Welcome to the this week’s edition of the NAISS training newsletter.   Since the last edition we have added the “Introduction to PDC systems”, the “NSC introduction”, “Matplotlib for Publication”, the “Introduction seminar for Alvis” and “Cluster architecture and job submission”.

We have created a new training page on the NAISS website. This page will provide an overview on planned NAISS training events.

The CodeRefinery workshop in late March is still taking registrations.

The next interactive support session Zoom-in is scheduled for 10 April 2025

Uppsala University and ENCCS asked us to share one of their events.

Overview

NAISS training

• Online workshop: Introduction to Bianca: Handling Sensitive Research Data, 19 March 2025
• Online course: Introduction to PDC Systems Course, 20 March 2025
• Online course: Introduction to running R, Matlab, and Julia in HPC, 24-26 March 2025
• Online course: Introduction to Linux, 3 April 2025, 09:00-12:00
• Online training course: Matplotlib for Publication, 8-9 April 2025
• Online training seminar: Introduction seminar for Alvis users, 10 April 2025
• Online training and support event: “NSC introduction to Tetralith/Sigma”, 15 April 2025 at 10:00
• Online training course: Using Python in an HPC environment, 24-25 and 28-29 April 2025
• Online course: Programming Formalisms, 5-9 May 2025
• Online training seminar: Cluster architecture and job submission, 27 May 2025 at 13:30

Online interactive support and discussion forum:

• NAISS Zoom-in - a virtual open-house, 10 April from 14:00 until 15:00

CodeRefinery

• Online workshop: CodeRefinery workshop, March 25-27, and April 1-3, 2025

University events

• Monthly Workshop Series: Whisper Transcription demonstration, continuing 4th March

ENCCS training

• Webinar: Practical Introduction to GPU Programming, 27 March
• Hybrid Workshop: PIC (BIT1) modelling of the fusion plasma edge. 7-9 April 2025
• Hybrid Workshop: Exploring Biomolecular Modelling and Simulations, 9-10 April
• Webinar: Development of algorithms for partial multi-label machine learning, 15 April
• Workshop: Practical Deep Learning, 6-8 May
• Webinar: Software Installation on HPC, 13 May

NAISS training

Online workshop: Introduction to Bianca: Handling Sensitive Research Data, March 19, 2025

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 the Bianca cluster.

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, March 19, 2025

Where: online via Zoom

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

Online course: Introduction to PDC Systems Course, 20 March 2025

This course focuses on utilising the Dardel high-performance computing (HPC) system provided by PDC. Throughout the course, we will cover fundamental information about Dardel and its usage, including an overview of the infrastructure, account management, logging in procedures, job execution, data storage, and code compilation.

Time: 9:00 - 12:00

For more information and access to registration please visit the PDC systems course page (PDC).

Online course: Introduction to running R, Matlab, and Julia in HPC, 24-26 March 2025

Learn how to run R, Matlab, and Julia at Swedish HPC centres, mainly using Tetralith on NSC as an example.  We will show you how to find and load the needed modules, how to write a batch script for R, Matlab, and Julia, 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 three days.  Each day starts at 9:00 and closes 16:00.  One day for each language.

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

Time and date: 09:00 - 16:00, 24-26 March 2025

Location: online via Zoom

For more information and registration, see:

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

Online course: Introduction to Linux, 3 April 2025, 09:00-12:00

This 3-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: 3 April 2025, 09:00-12:00

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

Online training course: Matplotlib for Publication, 8-9 April 2025

Matplotlib is among the most popular and advanced function libraries for the production of journal-quality data visualisations. In this course, participants will first learn/review how to use Matplotlib and what plotting options. Then, participants will be introduced to resources and techniques to make their plots both richer in content and more accessible.

This course will run for 2 days, fika-to-fika (10:00-15:00 with a lunch break) and consists of alternating blocks of lectures with demonstrations and exercises via Jupyter notebooks for students to practice with prepared data. The course will be taught in English via zoom.

Dates: 8-9 April 2025, 10:00 - 15:00 each day

For more information and access to registration visit the Matplotlib for publication course page (LUNARC).

Online training seminar: Introduction seminar for Alvis users, 10 April 2025

Description: 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: 10 April 10:00-11:45

Registration: Introduction Alvis registration page (Chalmers)

Online training and support event: “NSC introduction to Tetralith/Sigma”, 15 April 2025 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: 15 Apr 2025, 10:00 - ca. 11:15 Introduction, ca 11:15 - Open session

For further information, please see the Tetralith/Sigma event page (NSC).

Online training course: Using Python in an HPC environment, 24-25 and 28-29 April 2025

This online 4-day workshop aims to give a brief, but comprehensive introduction to using Python in a Swedish academic High-Performance Computing (HPC) environment. It covers a wide range of levels in using Python and you can decide which days to follow.

The goals of the different days are:

Day 1:

• Log in to a cluster and load python interpreter
• Use variables, expressions and statements with Python

Day 2:

• Load and use site-installed Python modules
• Use and install python packages with pip and/or Conda
• Use virtual environments

   

• Ask for compute resources, write batch scripts
• Do basic analysis with Matplotlib in Jupyter

Day 3-4:

• Use compute resources and batch jobs, including parallelism, GPUs and big data
• Use Pandas and Seaborn
• Use Python for ML

Where: online via Zoom

Date and time: 24-25 & 28-29 April, 9-17 each day.

For more info and registration, please visit

• the Python-HPC course page at HPC2N
• the Python-HPC course page at LUNARC

Online course: Programming Formalisms, 5-9 May 2025

Collaboration with NBIS

The goal of this highly-interactive 5-day course is to be able to develop academic software that you can trust to be 'good enough'. We assume you have written code 'that (sometimes) just works'.

The course follows a formal development process from start to finish, with a selection of topics and best practices we think are most important, with the goal of developing academic software that is actually good enough.

When: May 5-9 from 9:00-16:00 each day

Where: online via Zoom

More info and registration, please visit the programming formalisms course page (UPPMAX).

Online training seminar: Cluster architecture and job submission, 27 May 2025 at 13:30

This event explains key features of a contemporary HPC cluster, such as deployed at LUNARC and throughout NAISS.  It will explain the principles behind the job scheduler and how the scheduler can be used to accomplish your computational work in an efficient manner.  The examples will utilise the SLURM scheduler, which is deployed on the NAISS resources.

The event is organised as an online seminar.  The seminar addresses users who have recently started using HPC systems and prospective users considering using an HPC system in the near future.

Time: 12 May at 13:30

For more information and registration visit the cluster architecture and job submission seminar page (LUNARC).

Online interactive support and discussion forum

Change of date: NAISS Zoom-in - a virtual open-house, 10 April 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 will be announced closer to the event.

The following NAISS Zoom-in is planned for 8 May 2025

CodeRefinery events

Online workshop: CodeRefinery workshop, March 25-27, and April 1-3, 2025

Organised by CodeRefinery and partners, including NAISS

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 25-27 March and 1-3 April 2025, for free and online.

The workshop covers good coding practices, reproducible research principles, and using Git for collaboration. It consists of streamed lectures and exercises. 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 CodeRefinery workshop page (GitHub).

University events

Monthly Workshop Series: Whisper Transcription demonstration, continuing 4th April

Collaboration between UPPMAX and CDHU

OpenAI’s Whisper model makes it possible run fast, accurate, and secure automatic transcriptions of audio locally through Uppmax. This is even possible for files that are several hours long and/or which contain sensitive or personal information. In this demonstration, an Uppmax applications expert working with Humanities and Social Sciences researchers and CDHU will provide information about getting started with Whisper on their systems.

When: choose among April 4, or May 5

Where: hybrid event (Uppsala and online)

For more information, please visit the event calendar of Digital Humanities and Social Science, Uppsala University.

ENCCS training

Please visit the ENCCS event page for more information on all ENCCS training events.

Webinar: Practical Introduction to GPU Programming, 27 March

Abstract: Graphical processing units (GPUs) are the workhorse of many high performance computing (HPC) systems around the world. The landscape of GPU hardware, software and programming environments is quite complicated. Multiple vendors compete in the high-end GPU market, with each vendor providing its own software stack and development toolkits, and even beyond that, there is a proliferation of tools, languages and frameworks that can be used to write code for GPUs. This webinar 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.

Detailed information at ENCCS event page, see above.

Time: March. 27, 12:00-13:30 (CET) (2025).

Hybrid Workshop: PIC (BIT1) modelling of the fusion plasma edge. 7-9 April 2025

BIT1 is an electrostatic Particle in Cell (PIC) Monte Carlo (MC) code optimized for plasma edge modelling. It is 1D in usual and 3D in velocity space. The code is capable of simulating large scale systems with finest resolution in time and space. During the workshop we will 1) introduce the BIT1 code; 2) explain its modelling capabilities; 3) perform training sessions for users of different level; 4) consider examples of other PIC and MC codes; 5) discuss future developments related to exascale and multi-dimensional versions of the code (BIT2,3).

Detailed information and access to registration on the ENCCS event page, see above.

Date: 7-9 April 2024

Hybrid Workshop: Exploring Biomolecular Modelling and Simulations, 9-10 April

BioExcel CoE, NCC Türkiye, and ENCCS will deliver an interactive training on biomolecular modeling and simulation. Four sessions will be covered in this workshop:

1) Integrative modeling of biomolecular complexes with HADDOCK;

2) Molecular Dynamics Simulations – GROMACS;

3) Interoperable and Reproducible Biomolecular Simulation Workflows using BioExcel Building Blocks (BioBB); and

4) Fundamentals and Practical Use Cases of Free Energy Calculations with PMX.

Detailed information at ENCCS event page, see above.

Time: 9-10 April 2025

Webinar: Development of algorithms for partial multi-label machine learning, 15 April

Abstract: Machine learning is a branch of artificial intelligence that enables computers to learn from data and make predictions or decisions without being explicitly programmed. Multi-label learning is a type of machine learning problem where each data instance can be associated with multiple labels simultaneously. Partial multi-label learning addresses problems where each instance is assigned a candidate label set and only a subset of these candidate labels is correct. In this webinar, we will talk about the general features of multiple partial multi-label methods, and then the development of learning algorithms to handle dataset with large noisy labels across different domains using varied frameworks, with a focus on the recently developed methods for partial multi-label learning based on the Encoder-Decoder framework.

Detailed information at ENCCS event page, see above.

Time: April 15, 12:00-13:30 (CET) (2025).

Workshop: Practical Deep Learning, 6-8 May

Abstract: Deep learning is a subset of machine learning that focuses on training artificial neural networks with multiple layers to recognize patterns and to simulate the complex decision-making power of the human brain. The use of deep learning has seen a significant increase of popularity and applicability over the last decade. While it serves as a powerful tool for researchers across various domains, taking the first steps into the world of deep learning can be somewhat intimidating. This workshop aims to provide beginners with a foundational understanding of deep learning concepts, network architectures, and applications on drug discovery, computer vision and large language models.

Detailed information at ENCCS event page, see above.

Time: May 6-8, 09:00-12:00 (CET) (2025).

Webinar: Software Installation on HPC, 13 May

Abstract: Installing software on High-Performance Computing (HPC) systems differs from typical installations on personal computers due to multi-user environments, shared resources, and system-wide configurations. Instead of installing software globally, users often work within shared or isolated environments while leveraging specialized tools for software management. There are multiple methods available to install software on HPC systems depending on specific configuration of HPC systems. This webinar is designed for new users of the HPC systems who want to install software by themselves. It will cover topics such as compiling code from source (make and cmake), utilizing "package managers" (conda, spack, and easybuild), and deploying executables with containers (Singularity) on the HPC systems.

Detailed information at ENCCS event page, see above.

Time: May 13, 12:00-13:30 (CET) (2025).