I’m currently learning how to run an R workflow on a supercomputer. I’ve never come across supercomputers before and didn’t even know how and where to start. It’s been quite the journey and I thought I’d compile this list of resources so anyone else who wants to learn how to use supercomputers can have a friendly guide to get them started.
Before I dive into it, I would like to distinguish between using supercomputers and high-performance computing (HPC). These terms (“supercomputing” and “HPC”) are often used interchangeably, as you will see me do in this post, but there is a distinction here in the context of advanced computing. Supercomputers are only a subset of HPCs. HPC is a broader term that encompasses the use of supercomputers and other powerful computing resources to solve advanced computational problems.
The following is an opinionated list of what I believe to be the most important concepts to learn when you’re first starting out with HPC. Of course, you can run programs on high-performance computers without necessarily needing to understand the following concepts, especially if you’ve been given pre-written scripts to run your programs. However, I still think it’s helpful to understand the following concepts if you’d like to optimise your HPC usage.
HPC concepts
Here are the concepts that I found most important.
- Basic skills in using the Linux command line and a text editor such as Vim.
- Understanding the HPC components such as login nodes, compute nodes, and data nodes.
- Understanding the job scheduling system, such as Slurm.
- A basic understanding of computer architecture.
- A basic understanding of networking concepts.
Let’s break them down one by one.
Linux command line and text editor skills
A basic understanding of how to use the command line is useful as you’ll mostly be using the command line when accessing HPCs. When you’re on the command line, you also want to be able to use text editors like Vim or Nano to edit scripts and configuration files.
The textbook I enjoyed most for this was The Linux Command Line by William Shotts (freely available here). It gives an accessible and friendly explanation of what’s going on.
My preferred text editor is Vim. Here are the resources I found most helpful in learning how to use Vim:
- A quick introduction to what’s going on when you really have no clue: this guide from the Linux Handbook.
- An interactive tutorial for learning Vim: OpenVim. I liked this because it allows you to actually see what happens on the screen as you’re typing things out. I preferred this over the game Vim Adventures as 1) you can clearly see the progression of what you’re learning; and 2) it’s free.
- Otherwise you could try out the built-in
vimtutorby typing invimtutorin your terminal (assuming Vim is already installed on your device). - For information on how to do more advanced things in Vim, this guide is pretty good.
HPC components
It’s important to understand the components of the supercomputer you’re using so that you have a general idea of how processes and data move between its components. As an example, the following is a simplified and generalised architecture of a supercomputer, courtesy of Pawsey (Pawsey Supercomputing Research Centre 2023).
It’s useful to understand how to access the compute nodes and storage nodes from the login node; how to move data to and from the storage system from your local computer; and how to use the job scheduling system, which is the next topic.
Job scheduling system (Slurm)
Slurm is the most widely used job scheduling system for HPC clusters, but there are other job schedulers used too. Familiarise yourself with them.
I found this to be a good guide to Slurm.
Computer architecture
The best way to understand how supercomputers work is to understand how computers work to begin with, including computer architecture and computer networks. Specifically, I would want to know how processors, memory, and storage components work.
I’ll write separate posts on these topics and link them here.
Networking concepts
Specifically, a basic understanding of how to use SSH for secure remote access and data transfer.
For file transfer tools specifically, I found it useful to understand how to use tools such as scp, sftp, or rsync for transferring data into and out of the HPC system.
Good starting points
If this is overwhelming: I get it! I only compiled this list after having spent over a month–every day–reading up and watching videos on how to use supercomputers.
What you could do is go to your supercomputer centre’s help page and see if they have user documentation that you can use and a support team you can reach out to. Pawsey, the supercomputing research centre I’m with, has an excellent and comprehensive user support documentation, a Supercomputing User Training playlist, and a responsive support team who helps us optimise our workflow. At one point I just needed to talk to someone and ask for help, so it was really good to have access to the support team.
I also think it’s helpful to simply talk to someone who’s used supercomputers before. That way you can: 1) have a general idea of what you need to do, tailored to your workflow; and 2) have it pointed out to you what you don’t know about supercomputers. I found it really helpful to chat with colleagues who have worked with supercomputers. Alternatively, drop me a line and I will do my best to help!