CVN Simulation Study

Included files:

• run.R: Script to run entire simulation study
• config.R and torque.tmpl: Config for the BIPS cluster -- don't change. See below.

Setup

You'll need some R packages:

install.packages(c("CVN", "CVNSim", "tidyverse", "hmeasure", "batchtools", "ggplot2"))
source("install-packages-github.R")

First time cluster setup

• To use R, you have to load the R module on the cluster:
  • List available R versions: module avail R
  • Before loading an R module, you need mpi: module load mpi/openmpi/1.8.5
• Automatically load modules on login by adding the following to your ~/.bashrc:

module load mpi/openmpi/1.8.5
module load R/4.0.2
module list

• Copy the config files config.R and torque.tmpl from above to your configuration directory:

# create directory if needed
mkdir -p ~/.config/batchtools/
cp  config.R ~/.config/batchtools/
cp  torque.tmpl ~/.config/batchtools/

More info on the cluster, see:

• https://mllg.github.io/batchtools/index.html
• https://github.com/bips-hb/batchtools_example