The Week in Review

By Tiffany Trader

May 6, 2010

Here is a collection of highlights from this week’s news stream as reported by HPCwire.

France’s GENCI Deploys SGI Supercomputers

PGI Accelerator Compilers Enhanced for Latest NVIDIA

Revolution Analytics Defines the Future of Predictive Analytics with R

SGI Announces Next-Generation Altix ICE Scale-Out Supercomputer

AMAX Launches 1,920-Core 4U GPU Server

Spectra Logic Doubles Capacity and Memory of High-Performance Disk Appliance

AMAX Intros GPU Cluster Based on ‘Fermi’ Architecture

Supermicro Ships 2nd Generation GPU Systems with New Double-Precision GPUs

Appro Introduces 1U Quad GPU Server Based on NVIDIA Tesla 20-Series GPUs

More GPU Routines Now Available from Numerical Algorithms Group

Bright Cluster Manager Leverages Latest NVIDIA Tesla GPUs

Appro Adds GPU Flexibility to Its GreenBlade System

Cray Reports First Quarter 2010 Financial Results

SGI Reports Q3 Fiscal 2010 Financial Results

D. E. Shaw’s Anton Supercomputer on Loan to PSC

This week, the Pittsburgh Supercomputing Center (PSC) received a $2.7 million grant from the National Institute of General Medical Sciences (NIGMS), part of the National Institutes of Health (NIH). The money, which comes from the stimulus funds, will allow PSC to host a specialized supercomputer for biomolecular simulation. The machine and the innovative software that runs on it were designed by D. E. Shaw Research (DESRES), an independent research lab that enables high-speed molecular dynamics simulations. The supercomputer was dubbed “Anton” after the Dutch inventor of the microscope Anton van Leeuwenhoek because it allows scientists to see how molecules interact “close-up.”

From the release:

Anton was designed to dramatically increase the speed of molecular dynamics (MD) simulations compared with the previous state of the art, allowing biomedical researchers to understand the motions and interactions of proteins and other biologically important molecules over much longer time periods than have previously been accessible to computational study.

Studying how molecules change over time can lead to the development of new therapeutic drugs, but the process is so compute-intensive that many important biological phenomena were, up to now, impractical to simulate. Anton makes it possible to run simulations that extend for more than a millisecond of biological time, which is about 100 times longer than demonstrated in any previously-published reports.

The Anton project is one of 14 awards made by NIGMS with funding from the American Recovery and Reinvestment Act of 2009 for what the NIH views as “Grand Opportunities” for major scientific progress. In fact, this is the first time NIH has provided funds to make a supercomputing system for MD simulations available as a national resource.

According to NIGMS Director Jeremy M. Berg, “By closing specific knowledge gaps, creating new technologies, or building community-wide resources, these awards will dramatically propel progress in key scientific fields.”

Starting in late 2010, Anton will be made available gratis for non-commercial research use by universities and other non-profit ventures. A Request for Proposals (RFP) for computer time on Anton will be issued in the coming months, and the information will be available here.

NCSA Global Warming Predictions Dire, But Reversible

First the bad news: recent climate models confirm what many already know, that human-caused global warming is real. But the good news is it’s not too late to do something about it. So shows research put out this week by the National Center for Supercomputing Applications (NCSA).

Donald Wuebbles, a professor of atmospheric sciences at the University of Illinois at Urbana-Champaign, has been studying atmospheric chemistry and climate change for 40 years, and shares the 2007 Nobel Peace Prize for his work with the Intergovernmental Panel on Climate Change (IPCC). He and his team use the NCSA supercomputing resources to create and study 3D models of the atmosphere.

Says Wuebbles: “The climate is changing, and the evidence clearly suggests it is largely being caused by human activities. The good thing is, although we cannot totally reverse it, at least during this century, we can — by our energy and transportation choices — choose to keep the largest impacts from occurring.”

The term “global warming” is used heavily in media reports, even debated, but Wuebbles prefers the term “global weirding.” The phrase is suggestive of the strange weather events that climate change gives rise to. To those who question whether the warming trend is human related or just a natural phenomenon, he responds:

Climate does of course vary naturally, but the large changes we have been seeing in recent decades have the fingerprints of the human emissions as being the primary driving force. The global temperatures of the last decade are larger than they have been in over 2,000 years — this would not happen without some form of forcing. The Earth clearly has a fever.

Using NCSA’s Cobalt and Abe supercomputers, Weubbles team studies the findings from 3D chemistry-climate models that include the effects of air pollution. The pollution is a result of energy, industrial, and transportation sources, from dust storms, and from biomass burning. The models show that over the next 90 years, the warming of the planet’s land mass will increase substantially even if carbon dioxide emissions remain at their present levels (currently they are increasing). The temperature of the oceans will also increase, although not as quickly.

From the release:

While global warming is complicated, the basic mechanism underlying it is not. Natural emissions of heat-trapping gases essentially form a blanket in the Earth’s atmosphere, allowing life on our planet as we know it. The problem is human emissions are adding another blanket. This blanket is holding in the heat and keeping the planet toasty — lately, a little too toasty. But don’t expect a cooling trend any time soon. The gases emitted today will affect the Earth’s atmosphere many years from now.

So what can we do to slow the warming trend?

Human activities have caused or contributed to increasing temperatures and it will take human action to being to turn things around. Whether the changes are small or large — from the lightbulbs we purchase to the cars we drive — practicing conservation and reducing energy use will help lower carbon dioxide emissions. New technology, renewable energy resources and a forward-thinking green energy policy are all part of the overall strategy.

According to a special government task force that assessed the potential impacts of climate change on the United States, if nothing is done to stop the warming trend, average temperatures across the country could be nearly 11.5°F higher than they are now by the end of the century. Professor Weubbles explains that for folks living in Champaign, Ill., it will feel like their city slid down to Austin, Texas.

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