Support for science

A public UK HPC knowledge base

Author: Andy Turner
Posted: 11 Nov 2019 | 08:49

Photo by Glen Noble on UnsplashIn this blog post I consider how we (as the UK HPC community) could create a community HPC technical knowledge base that would allow us to share and reuse useful technical information. Much of these thoughts came out of discussions at the HPC Champions meeting that took place on 16 September 2019 alongside the UK RSE Conference 2019 in Birmingham, UK along with subsequent discussions at the monthly HPC RSE calls.

Online LAMMPS training for ARCHER

Author: Julien Sindt
Posted: 31 Oct 2019 | 15:56

In October I ran an online training course teaching current and potential ARCHER users how to run LAMMPS. LAMMPS is a widely-used open-source molecular dynamics (MD) software developed at the National Sandia Laboratories, and is optimised to run well on HPC facilities. It consistently ranks in the top 10 most used programs on ARCHER. Although the course was run on ARCHER and with ARCHER users in mind, I tried to teach users how to use LAMMPS on any platform.

Mining digital historical textual data

Author: Rosa Filgueira
Posted: 23 Oct 2019 | 10:43

Over the last three decades the collections of libraries, archives and museums have been transformed by large-scale digitisation. The volume and quality of available digitised text now makes searching and linking these data feasible, where previous attempts were restricted due to limited data availability, quality, and lack of shared infrastructures. One example of this is the extensive digital collection offered by the National Library of Scotland (NLS) (see Figure 1) [1], which can be accessed online and also downloaded for further digital humanities research.

Society of Research Software Engineering launches

Author: Neil Chue Hong
Posted: 23 Sep 2019 | 12:26

The Society of Research Software Engineering launched on 18th September. You can now become a member of the Society and, in doing so, help support software in research and the people who develop it.

ARCHER Embedded Computational Science and Engineering projects

Author: Chris Johnson
Posted: 18 Sep 2019 | 16:01

Since the start of the ARCHER UK National Supercomputing Service service, one hundred eCSE (embedded Computational Science and Engineering) projects have been awarded funding to carry out code improvements for software running on ARCHER and future Tier-1 services. Projects have come from a diverse range of disciplines with principal investigators (PIs), Co-Investigators (Co-Is) and technical staff involved from 44 different institutions across the UK.

Analysing historical newspapers and books using Apache Spark and Cray Urika-GX

Author: Mike Jackson
Posted: 16 Aug 2019 | 16:25

Library booksIn our October 2018 blog post on Analysing humanities data using Cray Urika-GX, we described how we had been collaborating with Melissa Terras of the College of Arts, Humanities and Social Sciences (CAHSS) at The University of Edinburgh to explore historical newspapers and books using the Alan Turing Institute's deployment of a Cray Urika-GX system ("Urika"). In this blog post we describe additional work we have done, to look at the origins of the term "stranger danger", find reports on the Krakatoa volcanic eruption of 1883, and explore the concept of "female emigration".

Active matter in an active city

Author: Guest blogger
Posted: 9 Jul 2019 | 13:39

Giuseppe Negro undertook an HPC-Europa3 visit based in Edinburgh from 15/04/19–27/05/19. He gives us a brief overview of his visit and the work he undertook.

Hi everyone! My name is Giuseppe Negro and I am a PhD student at the University of Bari in Italy. I work in computational modelling of soft matter systems with Prof. Giuseppe Gonnella and with my collegue Livio Nicola Carenza, who was also an HPC-Europa3 visitor in Edinburgh, at the Department of Physics in Bari. I visited EPCC under the HPC-Europa3 transnational access programme, and I was hosted by Prof. D. Marenduzzo at the Department of Physics and Astronomy of the University of Edinburgh located at the James Clerk Maxwell Building.

HPC for urgent decision-making

Author: Nick Brown
Posted: 5 Jul 2019 | 11:13

The EU VESTEC research project is focused on the use of HPC for urgent decision-making and the project team will be running a workshop at SC’19.

VESTEC will build a flexible toolchain to combine multiple data sources, efficiently extract essential features, enable flexible scheduling and interactive supercomputing, and realise 3D visualisation environments for interactive explorations.

Taking the sting out of gout

Author: Amy Krause
Posted: 1 Jul 2019 | 10:48





Gout is estimated to affect 2.5% of the UK population, and is increasing globally in association with cardiovascular disease and obesity. EPCC has been working with Dr Philip Riches of the MRC Institute of Genetics and Molecular Medicine to develop a new app that could lead to improved treatment and better quality of life for patients.

Gout is a type of arthritis caused by excess uric acid in the blood. It is characterised by sudden attacks of intense pain that result in reduced quality of life, work absence and disability. The standard treatment for the condition involves close monitoring of blood urate levels and medication, but the high level of health professional support required to ensure a long term cure of gout is rarely delivered: fewer than half of eligible patients receive preventive treatment and fewer than half of those on treatment receive an adequate dose of medication.

Computing for extreme conditions

Author: Rosa Filgueira
Posted: 27 Jun 2019 | 10:06

The DARE project is addressing the challenges of combining extreme data, extreme computation and extreme complexity in scientific research.

Virtually every scientific domain is experiencing an increase in the volume of data it produces, with growing computational power enabling more complex simulations. Although comparing these simulations with observation can improve models and understanding, it is highly data-intensive.