NESO-Tokamak

A NESO-based solver for modelling MAST-U.

Building

The easiest way to build the app is to use the Spack package manager. The build process has been tested with Spack v0.24.0; later versions may also work, but aren't recommended.

Install Spack v0.24.0, via the official instructions.

On Debian-based systems (e.g. Ubuntu) the following should work:

git clone -b releases/v0.23 --single-branch https://github.com/spack/spack.git

# Initialise spack
export SPACK_ROOT=$HOME/.spack
source $SPACK_ROOT/share/spack/setup-env.sh

# Optionally modify .bashrc such that spack is always initialised in new shells
echo 'export SPACK_ROOT=$HOME/.spack' >> $HOME/.bashrc
echo 'source $SPACK_ROOT/share/spack/setup-env.sh' >> $HOME/.bashrc

Install intel compilers

spack install intel-oneapi-compilers
spack compiler add `spack location -i intel-oneapi-compilers`/compiler/latest/bin

Or if they are already installed elsewhere and version < 2024, add them

spack compiler add `spack location -i intel-oneapi-compilers`/compiler/latest/linux/bin/intel64
spack compiler add `spack location -i intel-oneapi-compilers`/compiler/latest/linux/bin

Build and clone NESO-Tokamak:

cd ..
git clone https://github.com/ExCALIBUR-NEPTUNE/NESO-Tokamak.git
cd NESO-Tokamak
git submodule update --init --recursive
spack env activate ./spack -p
spack install

N.B.

spack install -j <nproc>

can be used to speed up compilation

Note that some of the dependencies (particularly nektar++) can take some time to install and have high memory usage.

Running examples

Configuration files for 2D and 3D examples can be found in the ./examples directory. An easy way to run the examples is (from the top level of the repository):

# Load the mpich spack module
spack load mpich
# Set up and run an example via the helper script
./scripts/run_eg.sh [example_name] [example_dimension]

• This will copy ./examples/[example_name]/[example_dimension] to ./runs/[example_name]/[example_dimension] and run the solver in that directory with 4 MPI processes by default.
• To run with a different number of MPI processes, use <-n num_MPI>
• The solver executable is assumed to be in the most recently modified spack-build* directory. To choose a different build location, use <-b build_dir_path>.

To change the number of openMP threads used by each process, use

# Run an example with OMP and MPI
OMP_NUM_THREADS=[nthreads] ./scripts/run_eg.sh [example_name]

Postprocessing

• Particle output is generated in an hdf5 file. See particle_velhist.py for an example of reading and postprocessing (requires these packages).
• Fluid output is generated as nektar++ checkpoint files. One way to visualise is them is to convert to .vtu using Nektar's FieldConvert tool and then use Paraview:

# Convert to vtu using FieldConvert (requires xml files as args)
cd runs/[example_name]/[example_dimension]
spack load nektar
FieldConvert [config_xml] [mesh_xml] [chk_name] [vtu_name]
# e.g. FieldConvert single_field.xml mastu.xml single_field_100.chk single_field.vtu