Welcome to the latest edition of the SNIC training newsletter. Today we newly list an introduction seminar to SNIC’s new Dardel system and an online training workshop on using Awk. We re-list training events on the Alvis system, using batch schedulers, Quantum Mechanical and Molecular Mechanics simulations, scientific visualisations in ParaView and the OpenFOAM CFD solver.

We highlight training events provided by the ENCCS, which are focusing on users who want to access pre-exascale systems, in particular LU

• Training for new users
• Introduction to the Dardel system at PDC: 6 December 2021 from 14:00 until 15:30
• Online training seminar: Cluster architecture and job submission, 8 December 2020 at 13:30
• Online training workshop: "Awk Workshop", Uppsala, 17 + 18 January 2022
• Training to use the Alvis system dedicated to machine learning
• Online training mini workshop: "Introduction to Alvis", 7 December 2021 at 13:00
• Application training
• Online training course: "QM/MM best practices" by HPC2N, 9 December 2021
• Online training course: “Scientific visualisation with ParaView - An introduction” by LUNARC, 15 December 2021
• PRACE advanced training centre online training course: OpenFOAM training workshop in collaboration with PDC and ENCCS, 7 December 2021
• Training events from ENCCS for users preparing for LUMI access
• ENCCS/NVIDIA GPU Hackathon, 6, 13 - 15 December 2021

Training for new users

Introduction to the Dardel system at PDC: 6 December 2021 from 14:00 until 15:30

You are invited to an online lecture on how to use the Dardel system that PDC provides. The lecture will focus on basic and advanced methods for using Dardel, including login, running software, storing data, compiling code, and more. After the lecture the participants can pose their own questions and have interactive discussion with PDC staff.

Zoom link for Dardel user introduction

Online training seminar: Cluster architecture and job submission, 8h December 2020 at 13:30

This event explains key features of a contemporary HPC cluster, such as widely deployed within SNIC and LUNARC. 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 SNIC resources.

Time: 8 December at 13:30

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

Online training workshop: "Awk Workshop", Uppsala, 17 + 18 January 2022

This 1+1 days 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 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.

When: January 17(+18)*, 2022

During the workshop, you will be able to register for the second day of the workshop.

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

Training to use the Alvis system dedicated to machine learning

Online training mini workshop: "Introduction to Alvis", 7 December 2021 at 13:00

An online event with two parts:

• An introductory presentation with demos, suitable for new users of Alvis.
• An optional workshop where users can go through a tutorial in machine learning on Alvis. To use workshop reserved resources, registration is required.

To register for the workshop part, request membership to SNIC 2021/7-120 at least two days before the seminar start. Alternatively if you are a member of an active project on Alvis, you can use that without reserved resources.

Link to request membership in SNIC 2021/7-120 in SUPR

Time: 7 December 2021

• 13:00 - ca. 15:00 Introduction to Alvis
• 15:00 - 17:00 Workshop with help available

Zoom link for Alvis user introduction

Application training

Online training course: "QM/MM best practices" by HPC2N, 9 December 2021

The aim of the course is to give an intro to classical Molecular Dynamics (MD) simulations and the combined Quantum Mechanical and Molecular Mechanics (QM/MM) simulations. We will start from scratch by setting a MD simulation, in the first half-day of the course, and then use this system to setup a QM/MM simulation. Regarding the software, we will use VMD, NAMD, ORCA, and GAUSSIAN for the full QM/MM protocol. We will also provide users with a set of best practices to improve the performance of their simulations.

This course will be one-day. It will have lectures interspersed with live-demo sessions where you get to try out what the instructor shows.

Time and date: 9 December 2021, 09:00-16:00.

For more information and registration, see the QM/MM course page at HPC2N.

Online training course: “Scientific visualisation with ParaView - An introduction” by LUNARC, 15 December 2021

This course is an introduction to Scientific Visualisation using the ParaView application. ParaView is an open source data analysis and visualisation application. ParaView provides state of the art algorithms and visualisation techniques. It can analyse extremely large data sets and supports a multitude of commonly used data file formats. ParaView is based on the Visualisation Toolkit (VTK), a powerful visualisation library for C++ and Python.

Time: 5 December, 9:00 until 12:30

For more information and access to registration visit the scientific visualisation course page at LUNARC.

PRACE advanced training centre online training course: OpenFOAM training workshop in collaboration with PDC and ENCCS, 7 December 2021

OpenFOAM is a widely-used open-source code in computational fluid dynamics (CFD). OpenFOAM uses finite volume method to solve governing equations of fluid motion through modules written in C++. This workshop will cover all foundational aspects of OpenFOAM, including an introduction to OpenFOAM enviroment as well as running on HPC resources. It will be useful for new users to broaden their basic knowledge of OpenFOAM.

The training will run on the KTH PDC Dardel system. For Dardel specs and the details, see the Dardel page at PDC.

Prerequisites: Basic knowledge of using Linux will be required. Participants are expected to know basic numerical analysis and have CFD theoretical background.

More information and registration at the OpenFOAM workshop page at ENCCS.

Online interactive support and discussion forum

SNIC zoom-in - a virtual open-house

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.

Zoom-in will restart in 2022. If you have any issues with SNIC services, please submit a support request.

Training events from ENCCS for users preparing for LUMI access

ENCCS/NVIDIA GPU Hackathon: 6, 13 - 15 December 2021

Together with NVIDIA and NSC, ENCCS orgnises GPU Hackathons to provide exciting opportunities for scientists to accelerate their AI research or HPC codes under the guidance of expert mentors from National Labs, Universities and Industry leaders in a collaborative environment. Teams of researchers are paired with experienced GPU mentors to learn and apply the accelerated and parallel computing skills needed by the scientific community. Both current or prospective users of large hybrid CPU/GPU HPC clusters who develop HPC and AI applications that could benefit from GPU acceleration are encouraged to participate!

The ENCCS hackathon will be designed for teams to work in productive sprint sessions with expert mentors for a full week. A wide variety of different projects are possible, for example:

• Accelerating applications written in common languages – C/C++, Fortran, Python
• Using OpenACC to gradually offload work to GPUs and incrementally improving the performance
• Identifying expensive kernels and porting them to CUDA
• Profiling already GPU accelerated applications to find hotspots for further acceleration

The event is supported by WASP and NSC through the access to BerzeLiUs system.

Please register at the ENCCS/NVIDIA GPU Hackathon page.

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.