Soft-Auto-HMC+RWMH tests scripts

Usage

Clusters

The nextflow.config file instructs Nextflow to use Apptainer with a custom Docker image, so the user only needs to run e.g.

./nextflow-sockeye.sh run funnel_scale.nf

for Sockeye or

./nextflow-alliance.sh run funnel_scale.nf

for the Alliance clusters.

Local

If you have Julia and cmdstan installed locally, you can run

./nextflow run funnel_scale.nf

Note: this assumes that there is an environment variable CMDSTAN pointing to the directory where cmdstan lives. You can do this via

export CMDSTAN=/full/path/to/cmdstan-vx.xx

Recommended .bashrc settings for Sockeye

Add the following at the bottom of your .bashrc, replacing

• YOUR_ALLOC_NAME with the name of the allocation you are assigned to, and
• YOUR_GITHUB_KEY with the filename of your private ssh key for accessing Github.

# export the name of the allocation you belong to
export ALLOC_NAME="YOUR_ALLOC_NAME"

# load modules
module load gcc/9.4.0
module load openjdk
module load git
module load apptainer

# start ssh-agent if not already started, then add keys
if [ -z "$SSH_AUTH_SOCK" ] ; then
  eval `ssh-agent -s` > /dev/null
  ssh-add $HOME/.ssh/YOUR_GITHUB_KEY >/dev/null 2>&1
fi