The Week in Review

By Tiffany Trader

April 22, 2010

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.

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At Long Last, Supercomputing Helps to Map the Poles

August 22, 2019

“For years,” Paul Morin wrote, “those of us that made maps of the Poles apologized. We apologized for the blank spaces on maps, we apologized for mountains being in the wrong place and out-of-date information.” Read more…

By Oliver Peckham

Xilinx Says Its New FPGA is World’s Largest

August 21, 2019

In this age of exploding “technology disaggregation” – in which the Big Bang emanating from the Intel x86 CPU has produced significant advances in CPU chips and a raft of alternative, accelerated architectures... Read more…

By Doug Black

Supercomputers Generate Universes to Illuminate Galactic Formation

August 20, 2019

With advanced imaging and satellite technologies, it’s easier than ever to see a galaxy – but understanding how they form (a process that can take billions of years) is a different story. Now, a team of researchers f Read more…

By Oliver Peckham

AWS Solution Channel

Efficiency and Cost-Optimization for HPC Workloads – AWS Batch and Amazon EC2 Spot Instances

High Performance Computing on AWS leverages the power of cloud computing and the extreme scale it offers to achieve optimal HPC price/performance. With AWS you can right size your services to meet exactly the capacity requirements you need without having to overprovision or compromise capacity. Read more…

HPE Extreme Performance Solutions

Bring the combined power of HPC and AI to your business transformation

FPGA (Field Programmable Gate Array) acceleration cards are not new, as they’ve been commercially available since 1984. Typically, the emphasis around FPGAs has centered on the fact that they’re programmable accelerators, and that they can truly offer workload specific hardware acceleration solutions without requiring custom silicon. Read more…

IBM Accelerated Insights

Keys to Attracting the Newest HPC Talent – Post-Millennials

[Connect with HPC users and learn new skills in the IBM Spectrum LSF User Community.]

For engineers and scientists growing up in the 80s, the current state of HPC makes perfect sense. Read more…

Singularity Moves Up the Container Value Chain

August 20, 2019

The enterprise version of the Singularity HPC container platform released this week by Sylabs is designed to allow users to create, secure and share the high-end containers in self-hosted production deployments. The e Read more…

By George Leopold

At Long Last, Supercomputing Helps to Map the Poles

August 22, 2019

“For years,” Paul Morin wrote, “those of us that made maps of the Poles apologized. We apologized for the blank spaces on maps, we apologized for mountains being in the wrong place and out-of-date information.” Read more…

By Oliver Peckham

IBM Deepens Plunge into Open Source; OpenPOWER to Join Linux Foundation

August 20, 2019

IBM today announced it was contributing the instruction set (ISA) for its Power microprocessor and the designs for the Open Coherent Accelerator Processor Inter Read more…

By John Russell

Ayar Labs to Demo Photonics Chiplet in FPGA Package at Hot Chips

August 19, 2019

Silicon startup Ayar Labs continues to gain momentum with its DARPA-backed optical chiplet technology that puts advanced electronics and optics on the same chip Read more…

By Tiffany Trader

Scientists to Tap Exascale Computing to Unlock the Mystery of our Accelerating Universe

August 14, 2019

The universe and everything in it roared to life with the Big Bang approximately 13.8 billion years ago. It has continued expanding ever since. While we have a Read more…

By Rob Johnson

AI is the Next Exascale – Rick Stevens on What that Means and Why It’s Important

August 13, 2019

Twelve years ago the Department of Energy (DOE) was just beginning to explore what an exascale computing program might look like and what it might accomplish. Today, DOE is repeating that process for AI, once again starting with science community town halls to gather input and stimulate conversation. The town hall program... Read more…

By Tiffany Trader and John Russell

Cray Wins NNSA-Livermore ‘El Capitan’ Exascale Contract

August 13, 2019

Cray has won the bid to build the first exascale supercomputer for the National Nuclear Security Administration (NNSA) and Lawrence Livermore National Laborator Read more…

By Tiffany Trader

AMD Launches Epyc Rome, First 7nm CPU

August 8, 2019

From a gala event at the Palace of Fine Arts in San Francisco yesterday (Aug. 7), AMD launched its second-generation Epyc Rome x86 chips, based on its 7nm proce Read more…

By Tiffany Trader

Lenovo Drives Single-Socket Servers with AMD Epyc Rome CPUs

August 7, 2019

No summer doldrums here. As part of the AMD Epyc Rome launch event in San Francisco today, Lenovo announced two new single-socket servers, the ThinkSystem SR635 Read more…

By Doug Black

High Performance (Potato) Chips

May 5, 2006

In this article, we focus on how Procter & Gamble is using high performance computing to create some common, everyday supermarket products. Tom Lange, a 27-year veteran of the company, tells us how P&G models products, processes and production systems for the betterment of consumer package goods. Read more…

By Michael Feldman

Supercomputer-Powered AI Tackles a Key Fusion Energy Challenge

August 7, 2019

Fusion energy is the Holy Grail of the energy world: low-radioactivity, low-waste, zero-carbon, high-output nuclear power that can run on hydrogen or lithium. T Read more…

By Oliver Peckham

Cray, AMD to Extend DOE’s Exascale Frontier

May 7, 2019

Cray and AMD are coming back to Oak Ridge National Laboratory to partner on the world’s largest and most expensive supercomputer. The Department of Energy’s Read more…

By Tiffany Trader

Graphene Surprises Again, This Time for Quantum Computing

May 8, 2019

Graphene is fascinating stuff with promise for use in a seeming endless number of applications. This month researchers from the University of Vienna and Institu Read more…

By John Russell

AMD Verifies Its Largest 7nm Chip Design in Ten Hours

June 5, 2019

AMD announced last week that its engineers had successfully executed the first physical verification of its largest 7nm chip design – in just ten hours. The AMD Radeon Instinct Vega20 – which boasts 13.2 billion transistors – was tested using a TSMC-certified Calibre nmDRC software platform from Mentor. Read more…

By Oliver Peckham

TSMC and Samsung Moving to 5nm; Whither Moore’s Law?

June 12, 2019

With reports that Taiwan Semiconductor Manufacturing Co. (TMSC) and Samsung are moving quickly to 5nm manufacturing, it’s a good time to again ponder whither goes the venerable Moore’s law. Shrinking feature size has of course been the primary hallmark of achieving Moore’s law... Read more…

By John Russell

Cray Wins NNSA-Livermore ‘El Capitan’ Exascale Contract

August 13, 2019

Cray has won the bid to build the first exascale supercomputer for the National Nuclear Security Administration (NNSA) and Lawrence Livermore National Laborator Read more…

By Tiffany Trader

Deep Learning Competitors Stalk Nvidia

May 14, 2019

There is no shortage of processing architectures emerging to accelerate deep learning workloads, with two more options emerging this week to challenge GPU leader Nvidia. First, Intel researchers claimed a new deep learning record for image classification on the ResNet-50 convolutional neural network. Separately, Israeli AI chip startup Hailo.ai... Read more…

By George Leopold

Leading Solution Providers

ISC 2019 Virtual Booth Video Tour

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Nvidia Embraces Arm, Declares Intent to Accelerate All CPU Architectures

June 17, 2019

As the Top500 list was being announced at ISC in Frankfurt today with an upgraded petascale Arm supercomputer in the top third of the list, Nvidia announced its Read more…

By Tiffany Trader

Top500 Purely Petaflops; US Maintains Performance Lead

June 17, 2019

With the kick-off of the International Supercomputing Conference (ISC) in Frankfurt this morning, the 53rd Top500 list made its debut, and this one's for petafl Read more…

By Tiffany Trader

AMD Launches Epyc Rome, First 7nm CPU

August 8, 2019

From a gala event at the Palace of Fine Arts in San Francisco yesterday (Aug. 7), AMD launched its second-generation Epyc Rome x86 chips, based on its 7nm proce Read more…

By Tiffany Trader

A Behind-the-Scenes Look at the Hardware That Powered the Black Hole Image

June 24, 2019

Two months ago, the first-ever image of a black hole took the internet by storm. A team of scientists took years to produce and verify the striking image – an Read more…

By Oliver Peckham

Cray – and the Cray Brand – to Be Positioned at Tip of HPE’s HPC Spear

May 22, 2019

More so than with most acquisitions of this kind, HPE’s purchase of Cray for $1.3 billion, announced last week, seems to have elements of that overused, often Read more…

By Doug Black and Tiffany Trader

Chinese Company Sugon Placed on US ‘Entity List’ After Strong Showing at International Supercomputing Conference

June 26, 2019

After more than a decade of advancing its supercomputing prowess, operating the world’s most powerful supercomputer from June 2013 to June 2018, China is keep Read more…

By Tiffany Trader

Qualcomm Invests in RISC-V Startup SiFive

June 7, 2019

Investors are zeroing in on the open standard RISC-V instruction set architecture and the processor intellectual property being developed by a batch of high-flying chip startups. Last fall, Esperanto Technologies announced a $58 million funding round. Read more…

By George Leopold

Ayar Labs to Demo Photonics Chiplet in FPGA Package at Hot Chips

August 19, 2019

Silicon startup Ayar Labs continues to gain momentum with its DARPA-backed optical chiplet technology that puts advanced electronics and optics on the same chip Read more…

By Tiffany Trader

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