June 2023 / Intro to Scientific Computing / HPC Summer Kickstart
Videos are on YouTube in this playlist.
Thanks to all who attended, we hope you enjoyed the course as much as we enjoyed giving it.
We know that this course was a lot. Learning scientific computing is a lot. If you felt overwhelmed, it’s OK: do what you can for your work, and keep referring back to our material as you work. Consider coming back next year for the course again - you’ll learn much more then.
You can still register to get HackMD access for Q&A. Sharing: You may definitely share the livestream with others!
Kickstart is a three × half day course for researchers to get started with high-performance computing (HPC) clusters. The first day serves as a guide to skills you need in your career: a map to the types of resources that are available and skills you may need in your career, so that you can be prepared when you need more in the future. This part is especially suitable to new researchers or students trying to understand computational/data analysis options available to them. It won’t go into anything too deep, but will provide you with a good background for your next steps: you will know what resources are available and know the next steps to use them.
The second and third days take you from being a new user to being competent to run your code at a larger scale than you could before using a computer cluster. This part is good for any researcher who thinks they may need to scale up to larger resources in the next six months, in any field - this is many new researchers in our departments. Even if you don’t use computing clusters, you will be better prepared to understand how computing works on other systems. If you are a student, this is an investment in your skills. By the end of the course you get the hints, ready solutions and copy/paste examples on how to find, run and monitor your applications, and manage your data.
If you are at Aalto University: the course is obligatory for all new Triton users and recommended to all interested in the field.
This is a livestream course with distributed in-person exercise and support. Everyone may attend the livestream at https://twitch.tv/coderefinery, no registration needed, and this is the primary way to watch all sessions. Aalto has an in-person exercise and support session (location TBA), as do some other partners, and a collaborative document is used for a continuous Q&A session.
Time, date: 6 – 8 June (Tue–Thu). 11:50-16:00 EEST
Place: Online via public livestream, Zoom exercise sessions for partners, and probably in-person discussion/practice rooms at some campus.
Registration: Please register at this link: https://link.webropol.com/ep/scicomphpc2023 . It’s OK to attend only individual sessions is fine.
Cost: Livestream is free to everyone. Aalto in-person is free of charge for FGCI consortium members including Aalto employees and students.
Additional course info at: firstname.lastname@example.org
If you can’t attend day 1 (Aalto CS Summer day)
Most of day 1 is good background information, but not strictly required. You will need the Triton connection set up before day 1. We recommend you look at the connecting tutorial and get this set up in advance (either by talking to a colleague or our daily garage). Then, try to watch the relevant videos Wednesday morning or Tuesday evening.
If you are not at Aalto University, you can follow along with the course and will learn many things anyway. The course is designed to be useful to people outside of Aalto, but some of the examples won’t directly work on your cluster (most will, anyway we will give hints about adapting). How to register if you are not at Aalto:
Regardless of where you are from, you may use the primary registration form to get emails about the course. You don’t get anything else.
Participants from University of Helsinki can follow how to connect to their Kale/Turso cluster by following their own instructions.
Participants from University of Oulu: please follow instructions on how to access the Carpo2 computing cluster.
Tampere: this course is recommended for all new Narvi users and also all interested in HPC. Most things should work with simply replacing triton -> narvi. Some differences in configuration are listed in Narvi differences
If you want to get your site listed here and/or help out, contact us via the CodeRefinery chat (#kickstart-aalto stream). We have docs for other sites’ staff to know what might be different between our course and your cluster.
All times are EEST (Europe/Helsinki time)!
The daily schedule will be adjusted based on the audience’s questions. There will be frequent breaks and continuous questions time going on, this is the mass equivalent of an informal help session to get you started with the computing resources.
Subject to change
Schedule may still have minor updates, please check back for the latest.
Day #1 (Tue 6.jun): Basics and background
11:50–12:00: Joining time/icebreaker
12:00–12:10 Introduction, about the course Richard Darst and other staff Materials: Summer Kickstart intro
12:10–12:25: From data storage to your science Enrico Glerean and Simo Tuomisto
Data is how most computational work starts, whether it is externally collected, simulation code, or generated. And these days, you can work on data even remotely, and these workflows aren’t obvious. We discuss how data storage choices lead to computational workflows. Materials: SciComp Intro
12:25–12:50: What is parallel computing? An analogy with cooking Enrico Glerean and Thomas Pfau
In workshops such as this, you will hear lots about parallel computing and how you need it, but rarely get a understandable introduction to how they relate and which are right for you. Here, we give a understandable metaphor with preparing large meals. Slides
13:00–13:25: How big is my calculation? Measuring your needs. Simo Tuomisto and Thomas Pfau
People often wonder how many resources their job needs, either on their own computer or on the cluster. When should you move to a cluster? How many resources to request? We’ll go over how we think about these problems. Materials: How big is my program?
13:25–13:50: Behind the scenes: the humans of scientific computing Richard Darst and Teemu Ruokolainen
Who are we that teach this course and provide SciComp support? What makes it such a fascinating career? Learn about what goes on behind the scenes and how you could join us.
14:00–14:45: Connecting to a HPC cluster Thomas Pfau and Jarno Rantaharju
Required if you are attending the Triton/HPC tutorials the following days, otherwise the day is done.
14:00–14:20?: Livestream introduction to connecting
14:??–15:00: Individual help time in Zoom (links sent to registered participants)
Break until 15:00 once you get connected.
Material: Connecting to Triton
15:00–15:25: Using the cluster from the shell (files and directories) Richard Darst and Teemu Ruokolainen
Once we connect, what can we do? We’ll get a tour of the shell, files diretories, and how we copy basic data to the cluster. Material: Using the cluster from a shell.
15:25–15:50: What can you do with a computational cluster? (Jarno Rantaharju and Richard Darst)
See several real examples of how people use the cluster (what you can do at the end of the course): 1) Large-scale computing with array jobs, 2) Large-scale parallel computing. Demo.
Preparation for day 2:
Remember to read/watch the “shell crash course” (see “Preparation” below) if you are not yet confident with the command line. This will be useful for tomorrow.
Day #2 (Wed 7.jun): Basic use of a cluster (Richard Darst, Simo Tuomisto)
11:50–12:00: Joining time/icebreaker
12:00–12:05: Introduction to days 2-3
12:05–12:30 Structure of a cluster: The Slurm queueing system
12:30–15:00: Running your first jobs in the queue
15:00–15:30: Other things you should know about the HPC environment
Day #3 (Thu 8.jun): Advanced cluster use (Simo Tuomisto, Richard Darst)
11:50–12:00: Joining time/icebreaker
12:00–12:30: What does “parallel” mean?:
12:30–14:00: Forms of parallelization
14:00–14:30: Laptops to Lumi
You now know of basics of using a computing cluster. What if you need more than what a university can provide? CSC (and other national computing centers) have even more resources, and this is a tour of them. Slides from 2022 here.
14:40–15:30: Running jobs that can utilize GPU hardware:
15:30–16:00: Ask us anything
We strongly recommend you are familiar with the Linux command line. Browsing the following material is sufficient:
How to attend: Online workshops can be a productive format, but it takes some effort to get ready. Browse these resources:
Attending a livestream workshop, good to read in detail (ignore the CodeRefinery-specific parts).
SSH client to connect to the cluster (+ be able to connect, see next point)
Zoom (if attending breakout rooms)
Cluster account and connection verification:
Next steps / follow-up courses
Each year the first day has varying topics presented. We don’t repeat these every year, but we strongly recommend that you watch some of these videos yourself as preparation.
Very strongly recommended:
Other useful material in previous versions of this course:
While not an official part of this course, we suggest these videos (co-produced by our staff) as a follow-up perspective:
Attend a CodeRefinery workshop, which teaches more useful tools for scientific software development.
Look at Hands-on Scientific Computing for an online course to either browse or take for credits.
Cluster Etiquette (in Research Software Hour): The Summer Kickstart teaches what you can do from this course, but what should you do to be a good user.
How to tame the cluster (in Research Software Hour). This mostly repeats the contents of this course, with a bit more discussion, and working one example from start to parallel.
We hope to make a good learning environment for everyone, and expect everyone to do their part for this. If there is anything we can do to support that, let us know.
If there is anything wrong, tell us right away - if you need to contact us privately, you can message the host on Zoom or contact us outside the course. This could be as simple as “speak louder / text on screen is unreadable / go slower” or as complex as “someone is distracting our group by discussing too advanced things”.
See the schedule