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Primeur weekly 2011-11-28

The Cloud

Shipping company signs $150 million-plus data centre services agreement with HP ...

Chinese genomics giant BGI releases latest bioinformatics software and datasets ...

New EMC Atmos Cloud Delivery Platform enhancements simplify delivery of Cloud Storage-as-a-Service - fully functional in minutes ...

UniCredit Global Information Systems S.p.A. Global Markets & Treasury selects Platform Computing to deliver a private Cloud environment ...

Adaptive Computing joins forces with SGI to deliver robust HPC and Cloud solutions ...

Fujitsu simplifies and unifies Cloud management with new ServerView Resource Orchestrator V3 ...

EMC OnDemand brings Captiva, Document Sciences and Documentum to the hybrid Cloud ...

UniCredit Global Information Systems S.p.A. Global Markets & Treasury selects Platform Computing to deliver a private Cloud environment ...

Desktop Grids

CERN has 2020 vision for LHC upgrade ...

Mersenne@home launched as new BOINC project ...

New Stanford software takes Folding@home's biological research to supercomputers ...

EuroFlash

projectiondesign launches 2nd Generation LED projector, the FL35 wqxga ...

PRACE awards 91 million processor core hours on the DECI call to 35 projects, new call open ...

Numascale, IBM and the University of Oslo together in European PRACE project for emerging technology ...

EMI 1 Update 10 now available ...

Fujitsu launches Hybrid Cloud Services for Microsoft Windows Azure customers ...

The impending revolution of low-power quantum computers ...

USFlash

K computer research results awarded ACM Gordon Bell Prize ...

Cray enters the integrated storage market ...

Adaptive Computing rocks the enterprise with new Moab HPC Suite - Enterprise Edition ...

3 DOE labs now connected with ultra-high speed network ...

Rankings released for supercomputers doing big data ...

NVIDIA Tesla GPUs again power world's greenest Petaflop supercomputer ...

Researchers get $7.5 million grant to combat nerve agents ...

K computer no. 1 in four benchmarks at HPC Challenge Awards ...

Whamcloud and Fujitsu to collaborate on Lustre development ...

SGI customers accelerate research efforts with new AMD Opteron 6200 series processors ...

HP to transform server market with single platform for mission-critical computing ...

EMC expands "no compromise" storage for High Performance Computing at SC11 ...

New Stanford software takes Folding@home's biological research to supercomputers

18 Nov 2011 Stanford - Vijay Pande's chemistry and structural biology group at Stanford has become known for Folding@home, a distributed computing project that borrows computing time from home computers to simulate how proteins take shape. Now, other researchers will be able to take advantage of the computing technology that Vijay Pande's group has developed over the last decade. The new distributed framework for supercomputers, called Copernicus, was presented at SC11, an international supercomputing conference, in Seattle.

Copernicus was developed in collaboration with the labs of Erik Lindahl at Sweden's KTH Royal Institute of Technology and Stockholm University and Peter Kasson at the University Virginia.

"We're bringing Folding@home to supercomputers", stated Vijay Pande, a professor of chemistry. Proteins control nearly all of life's functions, but how they self-assemble, or fold, is an unsolved problem in biology. Understanding how folding goes awry could lead to cures for diseases caused by protein misfolding, like Alzheimer's and Parkinson's.

By modelling protein folding, Vijay Pande said, "We hope to get exquisite detail and information that you might not be able to get from experiments."

Folding@home uses processor time donated by millions of home computer and video game console users. It has advanced the field of molecular dynamics by cutting protein-folding simulation times from years to days. Recently, Vijay Pande's group used Folding@home simulations to investigate new therapeutic approaches for Alzheimer's.

The vast computing resources of Folding@home have been available to Vijay Pande and his collaborators. With open-source Copernicus software, other researchers can run simulations, including molecular models, using processer time on multiple supercomputers or computing clusters, rather than home computers.

"It opens the door to huge crowds of people using these methods, which have matured with Folding@home", Vijay Pande stated.

With an interest in solving protein structures and having large computing clusters on hand, pharmaceutical companies are an example of one potential Copernicus user-group.

The advantage of Copernicus comes from how it uses the fast communication available between supercomputers, combined with statistical sampling techniques, to run parallel simulations within or between computing clusters or between supercomputers.

Copernicus allows for each additional processor in the system to aid the calculation to run faster and faster, something known as strong scaling. Previously, when using supercomputers to understand molecular dynamics, it has been very difficult to achieve strong scaling on a single machine.

"This method should be able to use any supercomputer on the planet completely", Vijay Pande stated. "Strong scaling to these extremes is unusual."

Folding@home is useful for molecular simulations that take place on relatively long timescales. But Copernicus will be a tool for shorter problems where researchers want a quick solution.

Computationally, using Copernicus is like taking a Lamborghini to run out for milk. Folding@home, on the other hand, "is kind of like a rocket. It takes a big deal to launch it and once you launch, it goes really far", Vijay Pande stated. "You don't use it to go to the corner store."
Source: Stanford University

Back to Table of contents

Primeur weekly 2011-11-28

The Cloud

Shipping company signs $150 million-plus data centre services agreement with HP ...

Chinese genomics giant BGI releases latest bioinformatics software and datasets ...

New EMC Atmos Cloud Delivery Platform enhancements simplify delivery of Cloud Storage-as-a-Service - fully functional in minutes ...

UniCredit Global Information Systems S.p.A. Global Markets & Treasury selects Platform Computing to deliver a private Cloud environment ...

Adaptive Computing joins forces with SGI to deliver robust HPC and Cloud solutions ...

Fujitsu simplifies and unifies Cloud management with new ServerView Resource Orchestrator V3 ...

EMC OnDemand brings Captiva, Document Sciences and Documentum to the hybrid Cloud ...

UniCredit Global Information Systems S.p.A. Global Markets & Treasury selects Platform Computing to deliver a private Cloud environment ...

Desktop Grids

CERN has 2020 vision for LHC upgrade ...

Mersenne@home launched as new BOINC project ...

New Stanford software takes Folding@home's biological research to supercomputers ...

EuroFlash

projectiondesign launches 2nd Generation LED projector, the FL35 wqxga ...

PRACE awards 91 million processor core hours on the DECI call to 35 projects, new call open ...

Numascale, IBM and the University of Oslo together in European PRACE project for emerging technology ...

EMI 1 Update 10 now available ...

Fujitsu launches Hybrid Cloud Services for Microsoft Windows Azure customers ...

The impending revolution of low-power quantum computers ...

USFlash

K computer research results awarded ACM Gordon Bell Prize ...

Cray enters the integrated storage market ...

Adaptive Computing rocks the enterprise with new Moab HPC Suite - Enterprise Edition ...

3 DOE labs now connected with ultra-high speed network ...

Rankings released for supercomputers doing big data ...

NVIDIA Tesla GPUs again power world's greenest Petaflop supercomputer ...

Researchers get $7.5 million grant to combat nerve agents ...

K computer no. 1 in four benchmarks at HPC Challenge Awards ...

Whamcloud and Fujitsu to collaborate on Lustre development ...

SGI customers accelerate research efforts with new AMD Opteron 6200 series processors ...

HP to transform server market with single platform for mission-critical computing ...

EMC expands "no compromise" storage for High Performance Computing at SC11 ...