Getting started#

This section goes through the process of getting, installing, and starting to run BOUT++.

The quickest way to get started is to use a pre-built binary. These take care of all dependencies, configuration and compilation. See section Docker image.

The remainder of this section will go through the following steps to manually install BOUT++. Only the basic functionality needed to use BOUT++ is described here; the next section (Advanced installation options) goes through more advanced options, configurations for particular machines, and how to fix some common problems.

  1. Obtaining a copy of BOUT++

  2. Installing dependencies

  3. Configuring BOUT++

  4. Configuring BOUT++ analysis codes

    1. Python

    2. IDL

  5. Compiling BOUT++

  6. Running the test suite

  7. Installing BOUT++ (experimental)

Note: In this manual commands to run in a BASH shell will begin with ’$’, and commands specific to CSH with a ’%’.

Pre-built binaries#

Docker image#

Docker is a widely used container system, which packages together the operating system environment, libraries and other dependencies into an image. This image can be downloaded and run reproducibly on a wide range of hosts, including Windows, Linux and OS X. Here is the starting page for instructions on installing Docker.

The BOUT++ docker images are hosted on dockerhub for some releases and snapshots. Check the list of BOUT-next tags if you want a recent version of BOUT++ “next” (development) branch. First download the image:

$ sudo docker pull boutproject/boutproject/bout-next:9f4c663-petsc

then run:

$ sudo docker run --rm -it boutproject/bout-next:9f4c663-petsc

This should give a terminal in a “boutuser” home directory, in which there is “BOUT-next”, containing BOUT++ configured and compiled with NetCDF, SUNDIALS, PETSc and SLEPc. Python 3 is also installed, with ipython, NumPy, Scipy and Matplotlib libaries. To plot to screen an X11 display is needed. Alternatively a shared directory can be created to pass files between the docker image and host. The following commands both enable X11 and create a shared directory:

$ mkdir shared
$ sudo docker run --rm -it \
   -e DISPLAY -v $HOME/.Xauthority:/home/boutuser/.Xauthority --net=host \
   -v $PWD/shared:/home/boutuser/bout-img-shared \
   boutproject/bout-next:9f4c663-petsc

This should enable plotting from python, and files in the docker image put in “/home/boutuser/bout-img-shared” should be visible on the host in the “shared” directory.

If this is successful, then you can skip to section Running BOUT++.

Obtaining BOUT++#

BOUT++ is hosted publicly on github at boutproject/BOUT-dev. You can the latest stable version from boutproject/BOUT-dev. If you want to develop BOUT++, you should use git to clone the repository. To obtain a copy of the latest version, run:

$ git clone https://github.com/boutproject/BOUT-dev.git

which will create a directory BOUT-dev containing the code:

$ cd BOUT-dev

To get the latest changes later, go into the BOUT-dev directory and run:

$ git pull

Development is done on the “next” branch, which you can checkout with:

$ git checkout next

Installing dependencies#

The bare-minimum requirements for compiling and running BOUT++ are:

  1. A C++ compiler that supports C++17

  2. An MPI compiler such as OpenMPI (www.open-mpi.org/), MPICH ( https://www.mpich.org/)

  3. The NetCDF library (https://www.unidata.ucar.edu/downloads/netcdf)

The FFTW-3 library (http://www.fftw.org/) is also strongly recommended. Fourier transforms are used for some derivative methods, as well as the ShiftedMetric parallel transform which is used in the majority of BOUT++ tokamak simulations. Without FFTW-3, these options will not be available.

Note

If you use an Intel compiler, you must also make sure that you have a version of GCC that supports C++17 (GCC 8+).

On supercomputers, or in other environments that use a module system, you may need to load modules for both Intel and GCC.

On a cluster or supercomputer#

If you are installing on a cluster or supercomputer then the MPI C++ compilers will already be installed, and on Cray or IBM machines will probably be called CC and xlC respectively.

On large facilities (e.g NERSC or Archer), the compilers and libraries needed should already be installed, but you may need to load them to use them. It is common to organise libraries using the modules system, so try typing:

modules avail

to get a list of available modules. Some instructions for specific machines can be found in Machine-specific installation. See your system’s documentation on modules and which ones to load. If you don’t know, or modules don’t work, you can still install libraries in your home directory by following the instructions below for FFTW and NetCDF.

Ubuntu / Debian#

On Ubuntu or Debian distributions if you have administrator rights then you can install the basic dependencies with:

$ sudo apt-get install libmpich-dev libfftw3-dev libnetcdf-c++4-dev git make

To additionally build the Python interface, you need some Python packages:

$ sudo apt-get install python3 python3-distutils python3-pip python3-numpy python3-netcdf4 python3-scipy
$ pip3 install --user Cython

Further, the encoding for python needs to be utf8 - it may be required to set export LC_CTYPE=C.utf8.

If you do not have administrator rights, so can’t install packages, then you need to install these libraries from source into your home directory. See Advanced installation options for details on installing some of these.

Arch Linux#

$ pacman -S openmpi fftw netcdf-cxx make gcc

Fedora#

On Fedora the required libraries can be installed by running:

$ sudo dnf build-dep bout++

This will install all the dependencies that are used to install BOUT++ for fedora. Feel free to install only a subset of the suggested packages. For example, only mpich or openmpi is required. To load an mpi implementation type:

$ module load mpi

After that the mpi library is loaded. Precompiled binaries are available for fedora as well. To get precompiled BOUT++ run:

$ # install the mpich version - openmpi is available as well
$ sudo dnf install bout++-mpich-devel
$ # get the python3 modules - python2 is available as well
$ sudo dnf install python3-bout++

Configuring BOUT++#

BOUT++ uses the CMake build system generator. You will need CMake >= 3.17.

Note

It is possible to get the latest version of CMake using pip:

$ pip install --user --upgrade cmake

or conda:

$ conda install cmake

You may need to put ~/.local/bin in your $PATH

CMake supports out-of-source builds by default, which are A Good Idea. Basic configuration with CMake looks like:

$ cmake -S . -B build

which creates a new directory build. You can call this directory anything you like, and you also put it anywhere you like, you just need to specify the path to the BOUT++ source directory with the -S argument. This makes it very easy to keep two build directories alongside one another, one with a debug build and one optimised, for example.

After configuring the build directory, you can then compile BOUT++ with:

# Build the library
$ cmake --build build
# Build the library with 8 threads
$ cmake --build build -j 8
# Build the "blob2d" example
$ cmake --build build --target blob2d

By default, CMake will use makefiles, and so it is possible to also build BOUT++ with make from the build directory – note that you must still run cmake once first to configure BOUT++:

$ cmake . -B build
$ cd build
$ make

Note

You might see some instructions in the documentation using make – they should be run from the build directory.

You can see what build options are available with:

$ cmake . -B build -LH
...
// Enable backtrace
BOUT_ENABLE_BACKTRACE:BOOL=ON

// Output coloring
BOUT_ENABLE_COLOR:BOOL=ON

// Enable OpenMP support
BOUT_ENABLE_OPENMP:BOOL=OFF

// Enable support for PETSc time solvers and inversions
BOUT_USE_PETSC:BOOL=OFF
...

CMake uses the -D<variable>=<choice> syntax to control these variables. You can set <package>_ROOT to guide CMake in finding the various optional third-party packages (except for PETSc/SLEPc, which use _DIR). Note that some packages have funny captialisation, for example NetCDF_ROOT! Use -LH to see the form that each package expects.

CMake understands the usual environment variables for setting the compiler, compiler/linking flags, as well as having built-in options to control them and things like static vs shared libraries, etc. See the CMake documentation for more infomation.

A more complicated CMake configuration command might look like:

$ CC=mpicc CXX=mpic++ cmake . -B build \
    -DBOUT_USE_PETSC=ON -DPETSC_DIR=/path/to/petsc/ \
    -DBOUT_USE_SLEPC=ON -DSLEPC_DIR=/path/to/slepc/ \
    -DBOUT_USE_SUNDIALS=ON -DSUNDIALS_ROOT=/path/to/sundials \
    -DBOUT_USE_NETCDF=ON -DNetCDF_ROOT=/path/to/netcdf \
    -DBOUT_ENABLE_OPENMP=ON \
    -DBOUT_ENABLE_SIGFPE=OFF \
    -DCMAKE_BUILD_TYPE=Debug \
    -DBUILD_SHARED_LIBS=ON
    -DCMAKE_INSTALL_PREFIX=/path/to/install/BOUT++

If you wish to change the configuration after having built BOUT++, it’s wise to delete the CMakeCache.txt file in the build directory. The equivalent of make distclean with CMake is to just delete the entire build directory and reconfigure.

If you need to debug a CMake build, you can see the compile and link commands which are being issued by adding --verbose to the build command:

$ cmake --build build --verbose

Common CMake Options#

The default build configuration options try to be sensible for new users and developers, but there are a few you probably want to set manually for production runs or for debugging:

  • CMAKE_BUILD_TYPE: The default is RelWithDebInfo, which builds an optimised executable with debug symbols included. Change this to Release to remove the debug symbols, or Debug for an unoptimised build, but better debug experience

  • CHECK: This sets the level of internal runtime checking done in the BOUT++ library, and ranges from 0 to 4 (inclusive). By default, this is 2, which aims to be a balance between useful checks and speed. Set this to 0 for faster production runs, and to 4 for more in-depth (and slower) checking.

  • BOUT_UPDATE_GIT_SUBMODULE: This is on by default, and ensures that the bundled git submodules are up-to-date. You should turn this off if you are using system versions, or if you run into problems updating the submodules.

  • NetCDF_ROOT: NetCDF is one of the few required, non-bundled dependencies. If CMake is having trouble finding netCDF, or the correct version, you should set this variable to the installed location of the netCDF C library.

  • BOUT_BUILD_EXAMPLES, BOUT_TESTS: These two options are particularly useful for developers of the BOUT++ library, and for new users. You can turn them off to save some time configuring the library. By default, these are on, but the examples and tests are not built unless you specifically ask for them, using the targets build-all-examples and build-check respectively.

Downloading Dependencies#

If you don’t have some dependencies installed, CMake can be used to download, configure and compile them alongside BOUT++.

For NetCDF, use -DBOUT_DOWNLOAD_NETCDF_CXX4=ON

For SUNDIALS, use -DBOUT_DOWNLOAD_SUNDIALS=ON. If using ccmake this option may not appear initially. This automatically sets BOUT_USE_SUNDIALS=ON, and configures SUNDIALS to use MPI.

For ADIOS2, use -DBOUT_DOWNLOAD_ADIOS2=ON. This will download and configure ADIOS2, enabling BOUT++ to read and write this high-performance parallel file format.

Bundled Dependencies#

BOUT++ bundles some dependencies, currently mpark.variant, fmt and googletest. If you wish to use an existing installation of mpark.variant, you can set -DBOUT_USE_SYSTEM_MPARK_VARIANT=ON, and supply the installation path using mpark_variant_ROOT via the command line or environment variable if it is installed in a non standard loction. Similarly for fmt, using -DBOUT_USE_SYSTEM_FMT=ON and fmt_ROOT respectively. To turn off both, you can set -DBOUT_USE_GIT_SUBMODULE=OFF.

The recommended way to use googletest is to compile it at the same time as your project, therefore there is no option to use an external installation for that.

Working with an active conda environment#

When conda is used, it installs separate versions of several libraries. These can cause warnings or even failures when linking BOUT++ executables. There are several alternatives to deal with this problem: * The simplest but least convenient option is to use conda deactivate before

configuring, compiling, or running any BOUT++ program.

  • You might sometimes want to link to the conda-installed libraries. This is probably not ideal for production runs on an HPC system (as conda downloads binary packages that will not be optimized for specific hardware), but can be a simple way to get packages for testing or on a personal computer. In this case just keep your conda environment active, and with luck the libraries should be picked up by the standard search mechanisms.

  • In case you do want a fully optimized and as-stable-as-possible build for production runs, it is probably best not to depend on any conda packages for compiling or running BOUT++ executables (restrict conda to providing Python packages for post-processing, and their dependencies). Passing -DBOUT_IGNORE_CONDA_ENV=ON (default OFF) excludes anything in the conda environment from CMake search paths. This should totally separate BOUT++ from the conda environment.

Natural Language Support#

BOUT++ has support for languages other than English, using GNU gettext. If you are planning on installing BOUT++ (see Installing BOUT++ (experimental)) then this should work automatically, but if you will be running BOUT++ from the directory you downloaded it into, then configure with the option:

cmake . -DCMAKE_INSTALL_LOCALEDIR=$PWD/locale

This will enable BOUT++ to find the translations.

See Natural language support for details of how to switch language when running BOUT++ simulations.

Configuring analysis routines#

The BOUT++ installation comes with a set of useful routines which can be used to prepare inputs and analyse outputs. Most of this code is now in Python, though IDL was used for many years. Python is useful In particular because the test suite scripts and examples use Python, so to run these you’ll need python configured.

When the configure script finishes, it prints out the paths you need to get IDL, Python, and Octave analysis routines working. If you just want to compile BOUT++ then you can skip to the next section, but make a note of what configure printed out.

Python configuration#

To use Python, you will need the dependencies of the boututils and boutdata libraries. The simplest way to get these is to install the packages with pip:

$ pip install --user boutdata

or conda:

$ conda install boutdata

You can also install all the packages directly (see the documentation in the boututils and boutdata repos for the most up to date list) using pip:

$ pip install --user numpy scipy matplotlib sympy netCDF4 future importlib-metadata

or conda:

$ conda install numpy scipy matplotlib sympy netcdf4 future importlib-metadata

They may also be available from your Linux system’s package manager.

For example on Fedora:

$ sudo dnf install python3-boututils python3-boutdata

To use the versions of boututils and boutdata provided by BOUT++, the path to tools/pylib should be added to the PYTHONPATH environment variable. This is not necessary if you have installed the boututils and boutdata packages. Instructions for doing this are printed at the end of the configure script, for example:

Make sure that the tools/pylib directory is in your PYTHONPATH
e.g. by adding to your ~/.bashrc file

   export PYTHONPATH=/home/ben/BOUT/tools/pylib/:$PYTHONPATH

To test if this command has worked, try running:

$ python -c "import boutdata"

If this doesn’t produce any error messages then Python is configured correctly.

Note that boututils and boutdata are provided by BOUT++ as submodules, so versions compatible with the checked out version of BOUT++ are downloaded into the externalpackages directory. These are the versions used by the tests run by make check even if you have installed boututils and boutdata on your system.

IDL configuration#

If you want to use IDL to analyse BOUT++ outputs, then the IDL_PATH environment variable should include the tools/idllib/ subdirectory included with BOUT++. The required command (for Bash) is printed at the end of the BOUT++ configuration:

$ export IDL_PATH=...

After running that command, check that idl can find the analysis routines by running:

$ idl
IDL> .r collect
IDL> help, /source

You should see the function COLLECT in the BOUT/tools/idllib directory. If not, something is wrong with your IDL_PATH variable. On some machines, modifying IDL_PATH causes problems, in which case you can try modifying the path inside IDL by running:

IDL> !path = !path + ":/path/to/BOUT-dev/tools/idllib"

where you should use the full path. You can get this by going to the tools/idllib directory and typing pwd. Once this is done you should be able to use collect and other routines.

Compiling BOUT++#

Once BOUT++ has been configured, you can compile the bulk of the code by going to the BOUT-dev directory and running:

$ cmake --build <build-directory>

where <build-directory> is the path to the build directory

At the end of this, you should see a file libbout++.so in the lib/ subdirectory of the BOUT++ build directory. If you get an error, please create an issue on Github including:

  • Which machine you’re compiling on

  • The output from make, including full error message

  • The CMakeCache.txt file in the BOUT++ build directory

Running the test suite#

BOUT++ comes with three sets of test suites: unit tests, integrated tests and method of manufactured solutions (MMS) tests. The easiest way to run all of them is to simply do:

$ cmake --build <build-directory> --target check

Alternatively, if you just want to run one set of them individually, you can do:

$ cmake --build <build-directory> --target check-unit-tests
$ cmake --build <build-directory> --target check-integrated-tests
$ cmake --build <build-directory> --target check-mms-tests

Note: The integrated and MMS test suites currently uses the mpirun command to launch the runs, so won’t work on machines which use a job submission system like slurm or PBS.

These tests should all pass, but if not please create an issue on Github containing:

  • Which machine you’re running on

  • The CMakeCache.txt file in the BOUT++ build directory

  • The run.log.* files in the directory of the test which failed

If the tests pass, congratulations! You have now got a working installation of BOUT++. Unless you want to use some experimental features of BOUT++, skip to section [sec-running] to start running the code.

Installing BOUT++ (experimental)#

Most BOUT++ users install and develop their own copies in their home directory, so do not need to install BOUT++ to a system directory. As of version 4.1 (August 2017), it is possible to install BOUT++ but this is not widely used and so should be considered experimental.

After configuring and compiling BOUT++ as above, BOUT++ can be installed to system directories by running as superuser or sudo:

$ sudo cmake --build <build-directory> --target install

Danger

Do not do this unless you know what you’re doing!

This will install the following files under /usr/local/:

  • /usr/local/bin/bout-config A script which can be used to query BOUT++ configuration and compile codes with BOUT++.

  • /usr/local/include/bout++/... header files for BOUT++

  • /usr/local/lib/libbout++.so The main BOUT++ library

  • /usr/local/lib/libpvode.so and /usr/local/lib/libpvpre.so, the PVODE library

  • /usr/local/share/bout++/pylib/... Python analysis routines

  • /usr/local/share/bout++/idllib/... IDL analysis routines

To install BOUT++ under a different directory, use the prefix= flag e.g. to install in your home directory:

$ cmake --build <build-directory> --target install -DCMAKE_INSTALL_PREFIX=$HOME/local/

You can also specify this prefix when configuring, in the usual way (see Configuring BOUT++):

$ cmake -S . -B <build-directory> -DCMAKE_INSTALL_PREFIX=$HOME/local/
$ cmake --build <build-directory> -j 4
$ cmake --build <build-directory> --target install

More control over where files are installed is possible by passing options to cmake, following the GNU conventions:

  • -DCMAKE_INSTALL_BINDIR= sets where bout-config will be installed ( default /usr/local/bin)

  • -DCMAKE_INSTALL_INCLUDEDIR= sets where the bout++/*.hxx header files wil be installed (default /usr/local/include)

  • -DCMAKE_INSTALL_LIBDIR= sets where the libbout++.so, libpvode.so and libpvpre.so libraries are installed (default /usr/local/lib)

After installing, that you can run bout-config e.g:

$ bout-config --all

which should print out the list of configuration settings which bout-config can provide. If this doesn’t work, check that the directory containing bout-config is in your PATH.

The python and IDL analysis scripts can be configured using bout-config rather than manually setting paths as in Configuring analysis routines. Add this line to your startup file (e.g. $HOME/.bashrc):

export PYTHONPATH=`bout-config --python`:$PYTHONPATH

note the back ticks around bout-config --python not quotes. Similarly for IDL:

export IDL_PATH=`bout-config --idl`:'<IDL_DEFAULT>':$IDL_PATH

More details on using bout-config are in the section on makefiles.