cmake git freeglut3-dev libloki-dev libboost-all-dev fakeroot \
dpkg-dev build-essential g++ python3-dev python3-ipython python3-matplotlib \
libsqlite3-dev python3-numpy python3-tk gnuplot libgts-dev python3-pygraphviz \
libvtk6-dev libeigen3-dev python3-xlib python3-pyqt5 pyqt5-dev-tools python3-mpi4py \
python3-pyqt5.qtwebkit gtk2-engines-pixbuf python3-pyqt5.qtsvg libqglviewer-dev-qt5 \
python3-pil libjs-jquery python3-sphinx python3-git libxmu-dev libxi-dev libcgal-dev \
help2man libbz2-dev zlib1g-dev python3-minieigen libopenblas-dev libsuitesparse-dev \
libmetis-dev python3-bibtexparser python3-future coinor-clp coinor-libclp-dev

• For Ubuntu 16.04 libqglviewer-dev-qt5 is to be replaced by libqglviewer-dev and python3-ipython by ipython3.

• For building documentation (the make doc invocation explained below) additional package texlive-xetex is required. On some multi-language systems an error Building format(s) --all. This may take some time... fmtutil failed. may occur, in that case a package locales-all is required.

Some of the packages (for example, cmake, eigen3) are mandatory, some of them are optional. Watch for notes and warnings/errors, which are shown by cmake during the configuration step. If the missing package is optional, some of Yade features will be disabled (see the messages at the end of the configuration).

Additional packages, which can become mandatory later:

sudo apt-get install python-gts


Some packages listed here are relatively new and they can be absent in your distribution (for example, libmetis-dev or python-gts). They can be installed from yade-dem.org/packages or from our external PPA. If not installed the related features will be disabled automatically.

If you are using other distributions than Debian or its derivatives you should install the software packages listed above. Their names in other distributions can differ from the names of the Debian-packages.

Warning

If you have Ubuntu 14.04 Trusty, you need to add -DCMAKE_CXX_FLAGS=-frounding-math during the configuration step of compilation (see below) or to install libcgal-dev from our external PPA. Otherwise the following error occurs on AMD64 architectures:

terminate called after throwing an instance of 'CGAL::Assertion_exception'
what():  CGAL ERROR: assertion violation!
Expr: -CGAL_IA_MUL(-1.1, 10.1) != CGAL_IA_MUL(1.1, 10.1)
File: /usr/include/CGAL/Interval_nt.h
Line: 209
Explanation: Wrong rounding: did you forget the  -frounding-math  option if you use GCC (or  -fp-model strict  for Intel)?
Aborted


### Compilation¶

You should create a separate build-place-folder, where Yade will be configured and where the source code will be compiled. Here is an example for a folder structure:

myYade/                 ## base directory
trunk/          ## folder for source code in which you use git
build/          ## folder in which the sources will be compiled; build-directory; use cmake here
install/        ## install folder; contains the executables


Then, inside this build-directory you should call cmake to configure the compilation process:

cmake -DCMAKE_INSTALL_PREFIX=/path/to/installfolder /path/to/sources


For the folder structure given above call the following command in the folder “build”:

cmake -DCMAKE_INSTALL_PREFIX=../install ../trunk


Additional options can be configured in the same line with the following syntax:

cmake -DOPTION1=VALUE1 -DOPTION2=VALUE2


As of Yade version git-2315bd8 (or 2018.02b release), the following options are available: (see the source code for a most up-to-date list)

• CMAKE_INSTALL_PREFIX: path where Yade should be installed (/usr/local by default)
• LIBRARY_OUTPUT_PATH: path to install libraries (lib by default)
• DEBUG: compile in debug-mode (OFF by default)
• ENABLE_LOGGER: use boost::log library for logging separately for each class (ON by default)
• MAX_LOG_LEVEL: set maximum level for LOG_* macros compiled with ENABLE_LOGGER, (default is 5)
• ENABLE_USEFUL_ERRORS: enable useful compiler errors which help a lot in error-free development.
• CMAKE_VERBOSE_MAKEFILE: output additional information during compiling (OFF by default)
• SUFFIX: suffix, added after binary-names (version number by default)
• NOSUFFIX: do not add a suffix after binary-name (OFF by default)
• YADE_VERSION: explicitly set version number (is defined from git-directory by default)
• ENABLE_GUI: enable GUI option (ON by default)
• ENABLE_CGAL: enable CGAL option (ON by default)
• ENABLE_VTK: enable VTK-export option (ON by default)
• ENABLE_OPENMP: enable OpenMP-parallelizing option (ON by default)
• ENABLE_MPI: Enable MPI enviroment and communication, required distributed memory and for Yade-OpenFOAM coupling (ON by default)
• ENABLE_GTS: enable GTS-option (ON by default)
• ENABLE_GL2PS: enable GL2PS-option (ON by default)
• ENABLE_LINSOLV: enable LINSOLV-option (ON by default)
• ENABLE_PFVFLOW: enable PFVFLOW-option, FlowEngine (ON by default)
• ENABLE_TWOPHASEFLOW: enable TWOPHASEFLOW-option, TwoPhaseFlowEngine (ON by default)
• ENABLE_LBMFLOW: enable LBMFLOW-option, LBM_ENGINE (ON by default)
• ENABLE_SPH: enable SPH-option, Smoothed Particle Hydrodynamics (OFF by default)
• ENABLE_LIQMIGRATION: enable LIQMIGRATION-option, see [Mani2013] for details (OFF by default)
• ENABLE_PROFILING: enable profiling, e.g., shows some more metrics, which can define bottlenecks of the code (OFF by default)
• ENABLE_POTENTIAL_BLOCKS: enable potential blocks option (OFF by default)
• ENABLE_POTENTIAL_PARTICLES: enable potential particles option (OFF by default)
• ENABLE_DEFORM: enable constant volume deformation engine (OFF by default)
• ENABLE_OAR: generate a script for oar-based task scheduler (OFF by default)
• runtimePREFIX: used for packaging, when install directory is not the same as runtime directory (/usr/local by default)
• CHUNKSIZE: specifiy the chunk size if you want several sources to be compiled at once. Increases compilation speed but RAM-consumption during compilation as well (1 by default)
• VECTORIZE: enables vectorization and alignment in Eigen3 library, experimental (OFF by default)
• USE_QT5: use QT5 for GUI (ON by default)
• CHOLMOD_GPU link Yade to custom SuiteSparse installation and activate GPU accelerated PFV (OFF by default)
• PYTHON_VERSION: force python version to the given one, set -1 to automatically use the last version on the system (-1 by default)

For using more extended parameters of cmake, please follow the corresponding documentation on https://cmake.org/documentation.

Warning

To provide Qt4→Qt5 migration one needs to provide an additional option USE_QT5. This option is ON by default but should be set according to the Qt version which was used to compile libQGLViewer. On Debian/Ubuntu operating systems libQGLViewer of version 2.6.3 and higher are compiled against Qt5 (for other operating systems refer to the package archive of your distribution), so if you are using such version, please switch this option ON. Otherwise, if you mix Qt-versions a Segmentation fault will appear just after Yade is started. To provide necessary build dependencies for Qt5, install python-pyqt5 pyqt5-dev-tools instead of python-qt4 pyqt4-dev-tools.

If cmake finishes without errors, you will see all enabled and disabled options at the end. Then start the actual compilation process with:

make


The compilation process can take a considerable amount of time, be patient. If you are using a multi-core systems you can use the parameter -j to speed-up the compilation and split the compilation onto many cores. For example, on 4-core machines it would be reasonable to set the parameter -j4. Note, Yade requires approximately 3GB RAM per core for compilation, otherwise the swap-file will be used and compilation time dramatically increases.

The installation is performed with the following command:

make install


The install command will in fact also recompile if source files have been modified. Hence there is no absolute need to type the two commands separately. You may receive make errors if you don’t have permission to write into the target folder. These errors are not critical but without writing permissions Yade won’t be installed in /usr/local/bin/.

After the compilation finished successfully, the new built can be started by navigating to /path/to/installfolder/bin and calling yade via (based on version yade-2014-02-20.git-a7048f4):

cd /path/to/installfolder/bin


For building the documentation you should at first execute the command make install and then make doc to build it. The generated files will be stored in your current install directory /path/to/installfolder/share/doc/yade-your-version. Once again writing permissions are necessary for installing into /usr/local/share/doc/. To open your local documentation go into the folder html and open the file index.html with a browser.

make manpage command generates and moves manpages in a standard place. make check command executes standard test to check the functionality of the compiled program.

Yade can be compiled not only by GCC-compiler, but also by CLANG front-end for the LLVM compiler. For that you set the environment variables CC and CXX upon detecting the C and C++ compiler to use:

export CC=/usr/bin/clang
export CXX=/usr/bin/clang++
cmake -DOPTION1=VALUE1 -DOPTION2=VALUE2


Clang does not support OpenMP-parallelizing for the moment, that is why the feature will be disabled.

### Supported linux releases¶

Currently supported [1] linux releases and their respective docker files are:

These are the bash commands used to prepare the linux distribution and environment for installing and testing yade. These instructions are automatically performed using the gitlab continuous integration service after each merge to master. This makes sure that yade always works correctly on these linux distributions. In fact yade can be installed manually by following step by step these instructions in following order:

1. Bash commands in the respective Dockerfile to install necessary packages,
2. do git clone https://gitlab.com/yade-dev/trunk.git,
3. then the cmake_* commands in the .gitlab-ci.yml file for respective distribution,
4. then the make_* commands to compile yade,
5. and finally the --check and --test commands.
6. Optionally documentation can be built with make doc command, however currently it is not guaranteed to work on all linux distributions due to frequent interface changes in sphinx.

These instructions use ccache and ld.gold to speed-up compilation as described below.

 [1] To see details of the latest build log click on the master branch.

### Python 2 backward compatibility¶

Python 2 support ends at the beginning of 2020. However, Yade can be compiled and used with python 2:

• On Ubuntu 18.04, 18.10, Debian 9, 10 and their derivatives install the python 2 version of the packages (and other required packages):

sudo apt install cmake git freeglut3-dev libloki-dev libboost-all-dev fakeroot \
dpkg-dev build-essential g++ python-dev ipython python-matplotlib python-mpi4py \
libsqlite3-dev python-numpy python-tk gnuplot libgts-dev python-pygraphviz \
libvtk6-dev python-numpy libeigen3-dev python-xlib python-pyqt5 pyqt5-dev-tools \
python-pyqt5.qtwebkit gtk2-engines-pixbuf python-argparse python-pyqt5.qtsvg \
libqglviewer-dev-qt5 python-pil libjs-jquery python-sphinx python-git python-bibtex \
libxmu-dev libxi-dev libcgal-dev help2man libbz2-dev zlib1g-dev python-minieigen \
libopenblas-dev libsuitesparse-dev libmetis-dev libopenmpi-dev openmpi-bin \
openmpi-common python-bibtexparser python3-future python-future python-gts \
coinor-clp coinor-libclp-dev

• For Ubuntu 16.04 libqglviewer-dev-qt5 is to be replaced by libqglviewer-dev, python-pil is to be replaced by python-imaging.

• force python 2 in the cmake command line: cmake -DPYTHON_VERSION=2 -DCMAKE_INSTALL_PREFIX=../install ../trunk

Note that the cmake PYTHON_VERSION option can be set to force any python version, for example -DPYTHON_VERSION=3.5 is valid.

Also see notes about converting python 2 scripts into python 3.

## Speed-up compilation¶

### Compile time¶

When spliting the compilation on many cores (make -jN), N is limited by the available cores and memory. It is possible to use more cores if remote computers are available, distributing the compilation with distcc (see distcc documentation for configuring slaves and master):

export CC="distcc gcc"
export CXX="distcc g++"
cmake [options as usual]
make -jN


In addition, and independently of distcc, caching previous compilations with ccache can speed up re-compilation:

export CC="ccache gcc"
export CXX="ccache g++"
cmake [options as usual]


The two tools can be combined very simply, adding to the above exports:

export CCACHE_PREFIX="distcc"


## Cloud Computing¶

It is possible to exploit cloud computing services to run Yade. The combo Yade/Amazon Web Service has been found to work well, namely. Detailed instructions for migrating to amazon can be found in the section Using YADE with cloud computing on Amazon EC2.

## GPU Acceleration¶

The FlowEngine can be accelerated with CHOLMOD’s GPU accelerated solver. The specific hardware and software requirements are outlined in the section Accelerating Yade’s FlowEngine with GPU.

## Yubuntu¶

If you are not running a Linux system there is a way to create an Ubuntu live-usb on any usb mass-storage device (minimum size 10GB). It is a way to boot the computer on a linux system with Yadedaily pre-installed without affecting the original system. More informations about this alternative are available here (see the README file first).

Alternatively, images of a linux virtual machine can be downloaded, here again, and they should run on any system with a virtualization software (tested with VirtualBox and VMWare).