June 2025 / Intro to Scientific Computing / HPC Summer Kickstart
Quick links
Registrations are open: https://link.webropol.com/ep/scicompsummer2025
News:
The course is over. We hope that you learned something and can keep studying as you need. There is a lot more written material available linked from the schedule, available for independent learning.
Other relevant courses as follow-ups:
Python for Scientific Computing (usually late autumn each year)
CodeRefinery covers version control (git) and related practical software tools.
Shell usage and scripting, though you should select the parts relevant to you.
Links
Livestream: https://twitch.tv/coderefinery
Notes docs: Archive day 1, Archive days 2-3.
Zoom: live zoom support for students from partner organisations
Videos: YouTube playlist, or git-annex to avoid YouTube.
Twitch archive (7 days only)
Kickstart: Introduction to HPC and Scientific Computing
Kickstart is a three half-day course for researchers and students who want to get started with high-performance computing (HPC) and scientific computing workflows.
Day 1: focuses on the basics of HPC through practical examples. You will learn how to connect to a supercomputer, how storage choices affect your workflow, how to transfer data, and run your first jobs with slurm.
Day 2 introduces tools and practices for efficient and responsible data science. Topics include Conda environments, batch and array jobs, job monitoring, software modules, parallel computing
Day 3 covers more advanced topics: GPU usage, working with real examples: local open-weights LLMs (large language models).
By the end of the course, you will be ready to use HPC clusters effectively with hands-on skills and ready-made examples.
If you are at Aalto University: the course is obligatory for all new Triton users and recommended to all interested in the field.
This course is part of Scientific Computing in Practice lecture series at Aalto University, supported by many others outside Aalto, and offered to others as part of CodeRefinery.
Schedule
Subject to change
Schedule may still have updates before the course, and also during as we adapt to audience questions and interests.
Times automatically converted to:
Day 1 (Tue 3 June)
: Joining time/icebreaker
Introduction, about the course Materials: SciComp kickstart intro (EG, )
Intro to SciComp and HPC: (Material, Video link from 2024)
The HPC Kitchen (RD, TP)
Connecting to the cluster (TP, SM)
Break
CSC resources for scientific computing (JL)
A special guest from CSC will talk about our national supercomputers Mahti/Puhti/LUMI and how to use them in practice.
Lunch break
Setting up for a new project (RD, ST)
Cluster shell, section Copy your code to the cluster (Exercise Shell-4 and Shell-5)
Exercise: Cloning our Gutenberg analysis code to the cluster.
Data storage - Exercise Storage-1
Remote access to data - Exercise RemoteData-1
Exercise: Copying the Project Gutenburg data to your work directory
What is Slurm? (ST, RD)
Break
Interactive jobs (RD, ST)
Interactive jobs - Exercise Interactive-2
Big example: Project Gutenburg n-gram analysis
First serial jobs (RD, ST)
Serial Jobs - Exercise Serial-2
Big example: Project Gutenburg n-gram analysis
End of day
Day 2 (4 June)
Connecting, icebreakers, Q&A
Behind the scenes: the humans of scientific computing (RD, SM)
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.
Conda (JR, YT)
Big example: Make a conda environment for LLMs
Break
Array jobs (ST, RD)
Big Example: Project Gutenberg book analysis in parallel
: Lunch break
Monitoring (ST, RD)
Applications (RD, ST)
Research integrity, security, compliance, and reproducibility (EG, TP)
Break
Parallel (ST, RD)
Big example: Calculating pi in parallel
End of day
Day 3 (5 June)
Connecting, icebreaker, Q&A
How to ask for help with (super)computers (RD, )
It’s dangerous to go alone, take us! Don’t waste time struggling, there are plenty of people here for you. Materials: Slides.
GPUs (ST, HF)
Break
LLM example (YT, HF)
Wrap up and summary, ask us anything
End of day
Practical information
This is a livestream course with distributed 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. There is constant Q&A via shared notes.
Time, date: 3 – 5 June 2025 (Tue–Thu). 10:00-12:00 EEST (days 1-3) and 13:00-15:00 EEST (days 1-2).
Place: Online via public livestream, Zoom exercise sessions for partners.
Registration: Please register at this link: https://link.webropol.com/ep/scicompsummer2025 . It’s OK to register and attend only individual sessions.
Cost: Livestream is free to everyone.
Additional course info at: scip@aalto.fi
Other organizations
If you are not at Aalto University, you can follow along and probably learn a lot. We design the course to be useful even to others outside of Aalto University, 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 Lehmus 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
CSC (Finland): Participants with CSC user account can try examples also in CSC supercomputers, see the overview of CSC supercomputers for details on connecting, etc.
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.
Preparation
We strongly recommend you are familiar with the Linux command line. Browsing the following material is sufficient:
Using the cluster from a command line (video, shorter video) - important background knowledge for command line work.
Watch this background info about why we use computer clusters. This is important information for why we are in this course, which we won’t cover directly. The most important videos are the intro (what is a cluster and why?), storage hierarchy (how the data looks), and the Slurm job scheduler (how the cluster runs things).
Technical prerequisites
Software installation
SSH client to connect to the cluster (+ be able to connect, see next point)
Zoom (if attending breakout rooms)
Cluster account and connection verification:
Access to your computer cluster.
Aalto: if you do not yet have access to Triton, request an account in advance. Others: Access to your computing cluster.
Attempt to Connect to your cluster (don’t worry, we will also go over this on day 1 anyway).
Next steps / follow-up courses
Keep the Triton quick reference close (or equivalent for your cluster), or print this cheatsheet if that’s your thing.
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:
Installing Python packages with Conda (Note that conda on new-Triton has changed. See Python Environments with Conda for details)
Git intro (useful)
Other useful material in previous versions of this course:
Scientific Computing workflows at Aalto - concepts apply to other sites, too (optional): lecture notes and video, reference material.
Tools of scientific computing (optional): lecture notes and video
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.
Community standards
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”.
Material
See the schedule