How to run a single simulation

For running the binary directly and seeing every intermediate file, see Your first simulation. This page is the shortcuts for doing it routinely.

Locally (blocks your terminal — use fidelity 3–4 only)

make run PARAMS=runs/my_run/params.json

Equivalent to cd runs/my_run && ../../build/BioReactor params.json, with one difference worth knowing: make run depends on build/BioReactor and will rebuild it first if the source is stale.

Via SLURM (non-blocking — production)

make submit PARAMS=runs/my_run/params.json

Or, with Python — which also waits for results.json and returns it:

uv run python scripts/simulate.py runs/my_run/params.json --slurm --wait --walltime 04:00:00

Preview the sbatch command without submitting anything:

make submit PARAMS=runs/my_run/params.json DRYRUN=1

Set up the run directory without running or submitting anything

launch.py writes params.json and a SLURM script into the run directory and stops there:

python scripts/launch.py path/to/params.json [runs_root]
# returns {"run_id": "...", "run_dir": "...", "slurm_script": "..."}

Useful when you want to inspect or hand-edit the generated SLURM script before it runs.