Welcome to the latest edition of the SNIC training newsletter. In this edition we newly advertise training events in R, Singularity and VeloxChem. In early April we offer a thematic zoom-in, focusing on questions regarding Electronic structure software, parallel programming in MPI/OpenMP and sensitive data handling on the Bianca system. ENCCS would like to draw the 2nd LUMI roadshow to your attention.

Contents of this issue

• Training aimed at new users of the SNIC infrastructure
• Online training and support event: “Introduction to NSC”, 31 March 2021 at 10:00
• Online training event: “C3SE Introductory Seminar”, 9 May 2020, 13:00
• General HPC training
• Training webinar: "Working effectively with HPC systems", 20 April 2021, 10:00 - 15:00
• Online Course: Analysing data in an HPC environment using R, 22 April 2021, 9:00 - 16:00
• Online training workshop: Basic Singularity: running and building Singularity containers, 3 May 2021
• Application specific training
• ENCCS/PDC VeloxChem Workshop: Quantum Chemistry from Laptop to HPC, May 6-7, 09:00-12:30 CEST
• Online interactive support and discussion forum:/li>
  • SNIC Thematic zoom-in - a virtual open-house: 8th April 2021 from 14:00 until 15:00
• Training events from ENCCS, recommended by SNIC
• ENCCS event: 2nd LUMI Roadshow, April 8-9 09:00-11:00
• ENCCS/CSC Workshop – HIP101. April 16, 09:00 - 13:00 CET

Training aimed at new users of the SNIC infrastructure

Online training and support event: “Introduction to NSC”, 31 March 2021 at 10:00

An online event with two parts:

• A short introduction to NSC, which is suitable for new users. The topics include
• the Sigma (LiU) and Tetralith (SNIC) clusters
• the module system
• submitting jobs
• allocating GPU:s for simulations or graphic
• 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: 31 Mar 2021, 10:00 - ca. 11:00 Short introduction to NSC, ca. 11:00 - Open session

The zoom link has been sent out with the email version of the SNIC Training news letter

The presentation will be available on the "Introduction to NSC" page at NSC.

Online training event: “C3SE Introductory Seminar”, 9th May 2020, 13:00

Introductory seminar describing know-hows for working with C3SE systems. This online event is intended for all new users providing a comprehensive overview on our systems and how to get started with using them.

Data and time: 9th May 2020, 13:00 - 15:00

For more information and access to registration please visit the events page at C3SE.

General HPC training

Training webinar: "Working effectively with HPC systems", 20 April 2021, 10:00 - 15:00

This NSC SNIC/PRACE webinar will present useful tools and best practices for working effectively on HPC systems. This will among other things cover methods and skills to help you use allocated resources effectively. It is expected to be of interest for a general HPC system user, both at a more familiar (intermediate) or starting (beginner) level.

Topics include:

• Tools at your end (e.g. terminal, ssh config., file transfer tools, VNC)
• HPC system anatomy (login and compute nodes, interconnect, storage)
• Properties and features of storage areas (e.g. quotas, performance, locality, backups, snapshots, scratch)
• Concept of parallelism (Amdahl’s law), scalability, scheduling and practical advice for good performance
• Software on an HPC system (OS, modules, python envs., concept of build envs., containers with Singularity)
• Ideas and strategies for organizing your workflow (data and file management, traceability and reproducibility)
• Interacting with the Slurm queueing system (requesting resources interactively or in batch)
• Practical examples (preparing, submitting, monitoring and evaluating job efficiency)

While the main part of the content and practices will be useful for HPC systems in general, we will also present examples and special tools specific for the NSC clusters, e.g. Tetralith and Sigma.

For more information and registration, see the HPC course page at NSC.

Online Course: Analysing data in an HPC environment using R, 22 April 2021, 9:00 - 16:00

Do you use R for analysing large amounts of data? Join us at this free SNIC-PRACE course on speeding up the performance of R code by parallelising it! In this course, which is being organised by PDC in its role as a SNIC PRACE training centre, you will learn what parallelisation means, and how to make your R code faster using parallelisation. We will also teach you how to run these codes on Tegner, which is a high-performance computing (HPC) cluster at PDC.

Lecturer: Henric Zazzi

Further information and a registration link can be found on the event page at PDC.

Online training workshop: Basic Singularity: running and building Singularity containers - toward reproducible research. 3 May 2021.

The online workshop is an introduction to the basic concepts of containerised software environment solution 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

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 of software: git, pip, conda, wget, curl ...

Please follow the workshop instructions at GitHub to install Singularity on your computer.

For more information and registration, please visit the singularity workshop page at UPPMAX.

Application specific training

ENCCS/PDC VeloxChem Workshop: Quantum Chemistry from Laptop to HPC, May 6-7, 09:00-12:30 CEST

Quantum molecular modeling of complex molecular systems is an indispensable and integrated component in advanced material design, as such simulations provide a microscopic insight into the underlying physical processes. ENCCS and PDC will offer training on using the VeloxChem program package This event is for researchers and students already familiar with quantum chemistry that want to learn how to:

• Perform quantum chemical simulations of ground- and excited-state properties on large systems and with efficient use of HPC resources.
• Use an interactive, computationally-oriented approach to teaching quantum chemistry.

Further information, a detailed schedule, and a registration link can be found on the VeloxChem Workshop page at ENCCS.

Online interactive support and discussion forum

SNIC Thematic zoom-in - a virtual open-house: 8th April 2021 from 14:00 until 15:00

You are invited to a virtual meeting room. This zoom-in will focus on three topics:

• Electronic structure software (e.g VASP, Wien2k, Gaussian, VeloxChem, QuantumESPRESSO
• Parallel programming using MPI and OpenM
• Bianca system and handling sensitive data

For this zoom-in, we will have SNIC application experts with relevant expertise in these topics available. SNIC users interested in one of these topic or question regarding these topics are highly encourage to join us via zoom.https://www.lunarc.lu.se/support/thematic-zoom-in/

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

A general zoom-in, where we will answer any questions regarding SNIC, SNIC systems and services is currently planned for the 22nd April.

Training events from ENCCS, recommended by SNIC

ENCCS event: 2nd LUMI Roadshow, April 8-9 09:00-11:00

Welcome to the second LUMI Roadshow event! Similar to the first Roadshow event, ENCCS will give an update on the LUMI (Large Unified Modern Infrastructure) pan-European pre-exascale supercomputer. In addition you will be informed of newly accepted access policies, valid for all the European High-Performance Computing Joint Undertaking (EuroHPC JU) systems. ENCCS will then continue to present possibilities of further support towards these systems both as applicants from academia as well as from industry and the public sector.

Further information, a detailed schedule and a registration link can be found on the LUMI Roadshow page at ENCCS.

ENCCS/CSC Workshop – HIP101. 16 April, 09:00 - 13:00 CET

With the upcoming LUMI supercomputer arriving this year in Finland, as well as the Dardel supercomputer arriving this and next year to PDC in Stockholm, ENCCS and CSC are providing a series of training events for future users of these new systems. The main partitions of both LUMI and Dardel will be based on AMD GPUs – users should thus be ready to port their applications to this new architecture.

This training event will be about porting CUDA applications to HIP. It will provide an extensive dive into the Hipify tools and showcase many examples. After this course, the participants will know how to use the AMD Hipify tools to convert CUDA codes to HIP. They will be familiar with the AMD architecture, issues that could arise from the code conversion, and the differences between CUDA and HIP.

In order to take the course, the participant should be familiar with GPU concepts and CUDA. Any experience with GPUs is welcome. Examples and exercises will be available in different programming languages, including Fortran and C.

Links

• LUMI supecomputer
• Dardel supercomputer
• ENCCS/CSC HIP101 workshop page with registration

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.