HPC research

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.

New exascale projects at EPCC

Author: Lorna Smith
Posted: 16 Jul 2018 | 11:36

The EU has recently funded a significant number of new projects to continue to drive forward Europe’s readiness for the transition to exascale computing. As a result EPCC will add another three projects to its portfolio of exascale activities.

March 2018 meeting of the MPI Forum

Author: Daniel Holmes
Posted: 21 Apr 2018 | 16:21

In the March 2018 meeting of the MPI Forum, the “Persistent Collectives” proposal began the formal ratification procedure, the “Sessions” proposal took a step forward, but the “Fault Tolerance” saga took a step side-ways.

The proposal to add persistent collective operations to MPI was formally read at the March meeting, and was well-received by all those present. The first vote for this proposal will happen in June and the second vote in September. If all goes well, this addition to MPI will be announced at SC18.

HPC-Europa 3 visit: Optimising the processing of food

Author: Guest blogger
Posted: 11 Apr 2018 | 10:49

Miriam Ruiz Ferrández was a recent HPC-Europa3 visitor to Edinburgh who used EPCC resources while being hosted by Napier University. In this article she relates some of her findings and experiences.

Hi everyone! I am a PhD student at the University of Almería, which is located in the south-east of Spain. I spent three months in Edinburgh funded by the HPC-Europa3 programme working on a project entitled: “A Parallel Multi-Objective Algorithm for Optimizing High-Pressure/Temperature Treatments in the Food Industry”. During this research stay, I was collaborating with Professor Ben Paechter at Edinburgh Napier University and I used computing resources provided by EPCC at the University of Edinburgh.

Event Driven Asynchronous Tasks

Author: Nick Brown
Posted: 5 Apr 2018 | 10:28

The INTERTWinE project has spent a lot of effort addressing interoperability challenges raised by task-based models. By rethinking parallelism in the paradigm of tasks, one reduces synchronisation and decouples the management of parallelism from computation.

This is really attractive but existing models typically rely on shared memory, where the programmer expresses input and output dependencies of tasks based upon variables, which in turn limits the technology to a single memory space – often a node of an HPC machine. So to then scale up beyond a single memory space we must combine a task model with distributed memory technology, such as MPI or GASPI, and this has been a focus for a number of activities in INTERTWinE.

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