NAISS Training Newsletter
No 16, 19 December 2023
– Published 19 December 2023
The NAISS training team wishes everyone a merry Christmas and a happy new year 2024
Welcome to the last NAISS training newsletter of the year 2023. In this newsletter we announce a number of training events for 2024
Overview
NAISS events
- UPPMAX Introductory Course, 15-18 January, 2024
- Online workshop: "Awk Workshop", January 22-23, 2024
- Online training seminar: An introduction to the UNIX/LINUX command-line, 6th February 2023 at 13:30
- Online workshop: Basic Singularity: Running and Building Singularity Containers, 13 February, 2024
- Online introduction to running R, Python, and Julia in HPC, 12-14 March 2024
Training events organised by HPC centres in Sweden
- Training course: "Introduction to Kebnekaise", 18 January 2024
ENCCS training
- Webinar: Practical intro to GPU programming in Python and Julia, 2nd February
- Workshop: Efficient materials modelling on HPC with QUANTUM ESPRESSO, SIESTA and Yambo, 11 - 15 March
- The N-ways to GPU Programming Bootcamp, 3-5 April
- The Multi-GPU Programming Bootcamp, 6-7 May
- The AI for Science Bootcamp, 25-26 June
- Publicly available training material
- Training events from around Europe
NAISS training
UPPMAX Introductory Course, 15-18 January, 2024
This 4-day course provides an introduction to the high-performance computing (HPC) environment offered at UPPMAX.
It offers an overview on how the systems work and covers skills from basic Linux usage to more advanced tips and tricks, including Python scripting.
Participation is open to all existing and prospective NAISS users.
When: 15-18 January, 2024
Where: online via Zoom
For more information and registration, please visit the UPPMAX introduction course page at UPPMAX.
Online workshop: "Awk Workshop", January 22-23, 2024
Awk is an interpreted programming language designed for text processing and typically used as a data extraction and reporting tool. This two-day workshop aims to promote and demonstrate the flexibility of the tool, where the overhead of more sophisticated approaches and programming languages is not worth the bother.
Learn how to use Awk as an advanced grep command, capable of arithmetic selection rules with control over the content of the matched lines perform simple conversions, analysis or filter you data on the fly making it easy to plot or read in your favorite research tool handle and take advantage of data split over multiple file data sets use Awk as simple function or data generator perform simple sanity checks on your results.
The workshop aims to promote the awk tool for use in everyday research work and urges you to find solutions yourself rather than expecting ready-made ones. The material given during the seminar will not be a complete guide or a manual but rather an overview of the capabilities, particular strengths, and common disadvantages.
When: January 22-23, 2024
Where: online via Zoom
For more information and registration, please visit the Awk Workshop page at UPPMAX.
Online training seminar: An introduction to the UNIX/LINUX command-line, 6th February 2023 at 13:30
This training seminar provides a first introduction to the UNIX/LINUX environment. It is aimed at new users of UNIX and will discuss UNIX skills required to work on a typical HPC cluster, such as provided by LUNARC, NAISS and other Swedish Universities. . Topics include manipulating files and directories, editing file contents and the development of simple scripts, such as required for job submission.
Time: 6th February at 13:30 - 16:00
Location: A zoom link will be provided to registered participants
For more information and registration visit the UNIX/LINUX introduction seminar at LUNARC.
Online workshop: Basic Singularity: Running and Building Singularity Containers, 13 February, 2024
The online workshop is an introduction to the basic concepts of containerised software environment solutions within the Singularity framework (Sylabs).
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 at the GitHub page for the Singularity workshop to install Singularity on your computer before the workshop.
When: 13 February, 2024
Where: online via Zoom
For more information and registration, please visit the Singularity workshop page at UPPMAX.
Online introduction to running R, Python, and Julia in HPC, 12-14 March 2024
HPC2N, in cooperation with UPPMAX, is offering a three-day ONLINE training course "Introduction to running R, Python, and Julia in HPC".
Learn how to run R, Python, and Julia 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, 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 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, 12-14 March 2024
Location: online via Zoom
For more information and registration, see the course websites:
Training events organised by HPC centres in Sweden
Training course: "Introduction to Kebnekaise", 18 January 2024
HPC2N is offering an ONLINE training course "Introduction to Kebnekaise". It will be given on 2024-01-18, 09:00 - 17:00.
We begin with a short OPTIONAL introduction to the Linux operating system (OS) that is used on HPC2N's compute cluster, and is the most common OS in HPC clusters. This part is only meant for complete beginners to the Linux operating system, and can be omitted if you are proficient already.
Then, we continue with an introduction to HPC and HPC2N, before going on to a walk-through of the Kebnekaise system, including the GPUs. In the afternoon 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 the CPUs as well as the different types of GPUs (V100s and A100s).
During the hands-on you will get the opportunity to load modules, try some of the installed applications, create a jobscript, and submit a job to the Kebnekaise cluster.
Eligibility: This course in only available to 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.
For more information and registration, see the Kebnekaise introduction page at HPC2N.
ENCCS training
Webinar: Practical intro to GPU programming in Python and Julia, 2nd February
Availability of Graphics Processing Units (GPUs) has transformed the way we work with machine learning and data science challenges in life sciences. The parallel processing capabilities of GPUs have allowed training of ever more complex models. As a result, it allows researchers to analyze large biological datasets with unprecedented efficiency. However, in order to make use of this potential we need to write fitting machine learning model code and analysis pipelines. In this webinar ENCCS will present some practical tips about what to keep in mind and how to optimize your code when running analyses on GPU hardware.
This webinar will be most useful to researchers who already work with large datasets and would like to improve their understanding of how to work with GPUs. At the end, the participants will learn about online materials and in-person courses where researchers can learn about this topic in depth.
Time: Feb. 2, 10:00-11:30 (2024).
For more information information and registration, see the event pages:
Workshop: Efficient materials modelling on HPC with QUANTUM ESPRESSO, SIESTA and Yambo, 11 - 15 March
Abstract: In recent years, computing technologies underlying materials modelling and electronic structure calculation have evolved rapidly. High-performance computing (HPC) is transitioning from petascale to exascale, while individual compute nodes are increasingly based on heterogeneous architectures that every year become more diversified due to different vendor choices. In this environment, electronic structure codes also have to evolve fast in order to adapt to new hardware facilities. Nowadays, state-of-the-art electronic structure codes based on modern density functional theory (DFT) methods allow treating realistic molecular systems with a very high accuracy.
This workshop will give a broad overview of important fundamental concepts for molecular and materials modelling on HPC, with a focus on three of the most modern codes for electronic structure calculations (QUANTUM ESPRESSO, SIESTA and Yambo). Participants will put their new knowledge to the test on the Leonardo EuroHPC JU supercomputer (https://leonardo-supercomputer.cineca.eu/hpc-system/) with theory sections and practical demonstrations and hands-on exercises.
Time: March 11-15, 9:00-13:00 (2024).
For more information and registration, see the materials modelling event page at ENCCS.
The N-ways to GPU Programming Bootcamp, 3-5 April
The N-Ways to GPU Programming Bootcamp covers the basics of how to use GPUs and provides an overview of different methods for porting scientific application to GPUs using NVIDIA® CUDA®, OpenACC, standard languages, OpenMP offloading, and/or CuPy and Numba.
Throughout the bootcamp, attendees with learn how to analyze GPU-enabled applications using NVIDIA Nsight™ Systems and participate in hands-on activities to apply these learned skills to real-world problems.
Time: April 3-5, 9:00-13:00 (2024).
For more information information and registration, see the event pages:
The Multi-GPU Programming Bootcamp, 6-7 May
Scaling applications to multiple GPUs across multiple nodes requires one to be adept at programming models and optimisation techniques, and proficient at performing root-cause analysis using in-depth profiling to identify and minimise bottlenecks.
Topics on GPU programming covers single node multi-GPU (P2P) and multi-Node multi-GPU (GPU Direct) programming, the NVIDIA Collectives Communications Library (NCCL), and the NVSHMEM, which is a parallel programming interface based on OpenSHMEM that provides efficient and scalable communication for NVIDIA GPU clusters).
The Multi-GPU Programming Bootcamp covers step-by-step ways to improve application performance using cues from profilers and provides an understanding of the underlying technologies and communication topology needed to leverage powerful NVIDIA® libraries to extract more performance from the system.
Time: May 6-7, 9:00-15:00 (2024).
For more information information and registration, see the event pages:
The AI for Science Bootcamp, 25-26 June
Abstract: The AI for Science Bootcamp provides a step-by-step overview of the fundamentals of deep neural networks and walks attendees through the hands-on experience of building and improving deep learning models for applications related to scientific computing and physical systems defined by differential equations.
The material will cover more advanced topics, such as physics-informed neural networks (PINNs) and operator learning and make use of tools like NVIDIA Modulus to develop and train the models. Furthermore, this online bootcamp is a hands-on learning experience where we will guide you through step-by-step instructions with teaching assistants on hand to help throughout.
Time: June 25-26, 9:00-13:30 (2024).
For more information information and registration, see the event pages:
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.