Welcome to the latest edition of the SNIC newsletter.  We newly advertise training on MD simulations and Singularity containers.   Please note the date and time change for the Alvis introduction seminar.  Registration closes soon for the data handling seminar and the Python at UPPMAX events.   Next week we will also have our open support session “zoom-in”.

• Training on application software
• Online workshop: "Python at UPPMAX", 10 March, 2022
• Online training course: "MD simulations with a focus on NAMD" in Umeå, 7-8 April, 2022
• Online training workshop: Basic Singularity - Running and building Singularity containers, 20 April 2022.
• Training to use the Alvis system, dedicated to machine learning
• Change of date and time for: Online introduction seminar for Alvis users, 16 March 2022
• Training in data handling
• Online training seminar: Handling large data within SNIC, using Swestore - 15 March 2022
• Online interactive support and discussion forum:
• SNIC zoom-in - a virtual open-house, 17 March from 14:00 until 15:00
• Training events from CodeRefinery
• CodeRefinery online workshop: Best practices and tools for research software, 22-24 and 29-31 March, 2022
• Training events from ENCCS
• ENCCS SYCL Workshop, 19-21 April, 9:00-12:10 CEST

Training on application software

Online workshop: "Python at UPPMAX", 10 March, 2022

UPPMAX is organizing a 1+1 hour interactive introduction on how to run and install additional Python packages on the computer resources provided by UPPMAX - Rackham, Snowy, and Bianca.

The following will be covered during the first hour:

• Loading the appropriate Python module from the software tree
• Installing additional packages in the common user space under $HOME
• Installing packages in Python virtual environments in project folders
• Using ‘conda’ to install packages in virtual environments - suitable approach for Bianca
• Alternative approaches

In the following hour, participants will be able to bring their particular software request for discussion with the UPPMAX application experts.

When: Thursday, March 10, 2022.

Time: 13:00 - 15:00.

Where: online.

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

Online training course: "MD simulations with a focus on NAMD" in Umeå, 7-8 April, 2022.

HPC2N is offering a course on "MD simulations with a focus on NAMD". The course will be ONLINE. We will use Zoom.

The aim of the course is to let participants learn how to use NAMD to set up basic molecular dynamics simulations, and to understand typical NAMD input and output files.

We will start from scratch by setting a MD Biomolecular (protein+water) simulation, in the first day of the course. During the second day, we will learn how to setup a steered molecular dynamics simulation (Na-Cl system) and use the results to compute the free energies of separation. Regarding the software, we will use software already installed at HPC2N, i.e. VMD, and NAMD for the full protocol. We will also provide users with a set of best practices to improve the performance of their simulations.

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

Date and time for the course: 7-8 April, 2022, 9:00 - 12:00 each day.

Deadline for signing up: 31 March 2022.

For more information and registration, see the MD course page at HPC2N.

Online training workshop: Basic Singularity - Running and building Singularity containers, 20 April 2022.

This online workshop is an introduction to the basic concepts of containerised software environment solutions within the Singularity framework (at 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 …

For more information and access to registration please visit the Singularity workshop page at UPPMAX.

Training to use the Alvis system, dedicated to machine learning

Change of date and time for: Online introduction seminar for Alvis users, 16 March 2022

In this online seminar we will show you how to use Alvis.  Zoom meeting will be at 8:00 - 12:00.   The second part of this seminar will be an optional workshop where users can go through a tutorial with help available and on reserved nodes on Alvis.  To get access to the reserved resources you need to request membership to project SNIC 2021/7-120 two days before the seminar at the latest.

Meeting URL

Visit the C3SE website for more information.

Training in data handling

Online training seminar: Handling large data within SNIC, using Swestore - 15 March 2022

This event addresses users handling large amounts of research data.  Users with large  amounts of research data, exceeding the storage available on the SNIC systems or requiring data access from multiple SNIC services, are encouraged to utilise SNIC’s Swestore system.

This seminar will discuss how to access Swestore from your laptop and from the SNIC clusters.  Tools discussed will include Winscp and Cyberduck for data access from your laptop as well as the Advanced Resource Connector (ARC) middleware.   The seminar will also show how to apply for Swestore storage.

The event is offered by LUNARC and NSC as part of the SNIC training.

For more information and access to registration, consult:

• Data handling seminar page at LUNARC
• Data handling seminar page at NSC

Online interactive support and discussion forum

SNIC zoom-in - a virtual open-house, 17 March 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.

Next zoom-in session: 17 March from 14:00 until 15:00

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

Training events from CodeRefinery

CodeRefinery online workshop: Best practices and tools for research software, March 22-24 and 29-31, 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, but we teach the tools you need to use 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.

For further information and registration, please visit the CodeRefinery workshop page at GitHub

Training events from ENCCS

ENCCS SYCL Workshop, April 19-21, 9:00-12:10 CEST

SYCL is a C++ abstraction layer for programming heterogeneous hardware with a single-source approach. SYCL is high-level, cross-platform, and extends standard ISO C++17. You will learn to:

• Use the hipSYCL compiler to generate executables for multiple hardware targets.
• Write hardware-agnostic code to express parallelism using the queue, command group, and kernel abstractions.
• Use buffer and accessors to handle memory across devices.
• Evaluate drawbacks and advantages of unified shared memory.

Further information and registration at the SYCL workshop page at ENCCS.

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.