Initialise Settings and Folders

Purpose

These instructions cover downloading the group-handbook repository, which contains bash scripts that configure the required folders and system environment variables.

Prerequisites

A SSO (Single Sign-On) account at the University of Oxford
VPN access to the University of Oxford network (required for off-site access)
An account on the project psyc-neuosc at ARC

Steps

Connect to the VPN
Connect to ARC (via remote desktop or SSH) — you will land on a gateway node
SSH into the login node: bash ssh -X htc-login

2. Download the `group-handbook` Repository

Download the repository into $DATA/git-repos. The scripts and functions in group-handbook will reside there.

cd $DATA
mkdir -p git-repos
cd git-repos
git clone https://github.com/Neuronal-Oscillations/group-handbook

3. Set Up the System Environment

Execute the setup script and reload your shell configuration:

bash group-handbook/code/hpc/setup_sysenv.sh
source ~/.bashrc

This defines the paths in ~/.bashrc needed to use the group functions and ensures a correct environment setup.

4. Configure RFS Credentials

The RFS credentials file allows nog_rfs (see nog_functions) to interact with RFS without prompting for your username and password each time.

Security note: The credentials file is stored in your ARC $HOME directory, which only you can access, so the security risk is minimal.

nog_rfs expects the credentials file at $HOME/.config/private/rfs_cred (no file extension). Create it using nano:

mkdir -p $HOME/.config/private

# create file and limit access to user only
touch $HOME/.config/private/rfs_cred
chmod 600 $HOME/.config/private/rfs_cred

# open the file and enter credentials
nano $HOME/.config/private/rfs_cred

The file should contain the following (replace with your own details):

username=AD-OAK\psycXXXX
password=YOUR-PASSWORD
domain=ox.ac.uk
projname=YOUR_PROJECT_NAME

Save with Ctrl+o and exit with Ctrl+x.

Note: projname should be the name of the project that you chose when requesting RFS storage.