ARCHER News

Wednesday 18th November 2020

• Supercomputers and molecular simulation in the fight against Covid19Today, Wed 18th November 15:00
• Reproducible computational environments using containers - Introduction to Docker and Singularity, Online 8 - 9 December 2020 10:00-16:00
• HPC Champions, Online, Tuesday 15 December 2020 13:00-17:00
• ARCHER, ARCHER2-4Cabinet and RDF : Service Outage 23-24 November
• Other upcoming ARCHER training

Supercomputers and molecular simulation in the fight against Covid19 :Exploring the binding site of the SARS-CoV-2 main protease using high performance computing

Wednesday 18th November 2020 15:00 - 16:00 BST

Syma Khalid and Jon Essex (both from the University of Southampton)

The UK biomolecular simulation community has come together to characterise a number of the key proteins within the virus in an effort identify targets for vaccines and antivirals. We will provide a brief overview of these activities before focusing on studying the binding site of the SARS-CoV-2 main protease.

The Coronavirus Disease of 2019 (COVID-19) is caused by a novel coronavirus known as the Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2). Despite extensive research since the outset of the pandemic it continues to spread with a high mortality rate. The main protease (MPro) of SARS-CoV-2 is an enzyme essential for virus replication through viral proteolytic activity and subsequent generation of infectious virus particles. Current computational efforts towards SARS-CoV-2MPro inhibitor design have often failed to consider the disruption of the His41-Cys145 catalytic dyad as a possible mechanism, and thus missed the opportunity to target the open conformational state. In this presentation, we use molecular dynamics and metadynamics simulations to sample this conformational change. We calculate a 1 +/- 0:45 kcal/mol free energy difference between the open and closed states of the SARS-CoV-2MPro active site. This indicates that favourable interactions with His41 over the Cys145-His41 dyad interaction can stabilise the open state, and that this state should be considered as part of inhibitor design efforts.

This online session is open to all.

Details and join link : https://www.archer2.ac.uk/training/#upcoming-training

Reproducible computational environments using containers - Introduction to Docker and Singularity

Online 8 - 9 December 2020 10:00-16:00

This course aims to introduce the use of containers with the goal of using them to effect reproducible computational environments. Such environments are useful for ensuring reproducible research outputs and for simplifying the setup of complex software dependencies across different systems. The course will introduce the use of Docker and Singularity containers but the material will be of use for whatever container technology you plan to, or end up, using.

On completion of this course attendees should:

• Understand what containers are and what they are used for
• Understand how to manage and create Docker containers
• Appreciate decisions that need to be made around containerising research workflows
• Understand the differences between Docker and Singularity containers and why Singularity is more suitable for multi-user systems (e.g. HPC)
• Understand how to manage and create Singularity containers
• Appreciate how containers can be used to enable and improve reproducibility in research

This course is aimed at researchers who have no (or very little) previous experience of using containers

Full details and registration : https://www.archer2.ac.uk/training/#upcoming-training

HPC Champions

Tuesday 15 December 2020 13:00-17:00

The next HPC Champions meeting will be held virtually on the afternoon of the 15th December 2020, and will involve talks and discussion sessions. We will confirm topics closer to the time but are likely to include updates from supercomputing services, training, and HPC software. The workshop will run between 1pm and 5pm GMT. If you have an idea for a 10minute presentation, a 3 minute lightning talk or discussion topic then please get in touch with the organiser: Andy Turner (a.turner@epcc.ed.ac.uk).

HPC Champions is a network of individuals with the goal of supporting HPC users in the UK to learn about HPC, find the most appropriate system for their purposes, and to get the most out of that system. The roughly bi-annual HPC Champions workshops play a key part in this, increasing the coordination between the different tiers of HPC in the UK and acting as a launching point for collaboration on projects related to training, outreach, reference materials and more.

The network includes a wide number of HPC communities including RSEs and system administrators from the local, regional and national supercomputing centres, as well representatives of HPC consortia, and we encourage anyone with an interest in supporting researchers and RSEs to make the best possible use of the HPC resources to attend. HPC Champions has been co-located with both the RSE Conference and HPC-SIG in the past, and this time is partnered with the ARCHER2 UK national supercomputing service.

If you have any questions, please contact the organiser: Andy Turner (a.turner@epcc.ed.ac.uk).

Full details and registration : https://www.archer2.ac.uk/training/courses/201215-champions/

ARCHER, ARCHER2-4Cabinet and RDF : Service Outage

0800 23rd November - 1700 24th November

Essential work on the main power settings to site requires a power down which will impact all equipment hosted in computer room 3 (CR3). Systems and services hosted in CR3 will be unavailable for approximately 24 hours.

The systems will be taken out of service at 0800 on Monday 23rd November, and returned to service following the power restoration. Given the complexity of the work, we are suggesting that services will be restored by 1700 on Tuesday 24th November. We will notify users if the services are returned to service earlier than expected.

Services which are affected are:

• ARCHER: Unavailable during this period which means that the login nodes and the compute nodes will not be available.
• RDF: Unavailable which includes the /epsrc and /general filesystems and the RDF login nodes.
• ARCHER2 4Cabinet: /home filesystem will be unavailable but queued jobs should continue to run. Access to the User Access Nodes (UAN) will be disabled as normal functionality will not be possible without the /home filesystem.

Other upcoming ARCHER2 Training

• Supercomputers and molecular simulation in the fight against Covid19 Wed 18th November 15:00-16:00
• ARCHER2 for software package users, Online, 7 December 2020 10:00 - 16:00 GMT
• Reproducible computational environments using containers - Introduction to Docker and Singularity, Online, 8 - 9 December 2020 10:00-16:00
• ARCHER2 for software package users, Online, 10 December 2020 10:00 - 16:00 GMT
• Introduction to ARCHER2 for software developers, Online, 14 - 15 December 2020 10:00 - 16:00 GMT
• HPC Champions, Online, Tuesday 15 December 2020 13:00-17:00

Further details https://www.archer2.ac.uk/training/#upcoming-training