Example simulation

This is an example framework for splitting up large simulations in parallel across a HPC cluster

Setup

git clone https://github.com/MRCIEU/example-simulation-framework.git

Explanation

• dgm.r - This has the functions to take a set of parameters and generate the data

• test.r - This reads in the functions in dgm.r and just checks that it's doing what it should

• params.r - this is gonna have all the parameters that are to be passed to dgm.r for the main simulation, writing the parameters to a csv. It also has batch column, which determins how to split up all the simulations for each run.

• run.r - takes an argument of which rows in params.r to run, and then runs just those simulations. Saves the results for that set of simulations

• run-parallel.r - alternative to run.r, but splits up into parallel across multiple cores within a batch

• run.sh - this is the script that will be submitted to the HPC cluster. It will run run.r for each batch, splitting up the whole set of parameters across the cluster

To run

sbatch run.sh