Execution with Quickrun

The planning and preparation of a campaign of alchemical simulations using the openfe package is intended to be achievable on a local workstation in a matter of minutes. The execution of these simulations however requires a large amount of computational power, and beyond running single calculations locally, is intended to be distributed across a HPC environment. Doing this requires storing and sending the details of the simulation from the local workstation to a HPC environment, this can be done via the Transformation.dump() function which creates a saved “json” version of the data. These serialised “json” files are the currency of executing a campaign of simulations, and contain all the information required to execute a single simulation.

To read this information and execute the simulation, the command line interface provides a quickrun command, the full details of which are given in the CLI reference section. Briefly, this command takes a “json” simulation as an input and will then execute the simulation contained within, therefore this command would execute a simulation saved to a file called “transformation.json”.

openfe quickrun transformation.json -o results.json

Which will produce a results file called results.json.

Executing within a job submission script

It is likely that computational jobs will be submitted to a queueing engine, such as slurm. The quickrun command can be integrated into as:

#!/bin/bash

#SBATCH --job-name="openfe job"
#SBATCH --mem-per-cpu=2G

# activate an appropriate conda environment, or any "module load" commands required to
conda activate openfe_env

openfe quickrun transformation.json -o results.json

See Also

For details on inspecting these results, refer to Working with Results.