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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Is Data Science the Fourth Pillar of the Scientific Method?

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At ASF 2019: The Virtuous Circle of Big Data, AI and HPC

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Google Open Sources TensorFlow Version of MorphNet DL Tool

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HPE Extreme Performance Solutions

HPE and Intel® Omni-Path Architecture: How to Power a Cloud

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IBM Accelerated Insights

Bridging HPC and Cloud Native Development with Kubernetes

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Interview with 2019 Person to Watch Michela Taufer

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By HPCwire Editorial Team

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Intel Gold U-Series SKUs Reveal Single Socket Intentions

April 18, 2019

Intel plans to jump into the single socket market with a portion of its just announced Cascade Lake microprocessor line according to one media report. This isn Read more…

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BSC Researchers Shrink Floating Point Formats to Accelerate Deep Neural Network Training

April 15, 2019

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Intel Extends FPGA Ecosystem with 10nm Agilex

April 11, 2019

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Nvidia Doubles Down on Medical AI

April 9, 2019

Nvidia is collaborating with medical groups to push GPU-powered AI tools into clinical settings, including radiology and drug discovery. The GPU leader said Monday it will collaborate with the American College of Radiology (ACR) to provide clinicians with its Clara AI tool kit. The partnership would allow radiologists to leverage AI techniques for diagnostic imaging using their own clinical data. Read more…

By George Leopold

Digging into MLPerf Benchmark Suite to Inform AI Infrastructure Decisions

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AI and Enterprise Datacenters Boost HPC Server Revenues Past Expectations – Hyperion

April 9, 2019

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By Doug Black

Intel Launches Cascade Lake Xeons with Up to 56 Cores

April 2, 2019

At Intel's Data-Centric Innovation Day in San Francisco (April 2), the company unveiled its second-generation Xeon Scalable (Cascade Lake) family and debuted it Read more…

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The Case Against ‘The Case Against Quantum Computing’

January 9, 2019

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Why Nvidia Bought Mellanox: ‘Future Datacenters Will Be…Like High Performance Computers’

March 14, 2019

“Future datacenters of all kinds will be built like high performance computers,” said Nvidia CEO Jensen Huang during a phone briefing on Monday after Nvidia revealed scooping up the high performance networking company Mellanox for $6.9 billion. Read more…

By Tiffany Trader

ClusterVision in Bankruptcy, Fate Uncertain

February 13, 2019

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Intel Reportedly in $6B Bid for Mellanox

January 30, 2019

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By Doug Black

It’s Official: Aurora on Track to Be First US Exascale Computer in 2021

March 18, 2019

The U.S. Department of Energy along with Intel and Cray confirmed today that an Intel/Cray supercomputer, "Aurora," capable of sustained performance of one exaf Read more…

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Looking for Light Reading? NSF-backed ‘Comic Books’ Tackle Quantum Computing

January 28, 2019

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IBM Quantum Update: Q System One Launch, New Collaborators, and QC Center Plans

January 10, 2019

IBM made three significant quantum computing announcements at CES this week. One was introduction of IBM Q System One; it’s really the integration of IBM’s Read more…

By John Russell

Deep500: ETH Researchers Introduce New Deep Learning Benchmark for HPC

February 5, 2019

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By John Russell

Leading Solution Providers

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IBM Bets $2B Seeking 1000X AI Hardware Performance Boost

February 7, 2019

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The Deep500 – Researchers Tackle an HPC Benchmark for Deep Learning

January 7, 2019

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Arm Unveils Neoverse N1 Platform with up to 128-Cores

February 20, 2019

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France to Deploy AI-Focused Supercomputer: Jean Zay

January 22, 2019

HPE announced today that it won the contract to build a supercomputer that will drive France’s AI and HPC efforts. The computer will be part of GENCI, the Fre Read more…

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Intel Launches Cascade Lake Xeons with Up to 56 Cores

April 2, 2019

At Intel's Data-Centric Innovation Day in San Francisco (April 2), the company unveiled its second-generation Xeon Scalable (Cascade Lake) family and debuted it Read more…

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Microsoft to Buy Mellanox?

December 20, 2018

Networking equipment powerhouse Mellanox could be an acquisition target by Microsoft, according to a published report in an Israeli financial publication. Microsoft has reportedly gone so far as to engage Goldman Sachs to handle negotiations with Mellanox. Read more…

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HPC Reflections and (Mostly Hopeful) Predictions

December 19, 2018

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Oil and Gas Supercloud Clears Out Remaining Knights Landing Inventory: All 38,000 Wafers

March 13, 2019

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By Tiffany Trader

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