Installation

The easiest way to build the PENKNIFE is to use the Spack package manager. The build process has been tested with Spack v1.2.0.dev0; later versions may also work, earlier than v1.0.0 is not recommended.

Get Spack

Install Spack via the official instructions. On Debian-based systems (e.g. Ubuntu) the following should work:

git clone --depth=2 https://github.com/spack/spack.git

Initialise Spack

source $SPACK_ROOT/share/spack/setup-env.sh
# Optionally modify .bashrc such that spack is always initialised in new shells (this only has to be done once)
echo 'source $SPACK_ROOT/share/spack/setup-env.sh' >> $HOME/.bashrc

Install intel compilers

Only required for the oneapi build

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

N.B. There is a known problem/conflict with the mkl libraries if the compilers come from the oneapi toolkit - it is recommended not to use this

Get PENKNIFE

cd ..
git clone https://github.com/ExCALIBUR-NEPTUNE/PENKNIFE.git
cd PENKNIFE
git submodule update --init --recursive
source ./scripts/activate.sh
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.

To leave the spack environment at any point run:

deactivate

Running a simulation

To run an example simulation, use the provided scripts

# Set up and run an example via the helper script
./scripts/run_eg.sh [EquationSystem] [Mesh] [Dimension] [Example] <-n num_MPI>
# e.g. ./scripts/run_eg.sh SingleField MASTU 2D CG -n 16

The script has an autocomplete option; use the TAB key to see the available options at each level.