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, HDF5, 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 https://github.com/boutproject/BOUT-dev. You can the latest stable version from https://github.com/boutproject/BOUT-dev/releases. 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 git://github.com/boutproject/BOUT-dev.git

which will create a directory BOUT-dev containing the code. 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++11
  2. An MPI compiler such as OpenMPI (www.open-mpi.org/), MPICH ( https://www.mpich.org/) or LAM (www.lam-mpi.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

Only GCC versions >= 4.9 are supported. This is due to a bug in previous versions.

Note

If you use an Intel compiler, you must also make sure that you have a version of GCC that supports C++11 (GCC 4.8+).

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 MPICH2 and the needed libraries by running:

$ sudo apt-get install mpich2 libmpich2-dev
$ sudo apt-get install libfftw3-dev libnetcdf-dev libnetcdf-cxx-legacy-dev

On Ubuntu 16.04:

$ sudo apt-get libmpich-dev libfftw3-dev libnetcdf-dev libnetcdf-cxx-legacy-dev

On Ubuntu 18.04:

$ sudo apt-get install mpich libmpich-dev libfftw3-dev libnetcdf-dev libnetcdf-cxx-legacy-dev git g++ make
$ sudo apt-get install python3 python3-distutils python3-pip python3-numpy python3-netcdf4 python3-scipy
$ pip3 install --user Cython

The first line should be sufficient to install BOUT++, while the 2nd and 3rd line make sure that the tests work, and that the python interface can be build. 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 sections on installing MPI, installing FFTW and installing NetCDF.

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++

To compile BOUT++, you first need to configure it. Go into the BOUT-dev directory and run:

$ ./configure

If this finishes by printing a summary, and paths for IDL, Python, and Octave, then the libraries are set up and you can skip to the next section. If you see a message “ERROR: FFTW not found. Required by BOUT++” then make sure FFTW-3 is installed (See the previous section on installing dependencies ).

If FFTW-3 is installed in a non-standard location, you can specify the directory with the –with-fftw= option e.g:

$ ./configure --with-fftw=$HOME/local

Configure should now find FFTW, and search for the NetCDF library. If configure finishes successfully, then skip to the next section, but if you see a message NetCDF support disabled then configure couldn’t find the NetCDF library. Unless you have another file format (like HDF5) installed, this will be followed by a message ERROR: At least one file format must be supported. Check that you have NetCDF installed (See the previous section on installing dependencies ).

Like the FFTW-3 library, if NetCDF is installed in a non-standard location then you can specify the directory with the --with-netcdf= option e.g.:

$ ./configure --with-fftw=$HOME/local --with-netcdf=$HOME/local

which should now finish successfully, printing a summary of the configuration:

Configuration summary
  PETSc support: no
  SLEPc support: no
  IDA support: yes
  CVODE support: yes
  ARKODE support: yes
  NetCDF support: yes
  Parallel-NetCDF support: no
  HDF5 support: yes (parallel: no)
  MUMPS support: no

If not, see Advanced installation options for some things you can try to resolve common problems.

CMake

There is now (experimental) support for CMake. You will need CMake > 3.9. CMake supports out-of-source builds by default, which are A Good Idea. Basic configuration with CMake looks like:

$ mkdir build && cd build
$ cmake ..

You can then run make as usual.

You can see what build options are available with:

$ cmake .. -LH
...
// Enable backtrace
ENABLE_BACKTRACE:BOOL=ON

// Output coloring
ENABLE_COLOR:BOOL=ON

// Enable OpenMP support
ENABLE_OPENMP:BOOL=OFF

// Enable support for PETSc time solvers and inversions
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). 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 .. \
    -DUSE_PETSC=ON -DPETSC_DIR=/path/to/petsc/ \
    -DUSE_SLEPC=ON -DSLEPC_DIR=/path/to/slepc/ \
    -DUSE_SUNDIALS=ON -DSUNDIALS_ROOT=/path/to/sundials \
    -DUSE_NETCDF=ON -DNetCDF_ROOT=/path/to/netcdf \
    -DENABLE_OPENMP=ON \
    -DENABLE_SIGFPE=OFF \
    -DCMAKE_BUILD_TYPE=Debug \
    -DBUILD_SHARED_LIBS=ON
    -DCMAKE_INSTALL_PREFIX=/path/to/install/BOUT++

You can write a CMake configuration file (CMakeLists.txt) for your physics model in only four lines:

project(blob2d LANGUAGES CXX)
find_package(bout++ REQUIRED)
add_executable(blob2d blob2d.cxx)
target_link_libraries(blob2d PRIVATE bout++::bout++)

You just need to give CMake the location where you installed BOUT++ via the CMAKE_PREFIX_PATH variable:

$ mkdir build && cd build
$ cmake .. -DCMAKE_PREFIX_PATH=/path/to/install/BOUT++

Natural Language Support

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

./configure --localedir=$PWD/locale

This will enable BOUT++ to find the translations. When configure finishes, the configuration summary should contain a line like:

configure:   Natural language support: yes (path: /home/user/BOUT-dev/locale)

where the path is the directory containing 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 NumPy and SciPy libraries. On Debian or Ubuntu these can be installed with:

$ sudo apt-get install python-scipy

which should then add all the other dependencies like NumPy. To test if everything is installed, run:

$ python -c "import scipy"

If not, see the SciPy website https://www.scipy.org for instructions on installing.

To do this, the path to tools/pylib should be added to the PYTHONPATH environment variable. 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.

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 (same as configure) and running:

$ make

(on OS-X, FreeBSD, and AIX this should be gmake). This should print something like:

----- Compiling BOUT++ -----
CXX      =  mpicxx
CFLAGS   =  -O -DCHECK=2 -DSIGHANDLE \
 -DREVISION=13571f760cec446d907e1bbeb1d7a3b1c6e0212a \
 -DNCDF -DBOUT_HAS_PVODE
CHECKSUM =  ff3fb702b13acc092613cfce3869b875
INCLUDE  =  -I../include
  Compiling  field.cxx
  Compiling  field2d.cxx

At the end of this, you should see a file libbout++.a in the lib/ subdirectory of the BOUT++ distribution. 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 make.config file in the BOUT++ root 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:

$ make check

from the top-level directory. Alternatively, if you just want to run one them individually, you can do:

$ make check-unit-tests
$ make check-integrated-tests
$ make check-mms-tests

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

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

  • Which machine you’re running on
  • The make.config file in the BOUT++ root 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 make 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++.a The main BOUT++ library
  • /usr/local/lib/libpvode.a and /usr/local/lib/libpvpre.a, the PVODE library
  • /usr/local/share/bout++/pylib/... Python analysis routines
  • /usr/local/share/bout++/idllib/... IDL analysis routines
  • /usr/local/share/bout++/make.config A makefile configuration, used to compile many BOUT++ examples

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

$ make install prefix=$HOME/local/

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

$ ./configure --prefix=$HOME/local/
$ make
$ make install

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

  • --bindir= sets where bout-config will be installed ( default /usr/local/bin)
  • --includedir= sets where the bout++/*.hxx header files wil be installed (default /usr/local/include)
  • --libdir= sets where the libbout++.a, libpvode.a and libpvpre.a libraries are installed (default /usr/local/lib)
  • --datadir= sets where idllib, pylib and make.config are installed (default /usr/local/share/)

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.