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Primeur live 2011-06-23

Blog

The K in K computer, the world's fastest supercomputer ...

Some insights in the TOP500 ...

Prospect Association presents report "High Performance Computing in Europe: a vision for 2020" to the European Commission ...

Hardware

Petaflop/s: The why, the how and the what for? ...

Panasas gives customers a treat with scalable ActivStor11 ...

Four important questions on energy consumption in HPC ...

Memory makers ready to help out but have no control over the infrastructure ...

Applications

What will it take to achieve the simulation of the human brain? ...

Russia accelerates scientific innovation with GPU supercomputers ...

hpc-ch at ISC'11 to present HPC activities in Switzerland ...

University of Hamburg to simulate large data applications with Distributed Simulation and Virtual Reality environment ...

German automotive industry heavily relies on HLRS simulation expertise ...

Massive simulation and sensing devices generate great challenges and opportunities ...

TOP500

Japan reclaims top ranking on latest TOP500 list of world's supercomputers ...

Supercomputer "K computer" takes first place in world ...

The new TOP500 in figures and percentages ...

AMD sees 15 percent growth in six months on newest list of TOP500 supercomputers ...

Tera 100 once again crowned as Europe's most powerful supercomputer ...

The Lomonosov Supercomputer Has Attained a New Level of Performance ...

SGI Altix supercomputer system at NASA achieves Petaflop scale ...

The 2010 HPC status and the 2011 HPC weather forecast in ten chapters ...

Around the world of HPC in 30 minutes ...

The Grid

RealityServer: A powerful platform for 3D visualization and rendering now accessible in the Cloud ...

You ask "What Cloud?" It's Enterprise IT! ...

Company news

Altair's PBS Professional celebrates 20th anniversary and exhibits at International Supercomputing Conference in Hamburg ...

Adapteva selects E.T. International's software for breakthrough high-performance, low-power multicore processor ...

T-Platforms signs strategic reseller agreement with AEON Computing ...

International Supercomputing Conference sessions to feature lively exchanges of ideas ...

SGI to unveil groundbreaking HPC solutions at 2011 International Supercomputing Conference ...

QLogic automates installation, verification, monitoring and management of InfiniBand fabrics ...

Panasas introduces ActiveStor 11, delivering cost-effective parallel storage for HPC and big data workloads ...

Appro nabs exclusive supercomputing deal with three US National Laboratories ...

QLogic wins major deployment in NNSA's Tri-Labs cluster ...

T-Platforms to participate in supercomputer industry's premier European event, ISC11 ...

NetApp bolsters management capabilities, provides common foundation for enterprise customers' private, public, and hybrid Clouds ...

Bull announces the creation of BUX, the Bull User group for eXtreme Computing ...

Bright Cluster Manager 5.2 shipping with support for CUDA 4, ScaleMP, SLURM, LSF and enhanced multi-cluster management ...

Experts from Russia and EU collaborate on HOPSA; a new project to boost the performance of supercomputers ...

Companies at ISC'11 exhibition show media the innovations they've got in store for user ...

Xyratex exhibiting at International Supercomputing Conference 2011 ...

Supermicro showcases portfolio of HPC optimized solutions at ISC'11 ...

Mellanox FDR InfiniBand selected to deliver PetaScale performance for Europe’s fastest supercomputer ...

NetApp E5400 meets extreme customer demands in high-performance environments ...

VMware introduces vFabric 5, an integrated application platform for virtual and Cloud environments ...

Adaptive Computing announces 10x scalability for high throughput computing and next-generation HPC systems ...

University of Birmingham uses Adaptive Computing technology to reduce HPC costs ...

Adaptive Computing HPC Technology advances research capabilities for Europe's leading cancer research centre ...

Penguin Computing's public HPC Cloud is now powered by Adaptive Computin's Moab Cluster Suite ...

Numascale announces support for Supermicro 1042G-LTF and IBM System x3755 M3 with multi socket 8/12 core AMD Opteron 6000 Series ...

Mellanox expands availability of InfiniBand and Ethernet solutions with NEC LX Series Supercomputer through NEC HPC Europe ...

Mellanox and Lawrence Livermore National Laboratory demonstrate leading performance and scalability for HPC applications ...

Mellanox announces complete end-to-end FDR 56Gb/s InfiniBand interconnect solutions for uncompromised clustering performance and scalability ...

SGI to deliver breakthrough exascale computing solution ...

Platform's collaboration with CERN recognized as 2011 Computerworld Honors Laureate ...

Bright Computing, NVIDIA and NextIO to drive panel discussion on use of GPUs in HPC at International Supercomputing Conference in Germany ...

GE Global Research gets a Cray supercomputer ...

Italy's largest computing centre selects DataDirect Networks (DDN) and IBM to accelerate international scientific collaboration and discovery ...

SGI launches InfiniteStorage 5500 for high performance data solutions ...

SGI announces fifth-generation Altix ICE high performance compute solution ...

IBM certifies 40 Gigabit Ethernet line card from Force10 Networks ...

Fusion-io technology advances bioinformatics research at San Diego Supercomputer Center ...

Fusion-io technology advances bioinformatics research at San Diego Supercomputer Center

22 Jun 2011 Hamburg - Fusion-io's technology has been utilized to realize significant performance improvements in MySQL database queries for bioinformatics research. The Protein Data Bank (PDB) research is being conducted at the University of California, San Diego, in collaboration with the San Diego Supercomputer Center (SDSC). Researchers at SDSC noted that replacing hard drive disks (HDDs) with Fusion-io technology in their database infrastructure reduced query times from 30 minutes to three minutes.

Fusion-io's memory technology is being utilized by the SDSC, an organized research unit of UC San Diego, in its data-intensive computing initiatives. As part of these efforts, researchers are using the technology to advance research on the Protein Data Bank, the world's most comprehensive repository for

three-dimensional structures of large molecules and nucleic acids. The research carried out for the PDB serves as a foundation for accelerating the development of life-saving drugs, synthetic proteins used in medicine and other treatments for illnesses.

"As SDSC strives to serve as a center for research excellence, we focus heavily on evaluating how flash-based technologies can improve scientific discovery", stated Allan Snavely, Associate Director of SDSC and co-Principal Investigator of the Center's upcoming data-intensive high-performance computing (HPC) system, Gordon, which is currently in development. "Through our research, we are finding that storage memory products like those offered by Fusion-io are considerably faster than hard drive disks for many large memory and data-intensive problems, and that flash-based storage memory has the potential to make supercomputing-level results accessible outside the traditional user base."

Using Fusion-io's server-deployed technologies, researchers were able to reduce the time required to conduct complex MySQL database queries that determine relationships between proteins and the effects proteins can have on each other. Using traditional hard drive disks, a query analyzing more than 200 million protein structures took 30 minutes.

"With Fusion-io's shared data decentralization technologies - which place the storage memory medium right next to the processor to significantly reduce latency and increase processing speed - the same query took just three minutes", stated Robert Sinkovits, SDSC computational scientist and Gordon Applications Lead.

Spencer Bliven, a graduate student in the Bioinformatics and Systems Biology Department at UC San Diego working with Allen Snavely on the research, stated: "The PBD is helping us gain a more theoretical and practical understanding of the foundations of biological science. With the reduced query times I've seen in conducting tests with Fusion's ioMemory technology, I'm able to stay more focused on my research. This allows the scientific discovery process to be more spontaneous and greatly helps me in eliminating potential errors."

The computer used to realize the performance gains includes two quad-core Intel Xeon E5530 2.40 GHz processors and 48 GB of DDR3-1066 memory. It includes four 320 GB ioDrives mounted and configured as a single 1.2 TB RAID 0 device running an XFS file system.

"Storing crucial data in the server where it is processed can greatly accelerate the analysis of large data sets to enable new scientific discoveries", stated Neil Carson, Chief Technology Officer of Fusion-io. "It's inspiring to see how SDSC is leveraging the performance gains and reduced latency made possible by Fusion-io technology to advance complex biological research that serves as the foundation for many improvements in science and medicine."
Source: Fusion-io

Back to Table of contents

Primeur live 2011-06-23

Blog

The K in K computer, the world's fastest supercomputer ...

Some insights in the TOP500 ...

Prospect Association presents report "High Performance Computing in Europe: a vision for 2020" to the European Commission ...

Hardware

Petaflop/s: The why, the how and the what for? ...

Panasas gives customers a treat with scalable ActivStor11 ...

Four important questions on energy consumption in HPC ...

Memory makers ready to help out but have no control over the infrastructure ...

Applications

What will it take to achieve the simulation of the human brain? ...

Russia accelerates scientific innovation with GPU supercomputers ...

hpc-ch at ISC'11 to present HPC activities in Switzerland ...

University of Hamburg to simulate large data applications with Distributed Simulation and Virtual Reality environment ...

German automotive industry heavily relies on HLRS simulation expertise ...

Massive simulation and sensing devices generate great challenges and opportunities ...

TOP500

Japan reclaims top ranking on latest TOP500 list of world's supercomputers ...

Supercomputer "K computer" takes first place in world ...

The new TOP500 in figures and percentages ...

AMD sees 15 percent growth in six months on newest list of TOP500 supercomputers ...

Tera 100 once again crowned as Europe's most powerful supercomputer ...

The Lomonosov Supercomputer Has Attained a New Level of Performance ...

SGI Altix supercomputer system at NASA achieves Petaflop scale ...

The 2010 HPC status and the 2011 HPC weather forecast in ten chapters ...

Around the world of HPC in 30 minutes ...

The Grid

RealityServer: A powerful platform for 3D visualization and rendering now accessible in the Cloud ...

You ask "What Cloud?" It's Enterprise IT! ...

Company news

Altair's PBS Professional celebrates 20th anniversary and exhibits at International Supercomputing Conference in Hamburg ...

Adapteva selects E.T. International's software for breakthrough high-performance, low-power multicore processor ...

T-Platforms signs strategic reseller agreement with AEON Computing ...

International Supercomputing Conference sessions to feature lively exchanges of ideas ...

SGI to unveil groundbreaking HPC solutions at 2011 International Supercomputing Conference ...

QLogic automates installation, verification, monitoring and management of InfiniBand fabrics ...

Panasas introduces ActiveStor 11, delivering cost-effective parallel storage for HPC and big data workloads ...

Appro nabs exclusive supercomputing deal with three US National Laboratories ...

QLogic wins major deployment in NNSA's Tri-Labs cluster ...

T-Platforms to participate in supercomputer industry's premier European event, ISC11 ...

NetApp bolsters management capabilities, provides common foundation for enterprise customers' private, public, and hybrid Clouds ...

Bull announces the creation of BUX, the Bull User group for eXtreme Computing ...

Bright Cluster Manager 5.2 shipping with support for CUDA 4, ScaleMP, SLURM, LSF and enhanced multi-cluster management ...

Experts from Russia and EU collaborate on HOPSA; a new project to boost the performance of supercomputers ...

Companies at ISC'11 exhibition show media the innovations they've got in store for user ...

Xyratex exhibiting at International Supercomputing Conference 2011 ...

Supermicro showcases portfolio of HPC optimized solutions at ISC'11 ...

Mellanox FDR InfiniBand selected to deliver PetaScale performance for Europe’s fastest supercomputer ...

NetApp E5400 meets extreme customer demands in high-performance environments ...

VMware introduces vFabric 5, an integrated application platform for virtual and Cloud environments ...

Adaptive Computing announces 10x scalability for high throughput computing and next-generation HPC systems ...

University of Birmingham uses Adaptive Computing technology to reduce HPC costs ...

Adaptive Computing HPC Technology advances research capabilities for Europe's leading cancer research centre ...

Penguin Computing's public HPC Cloud is now powered by Adaptive Computin's Moab Cluster Suite ...

Numascale announces support for Supermicro 1042G-LTF and IBM System x3755 M3 with multi socket 8/12 core AMD Opteron 6000 Series ...

Mellanox expands availability of InfiniBand and Ethernet solutions with NEC LX Series Supercomputer through NEC HPC Europe ...

Mellanox and Lawrence Livermore National Laboratory demonstrate leading performance and scalability for HPC applications ...

Mellanox announces complete end-to-end FDR 56Gb/s InfiniBand interconnect solutions for uncompromised clustering performance and scalability ...

SGI to deliver breakthrough exascale computing solution ...

Platform's collaboration with CERN recognized as 2011 Computerworld Honors Laureate ...

Bright Computing, NVIDIA and NextIO to drive panel discussion on use of GPUs in HPC at International Supercomputing Conference in Germany ...

GE Global Research gets a Cray supercomputer ...

Italy's largest computing centre selects DataDirect Networks (DDN) and IBM to accelerate international scientific collaboration and discovery ...

SGI launches InfiniteStorage 5500 for high performance data solutions ...

SGI announces fifth-generation Altix ICE high performance compute solution ...

IBM certifies 40 Gigabit Ethernet line card from Force10 Networks ...

Fusion-io technology advances bioinformatics research at San Diego Supercomputer Center ...