high-performance computing
Shaping high-performance computing for small companies
At PRACEdays14, held in Barcelona from 20 to 22 May,
Robert Roe heard that high-performance computing is not just for the big boys – but that it can help smaller companies secure competitive advantage.
F
rom the sails of transatlantic racing yachts, through pharmaceutical industry clean-rooms, to rotary turbines, high-performance computing
(HPC) is helping improve the efficiency and competitiveness of Europe’s small to medium sized enterprises (SMEs). Although the commercial application of HPC is more usually associated with the behemoths of aerospace and automobile manufacturing, the EU-funded Partnership for Advanced Computing in Europe (Prace) showcased how HPC can help SMEs at its recent PRACEdays14 event held in Barcelona from 20 to 22 May. Prace is a transnational organisation
offering European researchers access to ‘Tier 0’ supercomputing facilities. Although it is aimed predominantly at academic researchers, it has also set up the SME HPC Adoption Programme in Europe (SHAPE) to support the adoption of HPC by SMEs. Te programme aims to raise awareness and equip European SMEs with the expertise necessary to take advantage of the innovation possibilities opened up by HPC, increasing their competitiveness. International yacht racing is a highly
competitive business, so Spanish naval architects Juan Yacht Design have been using simulation soſtware to improve the design of their sails. As an aerofoil, a yacht sail inevitably produces turbulence, which produces drag and reduces the efficiency of the sail. But turbulence simulation is an inherently difficult, non-linear problem with no analytical solutions. Juan Yacht Design has been using a combination of Reynolds- averaged Navier–Stokes equations (RANS) CFD and large eddy simulations (LES) to understand the turbulence produced at the edge of the sails. As Herbert Owen from the Barcelona Supercomputing Centre (BSC) explained, RANS alone can be ineffective when there are large regions of separated flow, which are present under certain wind conditions. For this project, the LES models were
implemented in the finite element CFD code 16 SCIENTIFIC COMPUTING WORLD
Alya, created in Barcelona, for the flow around the boat sails in conditions where the RANS models would typically fail. Alya makes use of a variational multiscale formulation that can take into account the LES modelling relying only on the numerical model. Te comparison of the LES models with the RANS results, using the same mesh, allowed the company to develop a better understanding of how to improve its design process. Te project illustrated the sometimes-hidden
difficulties in porting code to a supercomputer. Te Alya model ran eight times faster on one supercomputer architecture compared to another. Te project compared the efficiency of running the code on the MareNostrum, located at the BSC; SuperMUC, which is part of the
Walsh, the founder and CTO of Nsilico. Genomic sequences contain large amounts of nucleotide data that must be accurately compared with similar sequences in order to determine functional, structural, and evolutionary relationships. ‘Tere are companies that can take tissue samples and very quickly spin out all of the genomic data from those samples,’ said Walsh. He added: ‘Tere is a lot of data being generated, and that data needs to be analysed and processed. Te sequencing technology is advancing, but the computational tools are not; so the tools are not really well adapted to this new slew of data.’ Nsilico partnered with CINES in France
(which provides researchers from universities and public research institutes with high- performance parallel computing platforms) and the Irish Centre for High-End Computing (ICHEC) using the SHAPE programme to develop a technique for rapid alignment of short DNA sequences. Te technique was to run a Smith-Waterman
algorithm on many-core technology – the Intel Xeon Phi Coprocessor. Te Smith–Waterman algorithm performs local sequence alignment:
RANS ALONE CAN BE INEFFECTIVE WHEN THERE ARE LARGE REGIONS OF SEPARATED FLOW, WHICH ARE PRESENT UNDER CERTAIN WIND CONDITIONS HERBERT OWEN
Leibniz Supercomputing Centre (LRZ); Juqueen, located at the Gauss Center for Supercomputing; and FERMI, the newest supercomputer in the CINECA, Italy. Both SuperMUC and MareNostrum use
Sandy Bridge, while the Juqueen and FERMI systems use Blue Gene processors. According to Owen: ‘Initially Alya was eight times slower on Blue Gene compared to Sandy Bridge.’ Although optimisation of the code improved performance, it was still 3.6 times slower than on Sandy Bridge machines. Nsilico, a company based in Ireland that
specialises in soſtware for life sciences, is trying to address the computation problems presented by the exponential growth of high-throughput genomic sequencing. ‘Te opportunity, at least for computer scientists, is that sequencing technology has really accelerated,’ said Paul
instead of looking at the total sequence, the algorithm compares segments of all possible lengths and optimises the similarity measure. Although it sounds like rarefied science,
the problems that Nsilico is trying to solve can sometimes be literally matters of life and death. Walsh gave as an example: a study of the genes present in a pathogen that was affecting new- born babies in a hospital. Te sample was known to be Staphylococcus but of an unidentified strain. ‘Without knowing anything about what it is, just by putting in the letters of the genomic sequence, we are able to identify what species of Staphylococcus was present,’ said Walsh. By identifying the pathogen early, specific treatments and antibiotics can be provided. ‘Te people at Prace are the ones that really
did the hard work on this. Tey analysed the algorithm that we were working with, and helped
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