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April 22, 2010

The Week in Review

by Tiffany Trader

Here is a collection of highlights from this week’s news stream as reported by HPCwire.

Chips, Worms and Grey Matter: More Similar Than You Think

NASA Announces a New Approach to Earth Science Data Analysis

Infinera Low Latency Solution Speeds Optical Transport

Panasas Intros Multi-Petabyte Scale-Out NAS Solution

JGI, NERSC Partner for Genomic High-Performance Computing

Mellanox Infiniband Available for Dell Blade Servers

DNAnexus Launches Web-Based Service for Next-Generation DNA Sequencing

CD-adapco Strengthens Partnership with Microsoft

Lightfleet Delivers First Optical Interconnect System to Microsoft Research

EStar Award Recognizes Innovative Supercomputer Cooling

TeraGrid Resources Help Harvard Team Gain Insights into Deafness

IBTA Announces RDMA over Converged Ethernet

Bright Cluster Manager Includes CUDA Toolkit 3.0

Altera Unveils 28-nm Stratix V FPGA Family

BLADE, Voltaire Partner on Highest-Density 10GbE Fabric Solution

Researcher Advances Understanding of Alzheimer’s Disease

As the most common neurodegenerative disorder, Alzheimer’s disease affects over 5 million people in America alone, according to the National Institutes of Health (NIH). University of Akron researcher Jie Zheng came a step closer this week to finding a cure for this devastating disease. Using supercomputing resources at the Ohio Supercomputer Center, Zheng created computer simulations that show how “misfolded” proteins in the brain contribute to degenerative disorders like Alzheimer’s.

The announcement includes an explanatory paragraph of the science involved:

In the nucleus of nearly every human cell, long strands of DNA are packed tightly together to form chromosomes, which contain all the instructions a cell needs to function. To deliver these instructions to various other cellular structures, the chromosomes dispatch very small protein fibers — called oligomers — that fold into three-dimensional shapes. Misfolded proteins — called amyloid fibrils — cannot function properly and tend to accumulate into tangles and clumps of waxy plaque, robbing brain cells of their ability to operate and communicate with each other, according to NIH.

Zheng explains computer simulations allow scientists to “see” the amyloid oligomers at the molecular level, enabling them to determine the exact mechanism of the amyloid formation and the origin of its toxicity. This degree of understanding was just not possible using traditional experimental techniques.

Says Zheng: “Molecular simulations…allow one to study the three-dimensional structure and its kinetic pathway of amyloid oligomers at full atomic resolution.”

Adding credibility to the potential for Zheng’s work with amyloid proteins is the fact that he recently received a CAREER Award from the National Science Foundation (NSF). This five-year award is one of the NSF’s most prestigious recognitions and comes with $400,000 honorarium.

Takeaway: This research is vital for understanding how plaque forms and accumulates in the brain, how it contributes to the breakdown of cells and, ultimately, how the process might be prevented.

Cray System Selected for Brazil’s National Institute for Space Research

This week, Cray was chosen by the Foundation for Space Technology, Applications and Science (FUNCATE) to outfit the National Institute for Space Research (INPE) with a Cray XT6 supercomputer. FUNCATE is the Brazilian agency responsible for the procurement of high performance computers in Brazil. The new Cray system will be used for weather forecasting and climate studies.

Once the Cray system is in place, Brazil will be home to one of the largest numerical weather prediction and climate research centers in the world. Haroldo Fraga de Campos Velho, associate director for space and environment at INPE, explains what this means for his agency:

“The INPE scientific team asserts that continued increase in supercomputing capacity is paramount to the advancement of simulation capabilities and improvement in forecast quality. The Cray XT6 supercomputer is designed to support the most challenging high performance computing workloads in demanding operational environments, and INPE scientists are looking forward to applying the system’s computational resources in their simulations of atmospheric phenomena.”

The contract, which is valued at more than $20 million, includes the supercomputer and multi-year services. The system is expected to be production ready later this year.

The Cray XT6 supercomputer, announced during SC09, is Cray’s highest performing system, the runup to the XT5, which occupies several of the top spots on the current TOP500 list, including the number one and number three spots. The XT6 features AMD Opteron 6100 Series processors and Cray’s Seastar interconnect, and the compute blades can be configured with up to 96 processor cores per blade or more than 2,300 processor cores per cabinet.

This deal marks Cray’s first foray into Brazil and comes on the heels of another big announcement for a contract with the National Nuclear Security Administration (NNSA) worth more than $45 million. That one is for Cray’s forthcoming next-generation “Baker” system, which builds on Cray’s XT architecture.