Contents

1. Packages
2. Running a MATLAB Script

Packages

Installing MATLAB packages on the HPC does not involve the lab’s default containers. Instead, you must manually copy all desired, supplemental scripts into your own local directory on the HPC. The steps below use installation of the MADE pipeline scripts as an example.

1. Download the EEGLAB scripts to your local machine.

2. Log in to the HPC and access the file navigator.

3. In your local directory, create a folder named “MATLAB” under your “Documents” folder, then click into it.

4. Use the “Upload” button to upload the entire EEGLAB folder to this new “MATLAB” folder.

5. Once upload is complete, navigate into the “plugins” folder: ~/Documents/MATLAB/eeglab/plugins.

6. Download the following plugins using their respective links, and upload each of them to this directory:

   • ADJUST1.1.1
   • bids-matlab-tools
   • FASTER1.2.4

Running a MATLAB Script

To run a script in the MATLAB programming language using the login node, log in to the Panther Shell Access. Use cd to navigate to the folder that contains your script. From that location, run the following command:

sh /home/data/NDClab/tools/lab-devOps/scripts/matlab/rmat.sh [--parallel] <your-script-name>

Notes:

• <your-script-name> is the name of your “.m” file, but without the file extension
• you can optionally attached the --parallel flag to specify that this job requires parallel processing

This will generate an Slurm script named after your script: your-script-name.sub. Run this file as you would any Slurm script.