Current NAISS Training Newsletter
NAISS training newsletter No 35, 17 February 2025
Welcome to the this week’s edition of the NAISS training newsletter. Registration for the ParaView event, the Python introduction and the C++ array computing course. We newly list a UNIX introduction, a Python in HPC course and the programming formalism course.
The CodeRefinery workshop in late March is still taking registrations.
The next interactive support session Zoom-in is scheduled for 13 March 2025
Uppsala University and ENCCS asked us to share one of their events.
NAISS training
- Online course: Using ParaView and Trame for Scientific Visualisation on HPC resources, 26 February 2025
- Online course: Introduction to Python, March 4, 2025
- Online course: Array computing in C++ using Eigen, 5 March 2025
- Online training seminar: Introduction seminar for Alvis users, 5 March 2025
- Online workshop: Transferring Files to/from HPC Clusters, 7 March 2025
- Online workshop: Introduction to Bianca: Handling Sensitive Research Data, 19 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: Using Python in an HPC environment, 24-25 and 28-29 April 2025
- Online course: Programming Formalisms, 5-9 May 2025
Online interactive support and discussion forum:
- NAISS Zoom-in - a virtual open-house, 13 March 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
- 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 course: Using ParaView and Trame for Scientific Visualisation on HPC resources, 26 February 2025
This training course introduces scientific visualization using the ParaView application. Participants will first learn the fundamentals of ParaView, including data loading, basic visualization techniques, and essential features for scientific data exploration. During the training, several example data sets will be examined and visualized. We will also show how ParaView can be run on the NAISS resources using hardware-accelerated graphics.
ParaView is a powerful but complex application. Sometimes, a simplified user interface for the visualization pipeline needs to be provided to make a visualization accessible. Kitware has developed the Python-based Trame framework for creating simplified web-based interfaces for visualization pipelines created in ParaView. An example visualization pipeline will be implemented using the Trame framework.
For more information and access to registration visit: https://www.lunarc.lu.se/learning-more/training-courses/using-paraview-and-trame-for-scientific-visualisation-on-hpc-resources-26-february/
Online course: Introduction to Python, March 4, 2025
This 1-day course helps you get started with Python, by working through an online and free book. We make use of HPC clusters to write and run Python code. The pace of this highly interactive course is set by the majority of learners, ensuring that any complete beginner has enough time for exercises. At the end of the day, you should feel comfortable with the basics of Python and feel familiar to a book on Python to help you on your next steps.
When: Tuesday, March 4, 2025, 09:00-16:00
Where: online via Zoom
For more information and registration, please visit: https://docs.uppmax.uu.se/courses_workshops/intro_to_python/
Online course: Array computing in C++ using Eigen, 5 March 2025
This course introduces students to high-performance array computing in C++ using the Eigen library, a versatile template library for linear algebra, matrices, and vectors. Participants will learn to leverage Eigen's expressive syntax and optimized computations for efficient numerical operations. The course covers fundamental concepts such as matrix operations, vector manipulations, and array broadcasting. Through hands-on exercises, students will discover how to use Eigen's powerful features for basic and advanced array operations, gaining essential skills for numerical programming in C++.
For more information and registration, please visit https://www.lunarc.lu.se/learning-more/training-courses/array-computing-in-c-using-eigen-5-march-2025/
Online training seminar: Introduction seminar for Alvis users, 5 March 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: January 15 13:15-15:00
Registration: https://indico.chalmers.se/event/185/
Online workshop: Transferring Files to/from HPC Clusters, March 7, 2025
In this 3-hour workshop you learn to transfer files to and from Swedish academic HPC clusters. We will cover graphical as well as terminal tools and you will work highly interactively. At the end of the day, you should be comfortable in transferring files between your local computer and a cluster and cross-clusters, and choosing the right tools for your use cases.
The workshop is intended for beginner users but with some Linux experience, see the course link below. You do not need to be a member of a NAISS project in order to join the workshop. A course project on one of the NAISS clusters will be available to those.
When: Tuesday, March 7 2025, 09:00-12:00
Where: online via Zoom
For more information and registration, please visit: https://docs.uppmax.uu.se/courses_workshops/naiss_transfer/
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: https://docs.uppmax.uu.se/courses_workshops/bianca_intro/.
Online course: Introduction to running R, Matlab, and Julia in HPC, 24-26 March 2025
Cooperation between HPC2N, LUNARC and UPPMAX
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: https://www.hpc2n.umu.se/events/courses/2025/spring/r-matlab-julia
https://docs.uppmax.uu.se/courses_workshops/R_matlab_julia/
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 course website: https://www.hpc2n.umu.se/events/courses/2025/spring/2/linux-intro
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: https://www.hpc2n.umu.se/events/courses/2025/spring/hpc-python
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 https://docs.uppmax.uu.se/courses_workshops/programming_formalisms/
Change of date: NAISS Zoom-in - a virtual open-house, 13 March 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 10 April 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 https://coderefinery.github.io/2025-03-25-workshop/.
University events
Monthly Workshop Series: Whisper Transcription demonstration, continuing 4th March
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 March 4, April 4, or May 5
Where: hybrid event (Uppsala and online)
For more information, please visit: https://www.uu.se/en/centre/digital-humanities-and-social-sciences/events.
ENCCS training
Please visit the ENCCS event page: https://enccs.se/events-at-enccs/ 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).
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).