HPC research

Preparing programming models for Exascale

Author: Daniel Holmes
Posted: 18 Jun 2019 | 15:03

To make future heterogeneous systems easier to use efficiently, the EPiGRAM-HS project is improving and extending existing programming models with Exascale potential. We are working with the MPI and GASPI programming models primarily, but also applying our changes to HPC applications like Nek5000, OpenIFS and iPIC3D, and AI frameworks like TensorFlow and Caffe. We expect the trend towards specialisation of hardware will continue and therefore large machines will become more and more heterogeneous.

NEXTGenIO at ISC High Performance 2019

Author: Catherine Inglis
Posted: 6 Jun 2019 | 14:34

The highly successful NEXTGenIO project is now drawing to a close after nearly four years. EPCC colleagues will be at ISC19 presenting the results of the project at a booth presentation, a BoF, and a workshop presentation. Come along and find out more!

Launch of EPCC’s Women in HPC UK chapter

Author: Lorna Smith
Posted: 28 May 2019 | 13:58

Women in HPC (WHPC) was set up in 2013 to tackle the problem of diversity in HPC through research and education. EPCC initiated the WHPC programme and EPSRC supported the initiative. We were therefore very pleased to be accepted as one of the first WHPC chapters, developing a chapter that encompasses all of the UK. We held a successful launch event in May, with attendees from different organisation from across the UK.

HPC Certification Programme: the HPC environment survey

Author: Weronika Filinger
Posted: 26 Apr 2019 | 13:31

We are embarking on a survey of the HPC environment and would appreciate your input! Jean-Thomas Acquaviva, DDN Storage, explains the background below.

Supercomputers are helping us to solve the world greatest challenges but who is helping us to harness the computational power of supercomputers?

The HPC Certification Forum is a community effort that aims to provide an international certification programme for the skills needed by practitioners  to harness supercomputers. It aims to clearly categorise, define, and examine competencies, which will be beneficial to all stake-holders involved in training and education. To make this effort relevant to the whole HPC community, a number of online surveys and polls will be created to capture and estimate the importance of the various tools, technologies, and skills expected from HPC practitioners. 

HPC-Europa3 visitor publishes paper in Physical Review Letters

Author: Guest blogger
Posted: 1 Mar 2019 | 12:33

Former HPC-EUROPA3 visitor Dr Mats Simmermacher, Dr Adam Kirrander (Mats' host from the University of Edinburgh's School of Chemistry), and their collaborators from Edinburgh and Copenhagen have recently published a paper in the prestigious Physical Review Letters where they discuss a new effect in ultrafast X-ray scattering. 

Spark-based genome analysis on Cray-Urika and Cirrus clusters

Author: Rosa Filgueira
Posted: 16 Jan 2019 | 11:06

Analysing genomics data is a complex and compute intensive task, generally requiring numerous software tools and large reference data sets, tied together in successive stages of data transformation and visualisation.

Typically in a cancer genomics analysis, both a tumour sample and a “normal” sample from the same individual are first sequenced using NGS systems and compared using a series of quality control stages. The first control stage, ‘Sequence Quality Control’ (which is optional), checks sequence quality and performs some trimming. While the second one, ‘Alignment’, involves a number of steps, such as alignment, indexing, and recalibration, to ensure that the alignment files produced are of the highest quality as well as several more to guarantee the variants are called correctly. Both stages compromise a series of intermediately computing and data-intensive steps that very often are handcrafted by researchers and/or analysts.

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.

VESTEC: saving the world one byte at a time

Author: Nick Brown
Posted: 15 Nov 2018 | 16:21

With jobs submitted to a batch system, supercomputing has traditionally been centred around an offline, non-interactive approach to running codes such as simulations. However, it is our belief that there is great potential in fusing HPC with real-time data for use as part of urgent decision-making processes in response to natural disasters and crises.

SpiNNaker arrives in the Bayes!

Author: Guest blogger
Posted: 6 Sep 2018 | 11:28

The SpiNNaker neuromorphic high-performance computing platform, which aims to run 1% of the human brain in real time, will arrive at EPCC in the Bayes building this year. SpiNNaker is a novel hardware platform due to its massive parallelism, multi-cast communication fabric and low power design.

HPC Europa3: My visit

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

Dr Martin Lepšík came on an HPC-Europa3 visit from 16-29 July 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.

Pages