high-performance computing ➤
outstrips increases in budgets, so the job falls to the computational physicists like Delaney to improve the performance of the soſtware. Delaney said: ‘We have lots and lots of data, and computers just can’t get fast enough as far as the oil industry is concerned. Te more horse power we can get our hands on, the more we can use at any given time. Small things matter, small improvements in resolution really do make a difference.’ Te team at Tullow has imposed vectorisation and improved the parallelisation of the code generally leading to a six-fold speed-up. NSilico provides data management and
analytics soſtware for the life sciences and healthcare industries. Its flagship program, Simplicity, is a cloud-based system for
SMALL THINGS
MATTER, SMALL IMPROVEMENTS IN RESOLUTION REALLY DO MAKE A DIFFERENCE
the automatic annotation, analysis, and visualisation of genetic data. Based in the city of Cork, to the south of Ireland, NSilico last year took part in the Prace SHAPE programme to encourage small and medium companies to use HPC to help develop their business, partnering with CINES in France and ICHEC to develop a technique for rapid alignment of short DNA sequences. NSilico uses the Smith-Waterman algorithm
to determine similar regions between two strings or nucleotide or protein sequences. According to Brendan Lawlor, a soſtware architect from NSilico: ‘Smith-Waterman is a data-dependent algorithm largely because some cells in the
matrix may rely on the results of others.’ NSilico has streamlined the code, rewriting the Smith- Waterman algorithm component into only 1,000 lines of Scala code and thus reducing opportunities for inefficiencies. However the team has so far only scaled the code across three cores, so they are just beginning investigations into how to scale across larger systems.
Supercomputing for small companies made simpler? Te most fragile part of the HPC ecosystem is the network of small firms, spin-out companies and open source soſtware service companies Oſten they are geographically dispersed and lack critical mass – so there could be a role for Prace as an ‘incubator’ for such companies and for the ‘early adopters’ of HPC among small to medium enterprises (SMEs), Lee Margetts, lecturer in computational mechanics at the University of Manchester, told the meeting. A special session of the meeting was devoted
to demonstrating how these smaller companies in the HPC ecosystem could encourage and support the wider use of high-performance computing both in industry and also in the public sector. In a hugely dynamic and enthusiastic
presentation, Stefano Cozzini, CEO of eXact Lab in northern Italy, offered some ideas and practical examples. His company exists to ease access to high performance computing for SMEs and for the public sector as well. It started as an HPC consultancy, but aſter
three years in business, Cozzini and his co- founders realised that consultancy ‘does not scale’ and that they needed a scalable solution to provide their services. Tis led to the eXact computing environment, targeting SMEs whose
Europe needs world-class computing, according to Augusto Burgueño Arjona, head of e-Infrastructure at the European Commission
HPC needs still have to be properly identified. Tese could range from CFD to rendering for media companies, he said. One fruit of their labours is XeRis – a cloud
platform for advanced analysis of seismic hazards with a web-based interface. Among the users have been a Swiss nuclear power plant and the Government of Trieste in Italy, which is using the service to assess the seismic safety of schools in the region. (As the destruction of Assisi due to two devastating earthquakes that shook Umbria in September 1997 testifies, earthquakes are a real risk in Italy.) But Cozzini admitted that it was a challenge
to find enough people who were trained in high-performance computing and to establish networks of small and medium sized companies who could provide the expertise needed. So, the University of Trieste is running a Masters programme in high-performance computing; and in early 2012, a group of Slovenian and Italian companies came together to form the High Performance and Cloud Computing Cross-Border Competence Consortium (HPC5) to provide businesses, researchers, and universities with advanced HPC and cloud computing services. Manuel Arenaz, from the Spanish company
HPC’s happy family in Europe: delegates to the Prace meeting in Dublin 20 SCIENTIFIC COMPUTING WORLD
Appentra Solutions, reminded his audience that ‘programming supercomputers is hard’. His company has therefore developed a soſtware tool, called ‘Parallware’, to find course-grain parallelism in sequential source code automatically, without intervention by the programmer. Speaking by video link as he was unable to attend the session in person, Parallware as another way of addressing the HPC ‘talent gap’ because it should allow engineers and scientists to focus on their science and engineering and decouple that task from the details of the underlying parallel hardware. l
@scwmagazine l
www.scientific-computing.com
Jason Clarke Photography
Jason Clarke Photography
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