Singularity Containers

This is a beginner tutorial on using Singularity COntainers

Setup

Navigate to rc.uab.edu in your preferred web browser and login.

From the dashboard, click "Jobs" and then "Job Composer" to open the job composer.

Create a new job from the default template. Then scroll down the page and select "Open Editor" at the bottom under "Submit Script"

Copy and paste the following code into the editor window. (Replace all current code with the pasted code)

#!/bin/bash
# JOB HEADERS HERE

mkdir -p /data/user/$USER/rc-training-sessions
folder=/data/user/$USER/rc-training-sessions/singularity_containers
URL=https://gitlab.rc.uab.edu/rc-training-sessions/singularity_containers.git

if [ -d "$folder" ] ; then
    cd "$folder"
    git pull "$URL"
else 
    mkdir -p "$folder"
    git clone "$URL" "$folder"
fi

Start Jupyter Notebook

Launch Jupyter Notebook through the interactive apps page in the OnDemand (rc.uab.edu) portal using following settings:

Environment Setup:

# Load required modules
module load Singularity/3.5.2-GCC-5.4.0-2.26
module load Anaconda3

Extra Jupyter Arguments:

--notebook-dir=/data/user/$USER/rc-training-sessions/singularity_containers