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Blue Waters' petascale computer cracks part of HIV's code

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June 4, 2013

The University of Illinois' National Center for Supercomputing Applications is now using its Blue Waters petascale computer for research, and is credited with cracking part of HIV's code.

And this could possibly help point the way to new treatments for patients as well.

Overall, several simulations carried out on Blue Waters's complex supercomputer allowed researchers and scientists to determine the precise structure of the HIV capsid-– the protein shell protecting the virus, which is an important part of its ability to attack the human immune system.

A sample of 64 million atoms was analysed, and according to the researchers, that's what's required for the petaflop capability of the supercomputer.

What scientists were looking for was a detailed atomic-level analysis of the 1,300 identical proteins that form a cone-like structure in the capsid. Previously, attempts to analyse the capsid couldn't capture the whole structure in one single simulation.

While preparing for the experiment, the researchers, led by Peijun Zhang of the University of Pittsburgh, had first conducted various physical experiments including cryo-electron tomography to slice the proteins up and gain a broad understanding of their shape.

They then used the Blue Waters supercomputer to conduct a simulation, run by University of Illinois physics professor Klaus Schulten and postdoctoral researcher Juan Perilla, called “molecular dynamic flexible fitting”.

Schulten says that the capsid is “one of the biggest structures ever solved”. Blue Waters was originally going to be constructed by IBM, but the company withdrew in 2011, realizing that it couldn't build the supercomputer together on budget. Then, Cray picked up the project, assembling XE6 Opteron blade server nodes and XK6 CPU-GPU nodes, linked with Cray's Gemini XE interconnect system.

The 237 XE cabinets house more than 22,000 compute nodes, while the 32 XK cabinets are home to 3,072 computer nodes. There's 26.4 PB of storage with an aggregate I/O of more than a terabit per second.

In other IT news

It took quite a bit of time, but Oracle has finally admitted to Java's numerous security issues and has now outlined three new security initiatives to set the record straight.

The first item certainly won't please everyone, as the company has committed to including Java updates among the quarterly Oracle Critical Security Patch Update it provides for all its products, as of the October 2013 update.

Java previously operated a twice-yearly patch cycle of its own, but not anymore, and the catalyst is the escalating security problems with Java.

To be sure, Oracle's critical patch update usually includes dozens of patches, so the inclusion of Java could swell the amount of work facing IT professionals and system admins when the update comes.

The second update modification is outlined here: “Local Security Policy features will soon be added to Java and system administrators will gain additional control over security policy settings during Java installation and deployment of Java in their organization. The policy feature will allow system administrators to restrict execution of Java applets to those found on specific hosts (e.g., corporate server assets, partners, etc) and thus reduce the risk of malware infection resulting from desktops accessing unauthorized and malicious hosts.”

This plan is expected to decrease the exploitability and severity of potential Java security vulnerabilities in the desktop environment and provide additional security protections for Java operating in the server environment.

The server side will also get the following security enhancements: “In the future, Oracle will explore stronger measures to further reduce attack surface including the removal of certain libraries typically unnecessary for normal server operation. Such significant measures cannot be implemented in current versions of Java since they would violate current Java specifications, but Oracle has been working with other members of the Java Community Process to enable such changes in future versions of Java.”

However, there's no specific timeframe for their advent or the arrival of the new Local Security Policy, although some in the security field say it should be sometime in October 2013.

In other IT news

As far back as in the 18th century, scientists began experimenting with electrochemical energy cells. But consumers only started buying their first low-density Lithium-ion batteries in the late 1980s, and then the industry became fixated on lithium in the 1990s.

However, despite a long waiting period and some significant advances in the state of the art, Lithium-ion batteries today still suffer the kind of serious issues that generate embarrassing headlines. And overheating has been the biggest issue.

Dell recalled more than four million of its laptops in 2006 after finding that their Lithium-ion cells were catching fire. Then Nokia also recalled 46 million phone batteries a year later in 2007, and Lenovo recalled tens of thousands of batteries in 2009, 2011 and 2012.

Then again, laptops and smartphones are one thing, but this year Boeing was forced to ground no less than fifty of its multi-million dollar 787 Dreamliner jets after a serious charging issue caused a battery fire on a Nippon Airways flight that could have crashed the plane with all its passengers.

So far, the most explosive incidents likely came as a result of iron filings, not lithium, entering batteries during the manufacturing process, possibly when crimping the batteries before shipping them. Over time, these pieces of metal managed to create short circuits between anodes and cathodes, causing rapid heating and thermal runaway-– essentially metal particles were short-circuiting the cells.

Manufacturers today are understandably concerned that it’s also possible to grow lithium dendrites across from a lithium metal anode to the cathode, again causing a short and potentially similar results.

Source: Cray Research.

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