June 2024 / Intro to Scientific Computing / HPC Summer Kickstart

Quick links

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 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.

Practical information

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 sometimes an in-person exercise and support session, as do some other partners, and a shared notes is used for a continuous Q&A session.

Time, date: 4 – 6 June 2024 (Tue–Thu). 11:50-16:00 EEST / 10:50-15:00 CEST

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/scicompsummer2024 . It’s OK to register and attend only individual sessions.

Cost: Livestream is free to everyone. Aalto in-person is free of charge for FCCI consortium members including Aalto employees and students.

Additional course info at: scip@aalto.fi

Other universities

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

  • [no active support] 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.

Schedule

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 as it happens.

  • Day #1 (Tue 4.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: SciComp 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: (Computational) reproducibility and open science Enrico Glerean and Samantha Wittke

      • Transparency in science is one of the core principles in research integrity. Did you know that half of published studies are actually not reproducible? Here we give an overview of CodeRefinery learning materials for those who want to start picking up good enough practices like git version control, clear project folder structure, conda environments, containers. Materials: Reproducible research (CodeRefinery)

    • 12:50–13:00: Break

    • 13:00–13:25: Behind the scenes: the humans of scientific computing Richard Darst and a special guest

      • 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.

    • 13:25–13:50: What can you do with a computational cluster? (Simo Tuomisto and Enrico Glerean)

      • A couple of real examples of how people use the cluster (what you can do at the end of the course): 1) Multi-cpu-node computations with LAMMPS, 2) Suprise demo.

    • 13:50–14:00: break

    • 14:00–14:50: 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 (ssh, openondemand)

      • 14:20–14:50: Individual help time in Zoom (links sent to registered participants for the affiliated HPC clusters)

      • Break until 15:00 once you get connected.

      • Material: Connecting to Triton

    • 14:50–15:00: Break

    • 15:00–15:25: How to ask for help with (super)computers Radovan Bast and Richard Darst

      • It’s dangerous to go alone, take us! Don’t waste time struggling, there are plenty of people here for you. Materials: Slides.

    • 15:25–15:50: VS Code on HPC Hossein Firooz and Richard Darst

      • One can use clusters also without the shell, but it comes with some extra care. Materials: VSCode on Triton

    • 15:50–16:00: Wrapping-up and getting ready for day 2 Richard Darst

    • 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 5.jun): Basic use of a cluster (Richard Darst, Simo Tuomisto)

  • Day #3 (Thu 6.jun): Advanced cluster use (Simo Tuomisto, Richard Darst)

Preparation

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:

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.

  • Then, connect and get it working

    • Aalto (and possibly useful to others): try to connect to Triton to be ready. Come to the Wednesday session for help connecting (required).

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:

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:

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