README.md

Apptainer containers

Containers for working with Apptainer or Singularity

Prerequisites

The container build requires apptainer and mksquashfs.

If not centrally available apptainer and mksquashfs can be installed using conda, e.g.

conda create -n apptainer apptainer squashfuse

export APPTAINER="conda run -n apptainer apptainer"
export MKSQUASHFS="conda run -n apptainer mksquashfs"

Building containers

A container can be built with

# Configure where environments are installed
export NGMOENVS_BASEDIR=~/ngmo-envs

# Configure the compiler and MPI to use
export NGMOENVS_COMPILER=gcc
export NGMOENVS_MPI=openmpi@4

# Install an environment
./site/apptainer/install.sh lfric

Building some packages will require passwordless access to MOSRS which will need to be set up separately.

Using container environments

Make sure the container environment's bin/ directory is on your PATH:

export PATH=${NGMOENVS_BASEDIR}/envs/lfric/bin:$PATH

Run commands inside the container using the envrun script. If you build an executable inside the container you must also run it inside the container.

envrun make
envrun mpirun -n 6 lfric

Using Host MPI

TODO