Welcome to the latest edition of the NAISS training newsletter.   This week we have a long list of events ranging from introduction events for new users of our systems to course in programming, parallel programming and code management.

Users who would like to discuss their issues in a face-to-face setting are invited to join our zoom-in on the 7th November.

ENCCS asked us to share some of their events.

Overview

NAISS training

• Online workshop: Basic Singularity: Running and Building Singularity Containers, 16 October, 2024
• Online training seminar: Introduction to Alvis, 17 October from 13:15 to 15:00
• Online course: Introduction to running R, Python, Julia, and Matlab in HPC, 22-25 October 2024
• Online hackathon: Bianca In-Depth: Improve Your Handling of Sensitive Research Data, 11 November
• Online course: Python for Scientific Computing, 5-7 November
• Online training and support event: “NSC introduction to Tetralith/Sigma”, 12 November 2024 at 10:00
• Online course: Programming Formalisms, 18-22 November
• Online training course: "Introduction to Git", 25-29 November 2024
• Online course: An introduction to parallel programming using Message Passing with MPI, 3, 4, 10 and 11 December 2024
• Online training course: Using Python in an HPC environment, 5-6 December 2024

CodeRefinery events

• Build Systems Course and Hackathon, October 8th-11th, 9:00-12:00 & October 15th-17th 10:00-16:00
• Online course: Python for Scientific Computing, 5-7 November

Online interactive support and discussion forum:

• NAISS Zoom-in - a virtual open-house, 7 November from 14:00 until 15:00

ENCCS training

• Online workshop: Best Practices in HPC Training, 21-22 October 2024
• Online event: The HPC Training Ecosystem in Europe, 22 October 2024
• alpaka and openPMD Workshop and Hackathon, 23 - 25 Oct
• GPU programming using Python – A practical intro webinar, 24 October
• GPU Programming. Why. When. How (Online), 12-14 November
• Hybrid event: Quantum Autumn School 2024, 2-4 December
• Julia for High-Performance Scientific Computing (Online), 9-12 December
• Publicly available training material
• Training events from around Europe

NAISS training

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 training seminar: Introduction to Alvis, 17 October 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: 17 October 13:15

Location: online via Zoom

For Zoom link and more information visit, please visit the events list at C3SE.

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:

• the R, Python, Julia, and Matlab course page at HPC2N
• the R, Python, Julia, and Matlab course page at UPPMAX
• the R, Python, Julia, and Matlab course page at LUNARC

Online hackathon: Bianca In-Depth: Improve Your Handling of Sensitive Research Data, 11 November

Are you already working with sensitive data in your research and feel that your workflows can be improved? If yes, welcome to 1-day hackathon where you'll learn smarter ways of working on the Bianca cluster. We will tell you how to do file transfer from a terminal, advanced SLURM, using IDEs (e.g. RStudio), and installing custom software and packages.

To attend this event, we expect you to be able to login to Bianca, submit a simple Slurm batch job, and know the basics of file transfer. A NAISS-SENS course project will be available to all participants.

When: Monday, November 11, 9.00-16.00

Where: online via Zoom

For more information and registration please visit the Bianca hackathon page (UPPMAX).

Online training and support event: “NSC introduction to Tetralith/Sigma”, 12 November 2024 at 10:00

An online event with two parts:

• A short introduction suitable for new users to the NSC Tetralith (NAISS) and Sigma (LiU) clusters. Topics include the module system, submitting jobs, working with Python, allocating GPU:s for simulations or graphics and other useful information.
• An open session for questions with several NSC application experts attending.

Feel free to join (and leave) whenever depending on your interest. The online event is open for all present and prospective NSC users.

Time: 12 Nov 2024, 10:00 - ca. 11:15 Introduction, ca 11:15 - Open session

Location: online via Zoom

The presentation will be available on the NSC event page.

Online course: Programming Formalisms, 18-22 November

Collaboration between UPPMAX and NBIS

This full 5-day course aims to give scientists, bioinformaticians and other research engineers  with some experience in programming and scripting an understanding of the underlying principles of software development, design, and programming. The course aims to strengthen the understanding of more advanced programming concepts, ability to produce more reusable scripts through modular programming and to enable a better understanding of how to evaluate a script or programs performance.

We will cover a formal development process form start to finish. We use Test-Driven Development as a good example of a development process, requirements modeling, risk assessment and structured design.

Some of the topics covered are modular development and (code) reusability, testing and optimization.

We will cover theory with bridging practical examples and applications to enhance the theoretical understanding of the principles.

When: November 18-22, onboarding: November 15

For more information and registration, please visit the programming formalisms course page (UPPMAX).

Online training course: "Introduction to Git", 25-29 November 2024

Collaboration between HPC2N and UPPMAX

The training course "Introduction to Git" will be given on 25-29 November 2024, 09:00 - 12:00 each day.  The course will be an introduction to version control, with a strong focus on Git.

Some of the main concepts, like repositories, commits, trees, branches, and merges will be covered, as will many of the basic commands, like clone, add, push, pull, commit, and fork.

The lectures will be complemented by demos, as well as hands-ons, during which the participants will learn both how to do simple Git commands as well as more complex cases. The hands-ons will mainly be done on your own computers and using GitHub.

This NAISS course is a cooperation between HPC2N and UPPMAX. It is open to NAISS users, prospective NAISS users and academics throughout the Nordic region.

For more information and registration, see the introduction to Git event page (HPC2N).

Online course: An introduction to parallel programming using Message Passing with MPI, 3, 4, 10 and 11 December 2024

Collaboration between HPC2N, LUNARC and PDC

Message Passing is presently a widely deployed programming model in massively parallel high performance computing. Message Passing is suitable for programming a wide range of current computer architectures, ranging from multi-core desk top equipment to the fastest HPC systems in the world, offering several hundred thousand processing elements.

This online course is at the beginners level and assumes no prior experience in parallel computing. The concepts behind message passing and distributed memory computing will be introduced and the syntax of the key MPI calls will be explained. The course will include point-to-point communications, non-blocking communication and the collective communications calls.  Live demonstrations and practical sessions to deepen the understanding of the lectures will be part of the course. At the end of the course participants should be able to write their own MPI programs at an intermediate level. The teaching language will be English.

For more information and access to registration, please refer to the event pages at HPC2N, LUNARC and PDC:

Online training course: Using Python in an HPC environment, 5-6 December 2024

• MPI event page at LUNARC
• MPI event page at HPC2N

Collaboration between UPPMAX, HPC2N and LUNARC

This two-day online course aims to give a brief, but comprehensive introduction to using Python in an HPC environment. You will learn how to use modules to load Python, how to find site installed Python packages, as well as how to install packages yourself. In addition, you will learn how to use virtual environments, write a batch script for running Python, use Python in parallel, and how to use Python for ML and on GPUs. In addition, the second day will be more advanced, with a focus on Pandas.

The course is a cooperation between UPPMAX, HPC2N, and LUNARC. The instructors will use UPPMAX's systems for demos and there will be hands-on exercises for the participants.

This course will consist of lectures interspersed with hands-on sessions where you get to try out what you have just learned.

Remote/online participation: The course will be completely online and we will use Zoom. More information about connecting and such will be sent to the participants close to the course.

The goal for the course is that you will be able to

• Load Python modules and site-installed Python packages
• Create a virtual environment and install your own Python packages to it
• Write a batch script for running Python
• Use Python in parallel
• Use Python for ML
• Use GPUs with Python
• Use pandas
• Learn about matplotlib

Prerequisites: familiarity with the LINUX command line, basic Python

Date and time: 5-6 December 2024, 9-17 each day.

For more info and registration, please visit the Python in HPC course page (HPC2N).

CodeRefinery events

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

• More information on part one and registration of the build systems course (PDC)
• More information on part two of the build systems course (PDC)

Online course: Python for Scientific Computing, 5-7 November

Organized by Aalto University, CodeRefinery, and partners

This is a medium-advanced course in Python tools such as NumPy, SciPy, Matplotlib, and Pandas. It is suitable for people who have a basic understanding of basic Python and want to know some internals and important libraries for science. Read the learner personas to see if the course is right for you.

The course streamed via Twitch (the CodeRefinery channel) so that anyone may follow along without registration. There is a "Notes" link (collaborative edited notes) which is used for asking questions during the course.

The course is organized by Aalto Scientific Computing in collaboration with CodeRefinery, and multiple Nordic partners.

For more information and registration, please visit the Python course page (Aalto University).

Online interactive support and discussion forum

NAISS Zoom-in - a virtual open-house, 7 November 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.

Location: Zoom-link for the NAISS Zoomin-in session on 7 November

ENCCS training

Online workshop: Best Practices in HPC Training, 21-22 October 2024

Abstract: The Best Practices in HPC training workshop focuses on helping competent practitioners and experts in various fields teach their knowledge to others. It also serves as a kickstart to teaching available open-source training material from ENCCS and other training providers. 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 ENCCS and well-known educational initiatives like The Carpentries and CodeRefinery.

Detailed information at the "Best Practices in HPC Training" page (ENCCS).

Time: Oct. 21-22, 10:00-16:00 (CET) (2024).

Online event: The HPC Training Ecosystem in Europe, 22 October 2024

Abstract: This event aims to unite HPC training providers and stakeholders to discuss current developments in the growing ecosystem of HPC training. We will share experiences, and identify collaboration opportunities.

Detailed information at the " HPC Training Ecosystem in Europe" page (ENCCS).

Time: Oct. 22, 14:15-17:15 (CET) (2024).

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).

GPU programming using Python – A practical intro webinar, 24 October

Abstract: In this webinar, we focus on GPU-accelerated computing with Python. Starting from familiar Python libraries such as Numpy and Pandas, we will guide you step-by-step into the world of GPU programming. Discover how to harness the power of GPU accelerators using libraries such as CuPy, cuDF, PyCUDA, Jax, and Numba, with a focus on their unique features and capabilities for high-performance computing.

Detailed information at the GPU programming using python page (ENCCS).

Time: Oct. 24, 12:00-13:30 (CET) (2024).

GPU Programming. Why. When. How (Online), 12-14 November

Abstract: This workshop is based on a multilateral collaboration between GPU programming specialists from the Nordic countries. 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.

Detailed information at the GPU programming why when how page (ENCCS).

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

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).

Julia for High-Performance Scientific Computing (Online), 9-12 December

Abstract: This workshop is an interactive online event, featuring live coding, demos, and practical exercises. We aim to equip you with the tools and knowledge to write efficient, high-performance code using Julia. In this four-half-day course, we will start with the basic features of Julia, and then delve into the specific topics on writing performant Julia code, multithreading, and distributed computing. Additionally, we will focus on Julia programming on HPC clusters using GPU accelerators, and the interfacing of Julia with other programing languages (C/C++, Fortran, Python, etc.).

Detailed information at the Julia workshop page (ENCCS).

Time: Dec. 9-12, 9:30-14:30 (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.