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NAISS Training Newsletter

No 26, 30 August 2024

– Published 30 August 2024

Welcome to the latest edition of the NAISS training newsletter.   Since last week we have a number of new events.  The topics of the new events include sensitive data handling,  parallel programming with OpenMP, Singularity containers.  Code refinery is newly offering an event on code build systems and ENCCS has added an event on GPU programming.   The next zoom-in, where you discuss directly with staff associated with the NAISS service is on the 19th September.

We remind on those previously advertised training events that are still open for registration.

Overview

NAISS training

  • Online training seminar: Introduction to Alvis, 9 September from 13:15 to 15:00
  • Mondays with Matlab - Nordic HPC workshops, 9, 16 and 25 September 2024
  • Online course: Introduction to Linux, 16 September 2024
  • Online workshop: Introduction to Bianca: Handling Sensitive Research Data, 25 September 2024
  • Online training course: “An introduction to shared memory parallel programming using OpenMP”, 25-27 September 2024
  • Online workshop: Basic Singularity: Running and Building Singularity Containers, 16 October, 2024
  • Online course: Introduction to running R, Python, Julia, and Matlab in HPC, 22-25 October 2024

CodeRefinery events

  • Online CodeRefinery workshop, 10-12 and 17-19 September 2024
  • Build Systems Course and Hackathon, October 8th-11th, 9:00-12:00 & October 15th-17th 10:00-16:00

Online interactive support and discussion forum:

  • NAISS Zoom-in - a virtual open-house, 19 September from 14:00 until 15:00

HPC centre events

  • Online course: Introduction to Kebnekaise, 16 September 2024, 11:15-17:00

ENCCS training

  • Online instructor training workshop: Best practices in HPC training, 21 - 22 October
  • alpaka and openPMD Workshop and Hackathon, 23 - 25 Oct
  • Online workshop: GPU Programming. Why. When. How, 12 - 14 November
  • Hybrid event: Quantum Autumn School 2024, 2-4 December
  • Publicly available training material
  • Training events from around Europe

NAISS training

Online training seminar: Introduction to Alvis, 9 September from 13:15 to 15:00

This seminar is for new and prospective users of the NAISS cluster for AI/ML, Alvis. You will learn all that you need to know to get started on the system.

Time: 9 September 13:15

Location: Alvis event Zoom link

For more information visit C3SE events page.

Mondays with Matlab - Nordic HPC workshops, 9, 16 and 25 September

Does your project involve large computations or training Machine Learning and Deep Learning models? Are you interested in speeding up your code by harnessing a High-Performance Computing (HPC) resource near you?

MathWorks is partnering with NAISS Sweden, DTU Denmark, CSC Finland, Sigma2 Norway, IHPC Iceland and RTU HPC, Latvia to bring you a three series workshop on parallel computing and AI using large compute resources –– including hands-on exercises where you will learn how to effectively use MATLAB and MATLAB Parallel Server to speed up your computations.

There will be three workshops in the series:

  • Workshop 1 (9th September 2024) will introduce the basics of parallel computing with MATLAB.
  • Workshop 2 (16th September 2024) will focus on building end-to-end AI systems with MATLAB, covering topics from no-code machine learning and low-code deep learning and Python. You will discover how MATLAB can simplify and enhance your AI research.
  • Workshop 3 (23rd September, 24th September and 25th September 2024) will involve hands-on sessions where participants will get to submit jobs on an HPC cluster that is most relevant to them based on their country.

More information and access to registration is available on the Mondays Matlab overview (MathWorks).

NAISS users are recommended to attend Workshop 3 on the 25th of September (MathWorks).

Online workshop: Introduction to Bianca: Handling Sensitive Research Data, 25 September 2024

Are you just beginning to work with sensitive data in your research? If yes, welcome to a 1-day introduction to handling sensitive data on the UPPMAX cluster, Bianca. We will tell you about NAISS-SENS, how to login to Bianca, transfer files via wharf, basics of the SLURM workload manager and the module system.

The workshop is intended for beginner users of Bianca.

You do not need to be a member of a NAISS-SENS project in order to join the workshop. A SUPR course project will be available to all participants. The workshop will consist of both lectures and exercise sessions.

When: Wednesday, September 25

Where: online via Zoom

For more information and registration please visit the sensitive data workshop page (UPPMAX).

Online course: Introduction to Linux, 16 September 2024

This 2-hour online course is an introduction to the Linux operating system (OS) that is used on most Swedish compute clusters, and is the most common OS in HPC clusters all over the planet. The course will consist of lectures, code-alongs, and interspersed exercises.

This NAISS course is meant for beginners to the Linux operating system, and is open to all users in Swedish academia.

Time and date: 16 September 2024, 09:00-11:00

More information and registration on the Linux introduction course page (HPC2N).

Online training course: “An introduction to shared memory parallel programming using OpenMP”, 25-27 September 2024

OpenMP provides an efficient method to write parallel programs in C, C++ and Fortran.  OpenMP programs are suitable for execution on shared memory architectures such as modern multi core systems or a single compute node of the HPC clusters deployed by LUNARC, HPC2N and within NAISS.

This course will introduce participants to the shared-memory model for parallel programming and the OpenMP application-programming interface.  In many cases OpenMP allows an existing serial program to be upgraded incrementally, starting with the parallelisation of the most time-consuming parts of the code.  Typically OpenMP programs are easily ported from one shared memory multi processor system to another one.

Venue: Online

For more information and access to registration visit:

Online workshop: Basic Singularity: Running and Building Singularity Containers, 16 October, 2024

Collaboration between UPPMAX and HPC2N

The online workshop is an introduction to the basic concepts of containerised software environment solutions within the Singularity framework (Sylabs).

The online workshop is an introduction to the basic concepts of containerised software environment solutions within the Singularity framework

During the workshop you will have the opportunity to follow the interactive guide on

  • how to run Singularity containers
  • how to build your own
  • good (and bad) practices on designing and building Singularity recipes
  • build and/or host container remotely and what are the limitations

To fully benefit from the workshop, basic Linux system administration experience is highly desirable i.e. knowledge of package management and common tools for building and managing software: git, pip, conda, wget, curl, etc.

Please follow the instructions to install Singularity (GitHub) on your computer before the workshop.

When: Wednesday, October 16, 2024

Where: online via Zoom

For more information and registration, please visit the singularity workshop page (UPPMAX).

Online course: Introduction to running R, Python, Julia, and Matlab in HPC, 22-25 October 2024

Learn how to run R, Python, Julia, and Matlab at Swedish HPC centres, mainly using Rackham on UPPMAX as an example.  We will show you how to find and load the needed modules, how to write a batch script, submitting jobs from inside Matlab, as well as how to install and use your own packages, and more.  The course will consist of lectures interspersed with hands-on sessions where you get to try out what you have just learned.

This course will consist of four days.  Each day starts at 9:00 and closes 15:00.  One day for each language.

Participation is free and open to all current and prospective users of NAISS.

Time and date: 09:00 - 15:00, 22-25 October 2024

Location: online via Zoom

For more information and registration, see:

CodeRefinery events

Online workshop: CodeRefinery workshop, September 10-12, and 17-19, 2024

Organised by CodeRefinery and partners

Are you writing code and managing data for your research?

Do you feel like wasting too much time on manual work?

Do you struggle to understand and reuse older code?

Join the CodeRefinery workshop 10-12 and 17-19 September 2024, for free and online.

The workshop covers good coding practices, reproducible research principles, and using Git for collaboration.

It consists of streamed lectures and breakout room exercises with team leaders.

You may register individually or as a team. In-person exercise sessions are available in some locations.

For registration and more information, please visit the September CodeRefinery workshop page (GitHub).

Build Systems Course and Hackathon, October 8th-11th, 9:00-12:00 & October 15th-17th 10:00-16:00

Hosted by PDC, ENCCS, CodeRefinery, CSC, and Aalto Scientific Computing

The development of modern computer hardware towards heterogeneous architecture that combines the compute capabilities of multicore central processing units (CPU) and graphics processing units (GPU), non-uniform memory access (NUMA), and high speed network interconnect, offers, on the one hand, the prospect of extreme computing power, and on the other hand, a challenge for developers and users of scientific software.

In this Build Systems Course and Hackathon you will learn how to make use of tools and frameworks for building and installing programs and libraries on modern personal computers and on supercomputers.

The event has two parts.

Part 1: Online course:

Tuesday 8 October - Friday 11 October 2024.  9:00-12:00

On the curriculum are:

  • Introduction to compilers, linkers, and libraries
  • The GNU make and autotools
  • The CMake build system
  • The Spack build system
  • The EasyBuild build system
  • SingularityCE / Apptainer

     

In the exercise sessions of the course you will get hands on experience on using these tools for a variety of open source scientific programs.

Part 2: Hackathon

The hackathon part of this event will be hosted at the KTH campus in Stockholm, Sweden, on three full days: Tuesday 15 October - Thursday 17 October 2024. The hackathon will be held in the conference rooms at the RISE office at the KTH campus, Drottning Kristinas väg 61, Stockholm.

The primary scope of the hackathon is for teams (consisting of one to five people) to work on their own code aiming to make it transferable to different computers using, for instance, the CMake build system, Spack, and containers.

Teams that would like to participate in the hackathon are welcome to submit an application. The organisers will review the applications and accept up to eight teams for participation. A team can have from one to five members. Preference will be given to teams working on scientific codes which are open source. In the application, please describe how the code is distributed, what the license for the code is, how the code can be built and installed currently, and how the team would like to extend the functionality of the code.

Note that participation in the hackathon is limited to a maximum of eight teams.

Links

Online interactive support and discussion forum

NAISS Zoom-in - a virtual open-house, 19 September from 14:00 until 15:00

You are invited to a virtual meeting room.  Inside the meeting room we like to discuss services offered by NAISS and how they can be used for your computational needs, help you process your data and visualise your results.  Participants are highly encouraged to pose their own questions.

We also expect to have experts available from C3SE, HPC2N and LUNARC, to discuss the University operated HPC services at Chalmers, Umeå and Lund University.

The zoom-link for the session on 19th September .

HPC centre events

Online course: Introduction to Kebnekaise, 16 September 2024, 11:15-17:00

In this course we begin with an introduction to HPC and HPC2N, before going on to a walk-through of the Kebnekaise system, including the new hardware.

After that, we go through the module system and take a look at how to submit jobs. During the hands-on you will get the opportunity to try loading modules, compile a program, and submit a job to the Kebnekaise cluster. We will look at how to use both the different types of CPUs, and the different types of GPUs.

Eligibility: since Kebnekaise is no longer a NAISS cluster, this course in only available to local users. This is defined as users who are current or future members of projects with a PI affiliated with HPC2N's partner sites (UmU, SLU, LTU, MIUN, IRF). Participation is free.

Time and date: 16 September 2024, 11:15-17:00

More information and registration on the Kebnekaise introduction course page (HPC2N).

ENCCS training

Online instructor training workshop: Best practices in HPC training, 21 - 22 October

Time: online, Oct. 21-22, 09:00-12:30 (CET), 2024

This online instructor training workshop is focused on helping competent practitioners and experts in various fields teach their knowledge to others. It also serves a kickstart to teaching ENCCS lessons. The two-half-day online workshop will present best practices in teaching technical topics both online and in-person and is based on past experiences from both ENCCS and well-known educational initiatives like The Carpentries and CodeRefinery. It will include a brief tour of the following topics:

  • Science and philosophy of teaching
  • How to teach interactive, hands-on workshops
  • How to design interactive, hands-on lessons

This workshop is organised by ENCCS, NCC Lithuania, NCC Finland and MultiXscale Centre of Excellence.

For further information and registration, please visit the instructor workshop page (ENCCS).

alpaka and openPMD Workshop and Hackathon, 23 - 25 Oct

Abstract: We are excited to invite you to a dynamic three-day workshop and hackathon focused on two powerful tools for high-performance computing: alpaka and openPMD. This event will bring together developers, researchers, and enthusiasts from diverse backgrounds to collaborate, learn, and innovate.

Detailed information at the alpaka and openPMD hackathon page (HLRS)

Time: Oct. 23-25, 09:00-17:30 (CET) (2024).

Online workshop: GPU Programming. Why. When. How, 12 - 14 November

Time: Nov. 12-14, 09:00-16:00 (CET) (2024).

Abstract: This workshop is based on a multilateral collaboration between GPU programming specialists from the Nordic countries. It is meant to help both software developers and decision makers navigate the GPU programming landscape and make more informed decisions on which languages or frameworks to learn and use for their projects. This workshop will cover basic aspects of GPU programming concepts and models including

  • GPU hardware and software ecosystem
  • GPU programming concepts & models
  • Directive-based models (OpenACC, OpenMP)
  • Portable kernel-based models (Kokkos, OpenCL, SYCL, *etc.*)
  • Non-portable kernel-based models I (CUDA, HIP)
  • High-level language support (Python, Julia)
  • Multi-GPU programming with MPI
  • Preparing code for GPU porting
  • Hand-on examples

In the final afternoon session, participants are invited to bring their own code, discuss it with experts and get concrete advice.

Detailed information at the GPU programming workshop page (ENCCS)

Hybrid event: Quantum Autumn School 2024, 2-4 December

Abstract: Experts from other organisations and industry will showcase the possibilities offered by quantum computing during the school. The school will cover more advanced topics and tutorials compared to QAS23, which serves as a good starting point for people interested in participating.

The QAS24 will include: 1)Overview of the main state-of-the-art QC hardware approaches; 2) Overview and update on recent developments in QC software stacks; 3) Integration of QC with classical computing: hybrid classical/quantum algorithms and HPC+QC systems; and 4) QC programming in high-level languages for scientific and industrial use cases.

Detailed information at the Quantum Autumn School page (ENCCS)

Time: Dec. 2-4, 09:00-17:00 (CET) (2024).

Publicly available training material

ENCCS develops and maintains a library of training material on topics in HPC, AI and Quantum Computing which is suitable for self-paced learning, see the training library at ENCCS.

Training events from around Europe

Many HPC centres and National Competence Centres around Europe offer diverse HPC training workshops open to anyone in Europe, many of which are online. Upcoming workshops can be found at the European HPC Portal.

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