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Cray Supercomputers Powering Scientific Research in Chemistry and Life Sciences

ISMB_Life Sciences Event

In recent months, several chemistry and life sciences organizations have turned to Cray supercomputers to power their scientific research. Among them we welcome Duke University, the National Institute of Environmental Health Sciences, Université Laval in Canada, S.N. Bose in India, and the PDC Center for High-Performance Computing at the KTH Royal Institute of Technology in Sweden, as well as a number of leading pharmaceutical companies and biotechs. These organizations are doing groundbreaking work, and providing them with Cray supercomputers is representative of our growing presence in this vitally important segment.

Chemistry and life sciences researchers are certainly no strangers to HPC. In fact, as part of the 2013 HPCwire Readers’ and Editors’ Choice Awards, the editors of HPCwire  gave the “Best Use of HPC in Life Sciences” award to the Cray® XK7™ “Blue Waters” system at NCSA for achieving breakthroughs in HIV capsid research. The online tech publication CNET had this to say about the groundbreaking research at NCSA: Blue Waters, a relatively new supercomputer at NCSA at the University of Illinois at Urbana-Champaign, is a rare breed of petascale supercomputers, which means it can manage one quadrillion floating point operations every second. It was able to piece together the entire HIV capsid — which consists of more than 1,300 identical proteins that form a cone-like structure — in atomic-level detail.”

We’re certainly no stranger to chemistry and life sciences either. It was in the late 1990s that professor Peter Kollman and his team at the Pittsburgh Supercomputing Center (PSC) paired their software with a Cray® T3E to simulate the folding of a small protein in water for a full microsecond — 100 times longer than previous simulations run at PSC. It’s just one example of how Cray has been helping scientists take that next quantum leap.

As for chemistry and life sciences, we see it as a vibrant and dynamic field that’s constantly evolving — from using nanotechnology and new materials to deliver drugs to unraveling the mysteries of how cells work. We definitely have our eye on those new technologies that are revolutionizing the field such as next generation sequencing (NGS). NGS allows for the analysis of genetic material with unprecedented speed and efficiency and is well suited for HPC.

Chemistry and life sciences are in our DNA, so it’s only natural for us to be one of the leading providers of solutions in the field. Here’s what our recent chemistry and life sciences customers are doing with their systems:

The PDC Center for High-Performance Computing (PDC) at the KTH Royal Institute of Technology provides leading HPC services to Swedish academia. They are already home to a Cray® XE6™ supercomputer and recently purchased a Cray® XC30™ system for neuroinformatics codes used to simulate large-scale models of neural systems. The system will allow Swedish scientists to participate in large-scale international efforts like the Human Brain Project.

The S.N. Bose National Centre for Basic Sciences in India is planning to use its new Cray XE6 supercomputer for the study of complex biomolecules and condensed matter. The Centre is a major institution for research and development in basic sciences.

National Institute of Environmental Health Sciences (NIEHS) has the mission to discover how the environment affects people to promote healthier lives. To accomplish this task, research initiatives at NIEHS in North Carolina include human studies of environmentally associated diseases, toxicological testing of environmental substances, and intervention and prevention studies to reduce the effects of exposures to hazardous environments. Gaining insight into these environmental factors requires simulations at the molecular level. NIEHS’s new Cray®CS300™ LMS system using vSMP Foundation from ScaleMP, will play a key role in providing that molecular insight.

Research initiatives at the National Institute of Environmental Health Sciences (NIEHS) in North Carolina include human studies of environmentally associated diseases, toxicological testing of environmental substances, and intervention and prevention studies to reduce the effects of exposures to hazardous environments. Gaining insight into these environmental factors requires simulations at the molecular level. NIEHS’s new Cray®CS300™ cluster supercomputer will play a key role in providing that molecular insight.

Professor Stefano Curtarolo from the department of mechanical engineering and materials science at Duke University said their new Cray CS300 system will be “used in an emerging area of materials science — one that combines advanced thermodynamic and electronic-structure methods with intelligent data mining to analyze enormous data repositories for the discovery of novel materials.”

Although Université Laval is the oldest center of education in Canada, it’s one of the newest universities to acquire a Cray CS300 system. Cray has worked closely with the university’s Jacques Corbeil, professor in the molecular medicine department. Dr. Corbeil leads a research group investigating the host-pathogen relationship. He also works on big data and advancing the development of their de novo assembler code which is used to assemble genomic data. Today, next generation sequencers produce large quantities of small fragments of DNA, assembling billions of small fragments requires high-performance computing resources. For a recent report on the work done in collaboration with Dr. Corbeil, see: http://online.liebertpub.com/doi/full/10.1089/big.2013.0031.

Researchers and scientists in chemistry and life sciences today are confronted with a new challenge —the “data deluge.” We’ve been working hard at solving this problem, designing and building systems capable of addressing the most complex computing, storage, and analytics challenges. By combining these attributes in systems that cover a range of products and sizes, Cray supercomputers continue to find homes with customers focused on turning great ideas into brilliant chemistry and life sciences discoveries worldwide.

To learn more about how our supercomputers are being used in chemistry and life sciences, please visit the Cray website. More information on the sessions can be found at http://www.cray.com/IndustrySolutions/LifeSciences.aspx

Carlos P. Sosa, Chemistry and Life Sciences Segment Manager 

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Comments

  1. James Myers says:

    Do SSDs help with supercomputing?

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