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High-Performance Hacks


For researchers with tight budgets, necessity is the mother of invention and innovation. These researchers are often forced to find alternative sources of computing power or experimental technology, so the do-it-yourself, hacker spirit has played a significant role in the scientific computing community, going all the way back to the first Beowulf compute cluster assembled by NASA in 1994. It is now a blueprint used across the world among those seeking to achieve cheap and powerful computing with low-cost commodity PCs instead of expensive traditional hardware.

In the last few years, high-performance computing innovators have looked beyond personal computers to electronic devices that were never intended for use in a lab. The most well-known to date is the use of the Sony PlayStation 3 gaming console for a range of molecular modeling projects, including [email protected], the distributed computing protein-folding project out of Stanford University. Since 2007 — when a team of researchers at North Carolina State University -constructed a cluster of eight PS3s that demonstrated processing capabilities as powerful as a small supercomputer for a fraction of the cost — the gaming consoles have been adopted by a number of research groups looking for cheap and powerful computing.

Not long after the Nintendo Wii gaming console arrived on the market in 2006, an MIT graduate student hacked and exploited the device for a range of uses, including an interactive whiteboard and a motion-sensing tracker. In 2009, researchers at the University of Warwick published a paper in Computational Biology and Chemistry that described the effectiveness of Microsoft's Xbox gaming console to study abnormal electrical activity in the heart.

Toward the unusual

More recently, efforts have ventured further afield to include devices that resemble traditional computing hardware even less. In March, a team of researchers at Ludwig Maximilian University in Munich announced that they were experimenting with Apple TV units — digital media receivers manufactured by Apple for accessing Internet television — for high-performance computing. The second-generation Apple TV units share their internal hardware with Apple's iPad device, including a 1 GHz processor, a PowerVR GPU, 8 GB of flash memory, and 256 MB of RAM, and it uses Apple's mobile device operating system iOS, which is similar to Unix. The device normally consumes about 6 watts, far less than the average server blade or workstation.

The initial motivation for trying out such an unusual piece of hardware for scientific computing came from the need to find a device that is power-efficient, inexpensive, and readily available. "We are interested in the future of high-performance computing, which is increasingly being dominated by concerns about energy efficiency. Servers based on energy-efficient ARM CPUs have been getting some interest from industry lately and we are interested in testing their suitability for the job," says Karl Fuerlinger, the LMU professor leading the project. "The Apple TV is a good starting point because it is affordable and fairly powerful. Having a big-iron supercomputer background, this is somewhat unfamiliar territory for us, but we wanted to get some real practical experience and the project has been a lot of fun so far."

Fuerlinger's team has built a six-node Apple TV cluster and is currently working on porting HPC essentials such as the Message Passing Interface specification that allows separate hardware units to share data processing tasks with one -another. He is confident that it will be possible to port traditional bioinformatics software or molecular modeling software to run on Apple TV units once his team works out the installation kinks. "We have encountered little difficulty so far getting to run software packages," Fuerlinger says. "The system offers a fairly standard Unix environment and we were able to get most of the benchmarks and other software working, so I think it should definitely be possible to run a molecular dynamics or bioinformatics app on the cluster."

A bigger challenge with using Apple TV units for scientific research is that, like iPhones, these devices are shipped "locked" — meaning that they must be hacked or "jailbroken" to free up the internal hardware for other purposes. There is currently a thriving community of hackers who post downloads and guide consumers on methods for unlocking Apple products. "The jailbreak community and Apple play a cat-and-mouse game, and the important thing is to have a firmware revision for which a jailbreak already exists. So we had to wait for several weeks before a jailbreak became available and we could proceed with our project," Fuerlinger says. "Once jailbroken, the devices come pre-installed with an SSH server, and creating a fully functional development platform is fairly straightforward from then on. Our project Web page contains some help on getting this step done."

Investigators at the University of Glasgow have incorporated Apple's iPad to help facilitate nanotechnology research by providing a user-friendly interface for controlling optical tweezers, instrumentation used to manipulate microscopic objects. "Consumer electronics give you an amazing amount of technology for surprisingly little money, so we are very keen to see what we can do with new technology," says Glasgow's Richard Bowman. "Our multi-touch interface interest started in Bristol with the team there — they needed to control several traps at once to work with nanorods to build tools. When the iPad came along we immediately saw its potential as a smaller, more convenient way of doing the same thing."

Bowman's team has developed an app called iTweezers that is freely available at the iTunes store. The app runs natively on the iPad — with no jailbreaking or hacking required — and makes use of the device's gesture recognition toolkit and powerful GPU processor to render holograms as a backdrop for enhanced particle manipulation. "One of the most useful features is that it's portable and wireless — we have to locate our computers away from the laser area for safety reasons — so it's really handy to be able to pick up the monitor and take it with you when you are aligning the optics, for example," Bowman says. "The other big advantage is that it's a much simpler, more intuitive interface than our usual program — so when we're doing experiments where we need to react quickly, it's really useful."

Bowman and the iTweezer team are currently working with collaborators in the chemistry department at Glasgow using optical tweezers to control crystal growth. Their hope is that the iPad will allow them to seamlessly interact with the structures as they grow, in real time.

Bowman says that this new trend is a direct result in the increasingly powerful processing capabilities of consumer electronics, and is definitely a new form of academic technology development that is here to stay. "For £100, you get a pocket super-computer with literally hundreds of processing cores and that would cost a huge amount if it was scientific equipment, but because it's sold to millions of people who want to play 3-D games, they can be manufactured incredibly cheaply," Bowman says. "Taking ordinary consumer electronics and pushing them to do cool stuff that they weren't designed for is just really fun."

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