Welcome to the latest edition of the SNIC newsletter.   The SNIC training team hopes you had a good summer break.

We have events focussing on new users of the infrastructure.  There are events on Awk, Python and MATLAB programming as well as building singularity containers.  We also like to draw your attention to the CodeRefinery event in September.

Please note the change of date for the next zoom-in.   This is now on the 8th September.

Overview

Introduction training for new users

• UPPMAX Introductory Course, 16-19 August 2022 (hybrid)
• Online training seminar: An introduction to the UNIX/LINUX command-line, 14 September 2022 at 13:30
• Online course: Introduction to HPC2N, 15 September 2022, HPC2N, Umeå University

Containers

• Online training workshop: Basic Singularity: Running and building Singularity containers, 28 September 2022

Programming training

• Awk Workshop, online, 29-30 August 2022 (hybrid)
• Using Python in an HPC environment, UPPMAX & HPC2N, 9 September 2022 (online)
• Mondays with MATLAB - online workshops, 12th September, 19th September and 26th September

Training events from CodeRefinery

• CodeRefinery online workshop: Best practices and tools for scientific software development, September 20-22 and 27-29, 2022

Online interactive support and discussion forum

• Change of date: SNIC zoom-in - a virtual open-house, 8 September from 14:00 until 15:00

Introduction training for new users

Online training seminar: An introduction to the UNIX/LINUX command-line, 14 September 2022 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 SNIC and LUNARC.  Topics include manipulating files and directories, editing file contents and the development of simple scripts, such as required for job submission.

Time: 14 September at 13:30

For more information and registration visit the UNIX/LINUX seminar page at LUNARC.

Online course: Introduction to HPC2N, 2022-09-15, HPC2N, Umeå University

We begin with a short (optional) introduction to the Linux operating system that is used on HPC2N's compute clusters. Then, we continue with a walk-through of the Kebnekaise system, including the GPUs and KNLs. After lunch, we go through the module system and take a brief 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.

The course will be completely online and we will use Zoom.

For more information and registration, please go to the HPC2N introduction course page.

Containers

Online training workshop: Basic Singularity: Running and building Singularity containers, 28 September 2022

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...

Please follow the instructions to install Singularity (UPPMAX) on your computer before the workshop.

For more information and access to registration, please visit the singularity workshop page (UPPMAX).

Programming training

Using Python in an HPC environment, UPPMAX & HPC2N, September 9, 2022 (online)

UPPMAX and HPC2N are organising a joint workshop on how to run Python codes and install additional Python packages on the computer resources provided by these two HPC centres. Participants are encouraged to bring their particular software request for discussion as well.

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

• Load Python modules and site-installed Python packages
• Create a virtual environment
• Install Python packages with pip (Kebnekaise, Rackham, Snowy)
• Install Python packages with conda (Bianca)
• Write batch scripts for running Python
• Use Python in parallel
• Use Python for ML
• Use GPUs with Python

Prerequisites: familiarity with the Linux command line, basic Python, and batch jobs.

For more info and registration, please visit the Python-HPC workshop page at UPPMAX or the Python-HPC workshop page at HPC2N.

Awk Workshop, online, August 29-30, 2022 (hybrid)

Awk is an interpreted programming language designed for text processing and typically used as a data extraction and reporting tool.

This two-days 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. Thus, the material given during the seminar will not be a complete guide or a manual. The purpose of the workshop is to give an overview of the capabilities of the awk language and to underline some of its particular strengths as well as its disadvantages.

Venue: Zoom + campus Polacksbacken, Uppsala (see Uppsala campus map)

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

Mondays with MATLAB - online workshops, 12th September, 19th September and 26th September

Are you interested in accessing MATLAB at a HPC center? Do you want to improve performance by parallelising your MATLAB code? Or are you interested in AI, Machine Learning or Deep Learning?

Mondays with MATLAB is a three-part online workshop series intended for users using MATLAB on HPC environments. Featuring in-depth, interactive sessions on Parallel Programming with MATLABand Machine and Deep Learning workflows with MATLAB, these workshops are aimed to provide you with the knowledge you need to scale up your computing needs by harnessing the power of a HPC center or a cluster near you.

A highlight or this series is the 3rd workshop where you will be taken through the steps required in accessing a HPC environment in a hands-on session. Participating HPC centers are SNIC (Sweden), DTU (Denmark) and CSC (Finland) – so users who intend to access these HPC centers will find it most useful.

The 2022 edition of Mondays with MATLAB will be held in September specifically on the 12th between 13.00 and 16.00, on the 19th between 13.00 and 17.00, and on the 26th between 13.00 and 16.00. All times CEST.

For more information and access to registration, visit the Mondays with MATLAB page at MathWorks.

Online interactive support and discussion forum

SNIC zoom-in - a virtual open-house, 8th September 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 the SNIC centres  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.

For more information and details on access, please visit the SNIC zoom-in page.

Training events from CodeRefinery

CodeRefinery online workshop: Best practices and tools for scientific software development, September 20-22 and 27-29, 2022

In this course, you will become familiar with tools and best practices for version control and reproducibility in modern research software development. The main focus is on using Git for efficiently writing and maintaining research software.

We will not teach programming languages, but we will teach the tools you need for programming well. We assume that you are familiar with the programming language that you use in your work and research. We try to keep the course as language-independent as possible but we will show some basic code examples in Python.

This is an informal and interactive online event with type-along type of presentations, live coding, and demos. Short tutorials alternate with practical exercises.

The event is offered in a collaboration between CodeRefinery, SNIC and ENCCS.

Further information and registration, please visit the CodeRefinery workshop page at GitHub.

Training overview

SNIC training webpage

In addition to these news letters we also provide a SNIC training webpage.

This webpage currently gives an overview on all courses currently planned. It provides links to more information and the actual registration. The webpage also includes training which is expected to be mostly of interest to individual SNIC centres. Information will be added to this page as it becomes available.