Welcome to a new edition of the NAISS training newsletter.  In this newsletter we newly advertise an introduction course at UPPMAX, training in AWK scripting and training in BASIC Singularity use.   We remind on training events on handling sensitive data and the use of job submission systems on our clusters.

The last Zoom-in of the year for the 7th December.  We have number of reminders on previously published training events.  We also advertise introduction training for users at HPC2N.

Overview

NAISS events

• Online workshop: Introduction to Bianca: Handling Sensitive Research Data, 11 December 2023
• Online training seminar: Cluster architecture and job submission, 12th December 2022 at 13:30
• Online hackathon: Bianca In-Depth: Improve Your Handling of Sensitive Research Data, 14 December 2023
• UPPMAX Introductory Course, 15-18 January, 2024
• Online workshop: "Awk Workshop", January 22-23, 2024
• Online workshop: Basic Singularity: Running and Building Singularity Containers, 13 February, 2024

Online interactive support and discussion forum

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

Training events organised by HPC centres in Sweden

• Training course: "Introduction to Kebnekaise", 18 January 2024

NAISS training

Online workshop: Introduction to Bianca: Handling Sensitive Research Data, 11 December 2023

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: Monday 11 December

Where: Online via Zoom

For more information and registration please visit the Bianca December introduction page at UPPMAX.

Online training seminar: Cluster architecture and job submission, 12th December 2022 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 December at 13:30

For more information and registration visit the cluster architecture and job submission training seminar page at LUNARC.

Online hackathon: Bianca In-Depth: Improve Your Handling of Sensitive Research Data, 14 December 2023

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 (i.e. RStudio and/or VSCode), and installing custom software and packages.

The workshop will consist of short lectures and the content will be driven by questions from the participants.

To attend this course, we expect you to be able to login to Bianca, submit a Slurm bash script, and know how to transfer files.

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.

When: Thursday 14 December

Where: Online via Zoom

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

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 Bianca January introduction 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 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

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 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 interactive support and discussion forum

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

Zoom link for the 7 December NAISS Zoom-in

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.