docker.rst

Docker image

The published Docker image includes ARC and RMG along with convenience entrypoints. Bind-mount your working directory and pass an input file path that exists inside the container. For best write access on bind mounts, pass your host UID/GID as PUID/PGID (the entrypoint remaps the mambauser account).

Run ARC non-interactively:

docker run --rm \
    -v "$PWD:/work" -w /work \
    -e PUID=$(id -u) -e PGID=$(id -g) \
    laxzal/arc:latest arc my_case/input.yml

Run RMG non-interactively:

docker run --rm \
    -v "$PWD:/work" -w /work \
    -e PUID=$(id -u) -e PGID=$(id -g) \
    laxzal/arc:latest rmg my_case/input.py

Manual RMG invocation:

docker run --rm \
    -v "$PWD:/work" -w /work \
    -e PUID=$(id -u) -e PGID=$(id -g) \
    laxzal/arc:latest \
    micromamba run -n rmg_env python /home/mambauser/Code/RMG-Py/rmg.py my_case/input.py

Manual ARC invocation:

docker run --rm \
    -v "$PWD:/work" -w /work \
    -e PUID=$(id -u) -e PGID=$(id -g) \
    laxzal/arc:latest \
    micromamba run -n arc_env python /home/mambauser/Code/ARC/ARC.py my_case/input.yml

Open an interactive shell:

docker run --rm -it \
    -v "$PWD:/work" -w /work \
    -e PUID=$(id -u) -e PGID=$(id -g) \
    laxzal/arc:latest

For job submission, the scheduler client tools must be available in the container or accessed via SSH on a remote host.

Aliases in interactive shells

When you open an interactive shell, the image provides these aliases:

rc              # reload ~/.bashrc
rce, erc        # edit ~/.bashrc with nano

mamba, conda    # micromamba
deact           # micromamba deactivate

rmge, arce      # activate rmg_env / arc_env

rmgcode         # cd to /home/mambauser/Code/RMG-Py
dbcode          # cd to /home/mambauser/Code/RMG-database
arcode          # cd to /home/mambauser/Code/ARC

rmg             # run RMG with input.py, tee logs
arkane          # run Arkane with input.py, tee logs
arc             # run ARC with input.yml, tee logs
arcrestart      # run ARC with restart.yml, tee logs