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Primeur weekly 2012-11-19

Exascale supercomputing

DataDirect Networks announces $100 million investment in Exascale computing ...

Intel and DataDirect Networks join forces to enable compute infrastructures 1,000 times larger than today's biggest systems ...

The Cloud

HP delivers industry's first purpose-built server for Big Data ...

DDN adds enterprise class Cloud Tiering, NAS and SSD capabilities to its parallel file system appliances, making them Big Data ready ...

Desktop Grids

Members of the public asked to help tend Feynman's Flowers ...

EuroFlash

EMI 2 - Matterhorn - 5th update is now available ...

German Federal Waterways Engineering and Research Institute (BAW) optimizes navigable waterways using a Bull supercomputer ...

Choreographing light ...

USFlash

New editions of Moab HPC Suite enhance HPC system efficiency ...

SGI ICE X selected by CRIEPI for electric power research ...

Supermicro debuts SuperServer and SuperBlade solutions supporting new AMD Opteron 6300 Series processor ...

Brocade collaborates with Dell to announce industry's first 16 Gbps Fibre Channel end-to-end solution ...

Department of Energy's ESnet rolls out world's fastest science network ...

New storage and management features for IBM PureSystems help clients reduce costs and increase utilization ...

Obsidian welcomes Mellanox and its MetroX product into the long haul InfiniBand ...

Commercial and technical HPC customers can achieve Big Data results faster with NetApp HPS Rack solution ...

Brocade and Hyve Solutions partner to deliver fully integrated Big Data solutions using industry-leading Brocade VCS Fabric network technology ...

AMD FirePro server graphics redefining supercomputing performance through power efficient, sustainable technology ...

Medic Vision introduces industry's first enterprise-wide iterative image reconstruction system ...

StackIQ announces release of StackIQ Enterprise HPC for high performance computing clusters ...

Heterogeneous systems re-claim Green500 list dominance ...

PNNL expertise highlighted at Supercomputing ...

Keeneland Project deploys new GPU supercomputing system for the National Science Foundation ...

Titan is also a green powerhouse ...

AMD delivers massive compute performance for world's top ranked supercomputer ...

PNNL expertise highlighted at Supercomputing

13 Nov 2012 Salt Lake City - From identifying common patterns in data to speeding up computers, researchers from the Department of Energy's Pacific Northwest National Laboratory (PNNL) shared their computational expertise at this year's Supercomputing conference.

Data is everywhere these days. Biologists sift through vast amounts of error-prone data to understand how our cells work. Even librarians slog through mountains of information to better understand the materials they catalog. The key to comprehending today's information explosion is finding meaningful patterns buried in the data - and then finding comparable data patterns in other, related sources. This technique is called network alignment. Computational scientists at PNNL and Purdue University have developed new methods to identify similar patterns in any type of data. Their procedures help find proteins that act the same in humans and mice, and help find ideas that act the same for librarians and Wikipedia editors.

The existing methods used to solve these kinds of problems have been too slow to cope with the growing amount of data, prompting the PNNL and Purdue team to make them faster. To do this, they developed a new algorithm that uses an approach called approximate matching, which saves time by matching nearly identical patterns instead of exactly identical ones. They also developed new computer implementations that enabled the algorithm to use all a computer's processors in parallel to quickly identify relationships between two different networks. Tests using both of these improvements showed that the algorithm found similar interactions between thousands of proteins in two species in just seconds and found comparable ideas between hundreds of thousands of topics in library systems and Wikipedia entries in less than a minute.

PNNL's Mahantesh Halappanavar led the research on how to quickly find approximate matchings with help from Purdue's Arif Khan and Alex Pothen. And, Purdue's David Gleich led the work on how to use approximate matchings to align networks. David Gleich presented a paper, titled "A multithreaded algorithm for network alignment via approximate matching", describing this research.

Large and complex networks in parallel computers can lead to inefficient communications between processors that also slows down computation. This makes it difficult to achieve exascale computing, which is one thousand times faster than today's fastest petascale supercomputers. Scientists are developing strategies to reduce the time it takes to compute data and communicate those results between parallel processors. A team of researchers from PNNL, University of California, San Diego, and Lawrence Livermore National Laboratory have developed new software called Bamboo to help do just that.

Traditionally, scientists have broken up a complex algorithm to speed things up. Different processors calculate bits of the algorithm and then each processor communicates its results to the others. Such division of labour is quicker than one processor doing all the work by itself. But communicating bunches of data between multiple processors can cause information bottlenecks that slow down the whole process.

One solution is to initially calculate a portion of a processor's data and communicate those results while the other portion is still being calculated. Called overlapping communications and calculations, this approach can reduce the overall time it takes to complete a job, but it requires extremely complex codes. That's where Bamboo comes in. Bamboo automatically translates standard MPI parallel codes into a format that can easily overlap communication with available computation. Without Bamboo, scientists have the onerous task of manually developing overlapping MPI code. Tests showed Bamboo-generated code was as good as or better than human-developed codes.

PNNL's Eric Bylaska drew on his experience developing complex code for NWChem, DOE's premier molecular modelling software package, to help develop realistic test programs for the Bamboo framework. The University of California, San Diego's Scott Baden, who led the project, presented a paper, titled "Bamboo - Translating MPI Applications to a Latency-Tolerant, Data-Driven Form", describing the team's results.

Source: DOE/Pacific Northwest National Laboratory

Back to Table of contents

Primeur weekly 2012-11-19

Exascale supercomputing

DataDirect Networks announces $100 million investment in Exascale computing ...

Intel and DataDirect Networks join forces to enable compute infrastructures 1,000 times larger than today's biggest systems ...

The Cloud

HP delivers industry's first purpose-built server for Big Data ...

DDN adds enterprise class Cloud Tiering, NAS and SSD capabilities to its parallel file system appliances, making them Big Data ready ...

Desktop Grids

Members of the public asked to help tend Feynman's Flowers ...

EuroFlash

EMI 2 - Matterhorn - 5th update is now available ...

German Federal Waterways Engineering and Research Institute (BAW) optimizes navigable waterways using a Bull supercomputer ...

Choreographing light ...

USFlash

New editions of Moab HPC Suite enhance HPC system efficiency ...

SGI ICE X selected by CRIEPI for electric power research ...

Supermicro debuts SuperServer and SuperBlade solutions supporting new AMD Opteron 6300 Series processor ...

Brocade collaborates with Dell to announce industry's first 16 Gbps Fibre Channel end-to-end solution ...

Department of Energy's ESnet rolls out world's fastest science network ...

New storage and management features for IBM PureSystems help clients reduce costs and increase utilization ...

Obsidian welcomes Mellanox and its MetroX product into the long haul InfiniBand ...

Commercial and technical HPC customers can achieve Big Data results faster with NetApp HPS Rack solution ...

Brocade and Hyve Solutions partner to deliver fully integrated Big Data solutions using industry-leading Brocade VCS Fabric network technology ...

AMD FirePro server graphics redefining supercomputing performance through power efficient, sustainable technology ...

Medic Vision introduces industry's first enterprise-wide iterative image reconstruction system ...

StackIQ announces release of StackIQ Enterprise HPC for high performance computing clusters ...

Heterogeneous systems re-claim Green500 list dominance ...

PNNL expertise highlighted at Supercomputing ...

Keeneland Project deploys new GPU supercomputing system for the National Science Foundation ...

Titan is also a green powerhouse ...

AMD delivers massive compute performance for world's top ranked supercomputer ...