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Primeur weekly 2015-03-16

Special

COMPSs superscaler helps deploy scientific applications on distributed infrastructures ...

Focus

2014 Another year on the road to Exascale - An Interview with Satoshi Matsuoka and Thomas Sterling - Part IV ...

The Cloud

GCHQ inspires next generation of computer programmers with launch of the world's biggest Raspberry Pi 'Bramble' ...

HP broadens compute portfolio for service providers with new open, hyperscale servers ...

Shinra Technologies announces Hardsuit Labs as the latest developer to join its Prototype Accelerator programme ...

IBM launches second Cloud centre in Australia ...

HP launches new investment solution suite and technology and services portfolio for service providers ...

Adobe and IBM Interactive Experience announce global partnership ...

Oracle Social Cloud adds support for Instagram and Weibo ...

EuroFlash

Atos launches the Self-Service Hadoop platform to meet the challenges of Big Data ...

Ghent University leads large-scale European training project on quantum dots ...

KIT physicist receives ERC Consolidator Grant of EU ...

Computer scientists from Saarland University simplify parallel programming ...

ANSYS collaborates with Intel to spur customer innovation ...

USFlash

Advancing accelerator science using Mira ...

Clemson to host leaders in computing infrastructure for campus research ...

Supercomputer speeds up genetics research at Clemson ...

Shinra Technologies debuts supercomputer technology at the Google Fiber Space in Austin ...

SDSC's CAIDA Group to explore the Internet's "uncharted territory" ...

SDSC announces 2015 Summer Internships for high school students ...

Intel packs power and intelligence of Xeon processor into System-on-Chip offering to target new, growing network opportunities ...

The climate is starting to change faster ...

HP granted FedRAMP authorization for government agencies to use HP Fortify on Demand ...

Dr. Steven Ashby named Director of Pacific Northwest National Laboratory ...

DDN announces record fourth quarter 2014 and 16 percent year-over-year growth and profitability ...

Supercomputer speeds up genetics research at Clemson


Clemson University
11 Mar 2015 Clemson - The next time you find yourself looking for a needle in a haystack, you might want to make friends with someone who can hook you up to a supercomputer. In the time it will take you to examine the first stem, the computer will have sorted through the entire stack, found the needle and returned everything to its original condition, neat as can be.

It just so happens that Clemson University has a supercomputer of its own. The Palmetto Cluster, the University's primary high-performance computing resource, is the 89th fastest computer in the world and among the top five fastest supercomputers at public academic institutions in the United States that don't have federally funded centres.

This is all good news for research scientists like Alex Feltus, associate professor of genetics and biochemistry. Alex Feltus, one of more than 1500 users of the machine since its inception in 2007, utilizes the supercomputer to find figurative needles in haystacks. In Alex Feltus' case, the "needles" are valuable traits, such as biomass production and disease resistance, that are hidden deep within the immensely intricate genetic material of plants.

Without a supercomputer, Alex Feltus and his fellow researchers could not function nearly as efficiently as they do.

"Only a supercomputer can handle the massive numbers of DNA sequences that are generated by new DNA sequencing technology", stated Alex Feltus, a member of a research team that recently received a $1.4 million grant from the National Science Foundation to enhance the capacity of genomic databases to process mind-boggling bundles of data.

"All crops are very, very complex. For instance, there are 55,000 genes in rice. We're trying to understand the genes and their pathways and how they are combining and interacting. You can't examine this level of complexity without using a supercomputer."

Alex Feltus is one of the leaders in an emerging field called systems genetics, which studies how genes in crops collectively interact using new computational technologies that Clemson University's Public Service and Agriculture programmes are helping to develop.

"Most agricultural traits in plants are controlled not just by one gene but by many genes", stated Alex Feltus. "We're trying to find the complexity 'sweet spot', the balance between being too reductionist and too holistic."

The majority of Clemson's computer research and production systems are housed in the Information Technology Center at the innovation campus in Anderson. Jay Harris, director of data centre facilities, explained that the cluster is not a single enormous computer but rather thousands of small computers stacked together like a really smart condominium complex. This highly intricate connection produces incredible speed.

"We have 100 gigabits per second connectivity to Internet2", stated Jay Harris, who has helped oversee a continuous updating and redesigning of the data centre that began in 2007. "To put that in perspective, a typical Internet service provider will sell you anywhere from 10 to 60 megabits per second for your residential service. Our 100 gigabits translates to 100,000 megabits per second. And that represents just one of our connections."

In other words, way fast. "The speed of a supercomputer is measured in teraflops - trillions of floating point operations per second", stated Jay Harris. "We have one room with about 2000 machines that can perform 550 trillion floating point operations in one second. And a second later, another 550 trillion and then another 550 trillion."

Internet2 - an international community of academic and government entities that includes Clemson University - plays a crucial role, as well. When compared to the number of users on the ordinary Internet, the Internet2's base is relatively tiny, which further increases the speed required by 21st century researchers and educators.

"On one of my research projects, our group was able to transfer DNA files from the National Center for Biotechnology Information in Maryland to Clemson University much faster due to Internet2", stated Alex Feltus. "That transfer of 7500 files took eight days. The same transfer can now be done in half a day. These are huge files, and some of our research is devoted to getting collaborators to use this really fast connection to share data."

Because Clemson's supercomputer has attained world-renowned status, it more than pays for itself, garnering millions of dollars in funding and attracting top talent from a variety of expertise. Grants that use the Palmetto cluster have been awarded from the U.S. Department of Agriculture, the U.S. Department of Energy, the National Science Foundation and other federal agencies.

"If the data centre hadn't been here, I would never have come to Clemson", stated Alex Feltus. "This is critical to my work. And it's becoming critical to a lot of people's work."

This material is based upon work supported by the National Science Foundation (NSF) under Grant nos. 1443040 and 1245936.
Source: Clemson University

Back to Table of contents

Primeur weekly 2015-03-16

Special

COMPSs superscaler helps deploy scientific applications on distributed infrastructures ...

Focus

2014 Another year on the road to Exascale - An Interview with Satoshi Matsuoka and Thomas Sterling - Part IV ...

The Cloud

GCHQ inspires next generation of computer programmers with launch of the world's biggest Raspberry Pi 'Bramble' ...

HP broadens compute portfolio for service providers with new open, hyperscale servers ...

Shinra Technologies announces Hardsuit Labs as the latest developer to join its Prototype Accelerator programme ...

IBM launches second Cloud centre in Australia ...

HP launches new investment solution suite and technology and services portfolio for service providers ...

Adobe and IBM Interactive Experience announce global partnership ...

Oracle Social Cloud adds support for Instagram and Weibo ...

EuroFlash

Atos launches the Self-Service Hadoop platform to meet the challenges of Big Data ...

Ghent University leads large-scale European training project on quantum dots ...

KIT physicist receives ERC Consolidator Grant of EU ...

Computer scientists from Saarland University simplify parallel programming ...

ANSYS collaborates with Intel to spur customer innovation ...

USFlash

Advancing accelerator science using Mira ...

Clemson to host leaders in computing infrastructure for campus research ...

Supercomputer speeds up genetics research at Clemson ...

Shinra Technologies debuts supercomputer technology at the Google Fiber Space in Austin ...

SDSC's CAIDA Group to explore the Internet's "uncharted territory" ...

SDSC announces 2015 Summer Internships for high school students ...

Intel packs power and intelligence of Xeon processor into System-on-Chip offering to target new, growing network opportunities ...

The climate is starting to change faster ...

HP granted FedRAMP authorization for government agencies to use HP Fortify on Demand ...

Dr. Steven Ashby named Director of Pacific Northwest National Laboratory ...

DDN announces record fourth quarter 2014 and 16 percent year-over-year growth and profitability ...