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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PRACEdays Reflects Europe’s HPC Commitment

May 25, 2017

More than 250 attendees and participants came together for PRACEdays17 in Barcelona last week, part of the European HPC Summit Week 2017, held May 15-19 at t Read more…

By Tiffany Trader

Russian Researchers Claim First Quantum-Safe Blockchain

May 25, 2017

The Russian Quantum Center today announced it has overcome the threat of quantum cryptography by creating the first quantum-safe blockchain, securing cryptocurr Read more…

By Doug Black

Google Debuts TPU v2 and will Add to Google Cloud

May 25, 2017

Not long after stirring attention in the deep learning/AI community by revealing the details of its Tensor Processing Unit (TPU), Google last week announced the Read more…

By John Russell

Nvidia CEO Predicts AI ‘Cambrian Explosion’

May 25, 2017

The processing power and cloud access to developer tools used to train machine-learning models are making artificial intelligence ubiquitous across computing pl Read more…

By George Leopold

HPE Extreme Performance Solutions

Exploring the Three Models of Remote Visualization

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PGAS Use will Rise on New H/W Trends, Says Reinders

May 25, 2017

If you have not already tried using PGAS, it is time to consider adding PGAS to the programming techniques you know. Partitioned Global Array Space, commonly kn Read more…

By James Reinders

Exascale Escapes 2018 Budget Axe; Rest of Science Suffers

May 23, 2017

President Trump's proposed $4.1 trillion FY 2018 budget is good for U.S. exascale computing development, but grim for the rest of science and technology spend Read more…

By Tiffany Trader

Hedge Funds (with Supercomputing help) Rank First Among Investors

May 22, 2017

In case you didn’t know, The Quants Run Wall Street Now, or so says a headline in today’s Wall Street Journal. Quant-run hedge funds now control the largest Read more…

By John Russell

IBM, D-Wave Report Quantum Computing Advances

May 18, 2017

IBM said this week it has built and tested a pair of quantum computing processors, including a prototype of a commercial version. That progress follows an an Read more…

By George Leopold

PRACEdays Reflects Europe’s HPC Commitment

May 25, 2017

More than 250 attendees and participants came together for PRACEdays17 in Barcelona last week, part of the European HPC Summit Week 2017, held May 15-19 at t Read more…

By Tiffany Trader

PGAS Use will Rise on New H/W Trends, Says Reinders

May 25, 2017

If you have not already tried using PGAS, it is time to consider adding PGAS to the programming techniques you know. Partitioned Global Array Space, commonly kn Read more…

By James Reinders

Exascale Escapes 2018 Budget Axe; Rest of Science Suffers

May 23, 2017

President Trump's proposed $4.1 trillion FY 2018 budget is good for U.S. exascale computing development, but grim for the rest of science and technology spend Read more…

By Tiffany Trader

Cray Offers Supercomputing as a Service, Targets Biotechs First

May 16, 2017

Leading supercomputer vendor Cray and datacenter/cloud provider the Markley Group today announced plans to jointly deliver supercomputing as a service. The init Read more…

By John Russell

HPE’s Memory-centric The Machine Coming into View, Opens ARMs to 3rd-party Developers

May 16, 2017

Announced three years ago, HPE’s The Machine is said to be the largest R&D program in the venerable company’s history, one that could be progressing tow Read more…

By Doug Black

What’s Up with Hyperion as It Transitions From IDC?

May 15, 2017

If you’re wondering what’s happening with Hyperion Research – formerly the IDC HPC group – apparently you are not alone, says Steve Conway, now senior V Read more…

By John Russell

Nvidia’s Mammoth Volta GPU Aims High for AI, HPC

May 10, 2017

At Nvidia's GPU Technology Conference (GTC17) in San Jose, Calif., this morning, CEO Jensen Huang announced the company's much-anticipated Volta architecture a Read more…

By Tiffany Trader

HPE Launches Servers, Services, and Collaboration at GTC

May 10, 2017

Hewlett Packard Enterprise (HPE) today launched a new liquid cooled GPU-driven Apollo platform based on SGI ICE architecture, a new collaboration with NVIDIA, a Read more…

By John Russell

Quantum Bits: D-Wave and VW; Google Quantum Lab; IBM Expands Access

March 21, 2017

For a technology that’s usually characterized as far off and in a distant galaxy, quantum computing has been steadily picking up steam. Just how close real-wo Read more…

By John Russell

Trump Budget Targets NIH, DOE, and EPA; No Mention of NSF

March 16, 2017

President Trump’s proposed U.S. fiscal 2018 budget issued today sharply cuts science spending while bolstering military spending as he promised during the cam Read more…

By John Russell

Google Pulls Back the Covers on Its First Machine Learning Chip

April 6, 2017

This week Google released a report detailing the design and performance characteristics of the Tensor Processing Unit (TPU), its custom ASIC for the inference Read more…

By Tiffany Trader

HPC Compiler Company PathScale Seeks Life Raft

March 23, 2017

HPCwire has learned that HPC compiler company PathScale has fallen on difficult times and is asking the community for help or actively seeking a buyer for its a Read more…

By Tiffany Trader

CPU-based Visualization Positions for Exascale Supercomputing

March 16, 2017

Since our first formal product releases of OSPRay and OpenSWR libraries in 2016, CPU-based Software Defined Visualization (SDVis) has achieved wide-spread adopt Read more…

By Jim Jeffers, Principal Engineer and Engineering Leader, Intel

Nvidia Responds to Google TPU Benchmarking

April 10, 2017

Last week, Google reported that its custom ASIC Tensor Processing Unit (TPU) was 15-30x faster for inferencing workloads than Nvidia's K80 GPU (see our coverage Read more…

By Tiffany Trader

Nvidia’s Mammoth Volta GPU Aims High for AI, HPC

May 10, 2017

At Nvidia's GPU Technology Conference (GTC17) in San Jose, Calif., this morning, CEO Jensen Huang announced the company's much-anticipated Volta architecture a Read more…

By Tiffany Trader

TSUBAME3.0 Points to Future HPE Pascal-NVLink-OPA Server

February 17, 2017

Since our initial coverage of the TSUBAME3.0 supercomputer yesterday, more details have come to light on this innovative project. Of particular interest is a ne Read more…

By Tiffany Trader

Leading Solution Providers

Facebook Open Sources Caffe2; Nvidia, Intel Rush to Optimize

April 18, 2017

From its F8 developer conference in San Jose, Calif., today, Facebook announced Caffe2, a new open-source, cross-platform framework for deep learning. Caffe2 is Read more…

By Tiffany Trader

Tokyo Tech’s TSUBAME3.0 Will Be First HPE-SGI Super

February 16, 2017

In a press event Friday afternoon local time in Japan, Tokyo Institute of Technology (Tokyo Tech) announced its plans for the TSUBAME3.0 supercomputer, which w Read more…

By Tiffany Trader

Is Liquid Cooling Ready to Go Mainstream?

February 13, 2017

Lost in the frenzy of SC16 was a substantial rise in the number of vendors showing server oriented liquid cooling technologies. Three decades ago liquid cooling Read more…

By Steve Campbell

MIT Mathematician Spins Up 220,000-Core Google Compute Cluster

April 21, 2017

On Thursday, Google announced that MIT math professor and computational number theorist Andrew V. Sutherland had set a record for the largest Google Compute Eng Read more…

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US Supercomputing Leaders Tackle the China Question

March 15, 2017

As China continues to prove its supercomputing mettle via the Top500 list and the forward march of its ambitious plans to stand up an exascale machine by 2020, Read more…

By Tiffany Trader

HPC Technique Propels Deep Learning at Scale

February 21, 2017

Researchers from Baidu's Silicon Valley AI Lab (SVAIL) have adapted a well-known HPC communication technique to boost the speed and scale of their neural networ Read more…

By Tiffany Trader

DOE Supercomputer Achieves Record 45-Qubit Quantum Simulation

April 13, 2017

In order to simulate larger and larger quantum systems and usher in an age of "quantum supremacy," researchers are stretching the limits of today's most advance Read more…

By Tiffany Trader

Knights Landing Processor with Omni-Path Makes Cloud Debut

April 18, 2017

HPC cloud specialist Rescale is partnering with Intel and HPC resource provider R Systems to offer first-ever cloud access to Xeon Phi "Knights Landing" process Read more…

By Tiffany Trader

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