Usage

Running locally

larest <config.toml> -o <output_dir>

Argument	Description
config	Path to your config.toml (required)
-o / --output	Directory where all results are written (default: ./output)
-v / --verbose	Increase console log verbosity

Example — run the example config and write results to ./output:

larest config/example.config -o output/

Running on HPC (Imperial College PBS)

A PBS job script (pipeline.sh) is included for Imperial College’s HPC service. Edit the resource directives and the MODIFY ME block at the top of the file, then submit from the LaREST root directory:

qsub pipeline.sh

Key variables to configure in pipeline.sh:

Variable	Description
CONDA_DIR	Path to the directory containing your conda binary
CONDA_ENV	Conda environment name (default: larest)
N_CORES	Number of cores, matching the PBS ncpus directive

Checkpointing

LaREST automatically checkpoints after each pipeline stage. If a run is interrupted, re-running the same command resumes from the first incomplete stage — completed stages are not re-executed.

Checkpoint state is inferred from the presence of result files on disk; no separate checkpoint file is written. To force a full re-run, delete the relevant molecule directory under the output folder.