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ARCHER2 Weekly Newsletter

By ARCHER2 Service on May 18, 2022

Tags: newsletters 

Centrally supported software list update

The CSE team is refreshing the list of centrally supported software, to prioritise popular and topical applications. These updates should be completed in the next couple of weeks.

Key changes are:

  • The suite of AMD Optimised CPU Libraries (AOCL) has been installed. These libraries provide common numerical techniques, optimised for AMD processors, and are a complement to the existing Cray LibSci libraries.
  • The ab-initio materials simulation package, FHI-aims, has been installed. This is a replacement for Elk, which will be removed from the list of centrally supported software.
  • An 8,192-core licence for ARM Forge debugger/ profiler (individually known as DDT and MAP) is being installed on a trial basis. ARM Forge is a commercial package for which CSE has secured funding for a licence, through until April 2023. CSE will monitor the use of ARM Forge and, if the software proves to be sufficiently useful, will aim to secure further funding – though availability of Forge beyond April 2023 is not guaranteed.
  • The SUNDIALS algebra library has been removed from the list of centrally installed software, due to lack of demand. It can be installed by individuals, if required.

More details on these changes will appear in the ARCHER2 documentation over the next couple of weeks, as the changes are progressed.

Dynamic hydrogen-bond networks for pH sensing at the membrane interface

Webinar, Wednesday 18th May 2022 15:00 - 16:00 BST

Ana-Nicoleta Bondar, University of Bucharest & Forschungszentrum Jülich

Hydrogen bonds and hydrogen-bond networks are of central interest for understanding protein structure, function, and dynamics. Recent developments in structural biology and computational methods enable access to the three-dimensional structures and dynamics of large proteins and protein complexes, but bring about the challenge of how to identify hydrogen-bond networks, study their dynamics, and rank hydrogen-bonding groups according to their importance in the network. To tackle these challenge, we developed highly efficient graph-based algorithms and graphical user interfaces, and apply these algorithms to study hydrogen-bond networks in proteins and lipid membrane interfaces. The HPC-Europe3 computing time allocation enabled prolonged computation of a pH-sensing ion channel described with different protonations relevant to physiology.

During my seminar I will present the applicability of the graph-based algorithms to analyses of dynamic hydrogen-bond networks of membrane transporters and receptors, including the pH-sensing ion channel studied with the HPC-Europe3 computing time allocation.

More details and join link: https://www.archer2.ac.uk/training/courses/220518-h-bond-networks-vt/

ARCHER2 Annual User Survey 2021-22

We are committed to continually improving the ARCHER2 Service and would like to request your input to help us understand what is important to you, where the Service is working well and where there is scope for improvement.

The ARCHER2 Annual User Survey consists of just a few questions and should take only a few minutes of your time to complete. There are opportunities to add more detailed comments if you wish.

For each survey response received, we will donate £1 to Save The Children.

We are also offering 5 prizes of 2000 CUs on ARCHER2 for users who complete the survey. Winners can choose to forgo the CU prize and for each winner that does this we will donate a further £20 to Save The Children. Winners will be drawn at random from all respondents who have left contact details after the closing date of Thursday 30th June 2022 and the winners notified by e-mail. The prizes are only available to people with existing ARCHER2 user accounts.

You can find the survey at:

https://bit.ly/ARCHER2-User-Survey-2021-2022

Thank you in advance for taking the time to complete this survey. The responses will be used to try and improve the service for you and to help identify key areas for service development.

ARCHER2 Embedded CSE (eCSE) call

We are very pleased to announce that the 7th ARCHER2 eCSE call (ARCHER2 eCSE07) is now open for proposals. The deadline for submitting documents for technical evaluation is 16:00 on 24th May 2022 with the final deadline for proposal submission being 16:00 on 14th June 2022.

Embedded CSE (eCSE) support provides funding of between 1 and 12 person months inclusive for RSEs (Research Software Engineers, PDRAs or equivalent) to carry out software development of codes to be run on the ARCHER2 system. The code(s) may already be running on ARCHER2, where the aim is to improve performance or scalability, to add functionality or to improve the usability and maintainability, or the code(s) may be running elsewhere (e.g. on a Tier-2 system) and the proposal could be to bring the software up to a level where it would perform well on ARCHER2.

For this call, software which results in research which is within the remit of EPSRC is eligible. Funding can be requested for staff located at the institution of the PI, third parties, or can include staff from the centralised CSE support team or a mixture of the above.

More details of how to apply are available by following the link to the eCSE calls page from here

https://www.archer2.ac.uk/ecse/

together with details of the application and review process, assessment criteria eligibility, etc.

eCSE call dates

Deadline for submitting eCSE07 documents for technical evaluation: 16:00 on Tuesday 24th May 2022

Deadline for final eCSE07 submission: 16:00 Tuesday 14th June 2022

A recent webinar can be found here: https://www.archer2.ac.uk/training/courses/210203-ecse-webinar/

which includes a walk through of the submission of a proposal.

eCSE Webinar Thurs 28th April at 3pm

This eCSE Webinar provides an overview of the eCSE programme, examples of work carried out during eCSE projects, and describes the submission process including all the technical and logistical aspects of putting together a proposal. There will be the opportunity to ask questions about any aspect of the programme.

Video of the session: https://www.archer2.ac.uk/training/courses/220428-ecse-webinar/

eCSE Tutorial - Preparing an eCSE Proposal (09:30-12:30 10th May 2022)

In addition to the eCSE webinar, we would like to invite you to this workshop which will take prospective candidates (PIs and RSEs) through the process of preparing a proposal from the initial idea, right through to submitting the final proposal. We will discuss how to put a project team together, how to deal with any associated costings, and will include all the various aspects of the application form within the SAFE and any additional documents required. There will be lots of time for questions.

Video of session : https://www.archer2.ac.uk/training/courses/220510-ecse-tutorial/

Recently added Known Issues

The “Known Issues” page of the ARCHER2 Documentation https://docs.archer2.ac.uk/known-issues/ lists all current open known issues including a description of the issue, its symptoms and any work-arounds.

  • No recent issues

Upcoming ARCHER2 Training

  • Message-passing Programming with MPI, Online, always-open self-service course
  • Shared Memory Programming with OpenMP, Online, always-open self-service course
  • QM/MM with GROMACS + CP2K, Online, Always open - self-service course

  • Dynamic hydrogen-bond networks for pH sensing at the membrane interface, Online webinar, Wednesday 18th May 2022 15:00 - 16:00 BST
  • A CFD tool for the simulation of renewable energy devices using GPU accelerated hardware, Online webinar, Wednesday 25th May 2022 15:00 - 16:00
  • Reproducible computational environments using containers, Western General Campus, Edinburgh, 20 - 21 June 2022 10:00 - 16:00 BST
  • GPU Programming with CUDA, The Open University, Milton Keynes, 27 June 2022 10:00 - 17:00 BST

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

Twitter: https://twitter.com/ARCHER2_HPC

Recordings of past courses and virtual tutorials can be found here: https://www.archer2.ac.uk/training/materials/