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CPL/OpenFOAM+LAMMPS containers with apptainer

Note

Install dependencies, if you do not already have them

  • Ansible
sudo apt update
sudo apt install software-properties-common
sudo add-apt-repository --yes --update ppa:ansible/ansible
sudo apt install ansible
  • Apptainer
sudo apt install -y wget
cd /tmp
wget https://github.com/apptainer/apptainer/releases/download/v1.3.4/apptainer_1.3.4_amd64.deb
sudo apt install -y ./apptainer_1.3.4_amd64.deb

Note

The CPL/OpenFOAM/LAMMPS container is set-up in way that favours continuous development. So, you can compile the socket and any solvers into your repo (check lib and bin folders after running the wmake commands bellow). This way, you can retain the binaries between separate runs of the container, which is the preferred way (compared to interactive shells inside the container) for reproducibility reasons.

If you want to alter the container itself in any way, create an overlay image and load it:

apptainer overlay create -s 1024 overlay.img #<- 1GB overlay image

Syntax to run a container with overlay image:

apptainer run --sharens --overlay overlay.img path/to/cpl-openfoam-lammps*.sif

Now to use the container via 2 methods

  • Build the container locally:
    1. Building the container
    git clone https://github.com/FoamScience/openfoam-apptainer-packaging /tmp/tainers
git clone https://github.com/FoamScience/cpl-openfoam-containers
cd cpl-openfoam-containers
ansible-playbook /tmp/tainers/build.yaml --extra-vars "original_dir=$PWD" --extra-vars "@config.yaml"
# Now a container is made in ./containers/projects/
    1. Run the source enter_container.sh script
    2. Type run_cpl, then press tab
    3. Type the location of the overlay image, if it is outside the repo path
    4. Press enter
  • Pull the container
# change to the repo directory
# Get the container
apptainer pull cpl-openfoam-lammps-2112-fcbc37d5a40e6dbd91148921378d28fca5294675-8.2.0.sif oras://ghcr.io/foamscience/cpl-openfoam-lammps-2112-fcbc37d5a40e6dbd91148921378d28fca5294675-8.2.0:latest

# enter the container
apptainer run --hostname cpl --sharens cpl-openfoam-lammps-2112-fcbc37d5a40e6dbd91148921378d28fca5294675-8.2.0.sif
# get cpl oF socket
git clone https://github.com/Crompulence/CPL_APP_OPENFOAM
cd CPL_APP_OPENFOAM
# modify Pstream includes since OpenFOAM is patched ON THE CONTAINER
# this will not affect openFOAM in host
find . -name options -exec sed -i 's;$(FOAM_CPL_APP_SRC)/CPLPstream/lnInclude;$(LIB_SRC)/Pstream/mpi/lnInclude;' {} \;

# make CPL APP
source SOURCEME.sh; wmake src/CPLSocketFOAM
source SOURCEME.sh; wmake src/solvers/CPLTestFoam
source SOURCEME.sh; cd examples/CPLTestFoam && ./run.sh
# (You will have to make adjustments to Makefile if you want to compile with make)

Post process can be done on the host machine (outside of the container). Or, add processing tools to projects/cpl-openfoam-lammps.def and rebuild the container.