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Using HPC Techniques to Accelerate NGS Workflows

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Next-generation sequencing (NGS) describes the modern nucleotide sequencing technologies that allow analysis of genetic material with unprecedented speed and efficiency. Its advent is shifting genome assembly from a problem of laboratory-based chemistry to one well suited to high performance computing (HPC). In simple terms, NGS involves breaking up long DNA or RNA molecules into millions of small, fragments (50 to 200 nucleotides), defined as a “reads” to be assembled into larger fragments called contigs. The process of taking genetic material, processing it on a sequencer, passing it to an HPC system for assembly, and outputting digital information in a form useful for research is contained in a “workflow,” the end-to-end flow … [Read more...]

Why Chapel?

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In previous articles for this blog, I’ve provided a high-level overview of Chapel, the parallel programming language that we’re developing at Cray Inc., and I’ve introduced Chapel’s iterators as a sample productivity-oriented feature. In this article (the first in a series), I’ll address some recurring questions about why we’re pursuing Chapel. Why develop a new language? My short answer to this question is that, quite simply, I believe programmers have never had a decent programming language for large-scale parallel computing. By “decent,” I mean one that contains sufficient concepts for expressing the parallelism and locality control required to leverage supercomputers, while also being as general, effective, and … [Read more...]

Cray Joins EU’s Push Toward Exascale Technologies

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Cray acquired the assets of Gnodal in Bristol, U.K. November of last year. From its start with sales and customer-support organizations in Europe, Cray has made significant additions to its R&D staff, its CTO office and other local teams. Acquiring Gnodal demonstrated Cray’s desire to grow this European R&D team, to collaborate and exchange information with other leaders in the European HPC environment as well as continue our push towards exascale technologies.  This collaboration is exemplified by Cray’s recent membership in the European Technology Platform for High-Performance Computing (ETP4HPC). European Technology Platforms are industry-led forums that collaborate with the European Commission (EC) in Brussels.  As … [Read more...]

Video Blog: Cray Application Performance Team Poised to Get the Most from HPC Systems

Supercomputing solutions are more than the hardware they run on. It is supercomputing applications that transform ideas into reality and answer previously unanswerable questions. With a wider variety of customer sectors demanding parallel computing and other sophisticated functions, Cray is committed to finding ways to get the most value and efficiency from our systems. As part of that effort, we have a team dedicated to working closely with customers and numerous independent software vendors (ISVs). Our application performance team is devoted optimizing application solutions that help our customers make the most of their investments. Here’s a brief look at their work. What is the Cray Application team’s area of expertise? Like … [Read more...]

INCITE Program Paves Way for Groundbreaking Research

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This year marks the seventh anniversary of the Innovative and Novel Computational Impact on Theory and Experiment (INCITE) program, which has given researchers from academia, government labs and industry access to some of the fastest supercomputers in the world. INCITE enables scientific discoveries and technological innovations by awarding time on multiple systems and is now accepting proposals for high-impact, computationally intensive research campaigns in a broad array of science, engineering and computer science domains. INCITE’s Multi-Discipline Research  Using one of the most powerful supercomputers in the world — “Titan,” a Cray® XK7™ system housed at Oak Ridge National Lab (ORNL) — researchers across the country … [Read more...]