Modelling & simulation

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.

Optimising sparse matrix-vector products at EPCC

Author: Guest blogger
Posted: 15 Aug 2019 | 11:35

Edoardo Coronado visited EPCC from 18th May–15th August 2019 under the HPC-Europa3 programme. 

Hi! My name is Edoardo Coronado. I am a Mexican PhD student in Technologies of Information at the "Centro Singular de Investigación en Tecnoloxías Intelixentes" (CiTIUS) at the "Universidad de Santiago de Compostela" in Spain. I work on the optimisation of iterative solvers on accelerator devices. I have spent three months at EPCC at the University of Edinburgh under the HPC-Europa3 transnational access programme with Mr Adrian Jackson acting as my host.

My HPC-Europa visit to Cambridge

Author: Guest blogger
Posted: 29 Jul 2019 | 16:27

Hi! My name is Concetta Cozza. I am a PhD student in Life Science at University ‘Magna Graecia’ of Catanzaro. This summer I visited the research group of Professor Michele Vendruscolo based at the University of Cambridge for three months with the HPC-Europa3 transnational access programme.

Computational optimisation of materials at St Andrews

Author: Guest blogger
Posted: 22 Jul 2019 | 11:53

EPCC staff supported Dr Rincon Bonilla in his HPC-Europa3 research visit to the University of St Andrews earlier this year. 

My name is Mauricio Rincon Bonilla. I work as a postdoctoral fellow at the Basque Centre for Applied Mathematics in Bilbao, Spain, where I combine advanced sampling methods with physico-chemical insights to investigate ion dynamics in advanced battery materials. With the sponsorship of an HPC-Europa3 grant, I was able to spend seven weeks at the University of St Andrews with my hosts Prof. Tanja van Mourik and Herbert Fruchtl, who have lots of expertise in density functional theory for biological and inorganic materials. 

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.

Accelerating cloud physics and atmospheric models using GPUs, KNLs and FPGAs

Author: Nick Brown
Posted: 24 Apr 2019 | 11:51

The blog post below is based on the abstract of a talk at the PASC mini-symposium 'Modelling Cloud Physics: Preparing for Exascale' (Zurich, 13 June 2019).

The Met Office NERC Cloud model (MONC) is an atmospheric model used throughout the weather and climate community to study clouds and turbulent flows. This is often coupled with the CASIM microphysics model, which provides the capability to investigate interactions at the millimetre scale and study the formation and development of moisture. One of the main targets of these models is the problem of fog, which is very hard to model due to the high resolution required – for context the main UK weather forecast resolves to 1km, whereas the fog problem requires 1metre or less.

My HPC-Europa visit to EPCC

Author: Guest blogger
Posted: 20 Nov 2018 | 09:08


Pablo C. Cañizares came on an HPC-Europa3 visit to EPCC from 23 July–24 October 2018. In this blog article he summarises his visit.

Hi there! I'm Pablo C. Cañizares, a PhD student in Computer Science from the Complutense University of Madrid (UCM), Spain. I work in the Design and Testing of Reliable Systems group in the Computer Science Faculty of the UCM. I visited EPCC for three months under the HPC-Europa3 transnational access programme and was hosted by EPCC's Dr David Henty.

New Prosperity Partnership to develop world first in high-fidelity engineering simulations

Author: Michele Weiland
Posted: 5 Nov 2018 | 14:44

A consortium led by Rolls-Royce and EPCC was recently awarded an EPSRC Prosperity Partnership worth £14.7m to develop the next generation of engineering simulation and modelling techniques, with the aim of developing the world’s first high-fidelity simulation of a complete gas-turbine engine during operation.

HPC-Europa3: My visit

Author: Guest blogger
Posted: 7 Aug 2018 | 10:28

Dr Martin Lepšík came on an HPC-Europa3 visit in July 2018 and was hosted by Dr Emanuele Paci at the University of Leeds. Martin started his visit by coming to Edinburgh.

My name is Martin Lepšík, and I am a Czech computational structural biologist. After 11 years of fruitful research in quantum mechanics-based drug design (at P. Hobza’s group at IOCB, Prague, CR), I decided to enrich my expertise with enhanced-sampling molecular dynamics of lectin-carbohydrate complexes, important for human health and disease.

Arnau Miro: an HPC-Europa visitor's report

Author: Guest blogger
Posted: 4 Jul 2018 | 10:22

Arnau Miró was an HPC-Europa visitor from 10th Jan–9th Apr 2018. He was hosted by Dr Charles Moulinec at STFC Daresbury Laboratory.

Hello everyone! My name is Arnau Miró and I am a third-year PhD student from Universitat Politècnica de Catalunya. I’m working in the Aerospace department in collaboration with the Barcelona Supercomputing Center Computer Applications in Science and Engineering department. I visited EPCC under the HPC-Europa3 transnational access programme, although I was mainly hosted by Dr Charles Moulinec at STFC Daresbury Laboratory.


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