Games consoles reveal the supercomputer within

February 16, 2008

WHEN Todd Martínez broke his son’s Sony PlayStation he didn’t realise this would change the course of his career as a theoretical chemist. Having dutifully bought a PlayStation 2 as a replacement, he was browsing through the games console’s technical specification when he realised it might have another use. “I noticed that the architecture looked a lot like high-performance supercomputers I had seen before,” he says. “That’s when I thought about getting one for myself.”

Six years on and Martínez has persuaded the supercomputing centre at the University of Illinois, Urbana-Champaign, to buy eight computers each driven by two of the specialised chips that are at the heart of Sony’s PlayStation 3 console. Together with his student Benjamin Levine he is using them to simulate the interactions between the electrons in atoms. Scaled up over entire molecules, the results could pave the way to predicting how a protein will interact with a drug.

Martínez and Levine are not the only researchers who have turned to gaming hardware to do their number crunching. That’s because the kinds of calculations required to produce the mouth-wateringly realistic graphics now seen in high-end video games are similar to those used by chemists and physicists as they simulate the interactions between particles in systems ranging in scale from the molecular to the astronomical. Rotating, enlarging or reflecting an object from one frame to the next in a game, for example, requires a technique called matrix multiplication. Modelling the interactions between thousands of electrons in a molecule calls for similar techniques.

Such simulations are usually carried out on a supercomputer, but time on these machines is expensive and in short supply. By comparison, games consoles are cheap and easily available, and they come with the added bonus of some innovative hardware. For example, the Wii, made by Nintendo, has a motion-tracking remote control unit that is far cheaper than a comparable device would be if researchers had to build it from scratch.

One key advance is the ease with which scientists can now program games consoles for their own purposes. Although consoles do a great job of rendering images, games programs don’t require software to save data once it has been used to render the image. Scientists, by contrast, need to be able to store the results of the calculations they have fed into their machines.

Things started to get easier in 2002, when demand from computer enthusiasts who wanted to use their PlayStations as fully fledged desktop machines prompted Sony to release software that allowed the PlayStation 2 to run the Linux operating system. That allowed scientists to reprogram the consoles to run their calculations. Then in 2006 came the big breakthrough, with the launch by IBM, Sony and Toshiba of the Cell chip that now drives Sony’s PlayStation 3 (see Timeline). With one central processor and eight “servant” processors (New Scientist, 19 February 2005, p 23), it is vastly more powerful than the PS2 chip, and was designed from day 1 to run Linux.

The release of the Cell has accelerated  research into black holes by Gaurav Khanna, an astrophysicist at the University of Massachusetts, Dartmouth. He has strung together 16 PS3 consoles to calculate the properties of the gravity waves that are expected to be produced when two black holes merge. Meanwhile, a collaboration between IBM and the Mayo Clinic in Rochester, Minnesota, is using the Cell’s ability to render high-resolution video graphics to do the same with data gathered by MRI and other medical scanning techniques. The aim is to make diagnosis easier and faster – by using the images to determine whether a tumour has grown or shrunk, for example.

Other researchers are pushing for even more speed. One of Martínez’s students, Ivan Ufimtsev, is experimenting with the NVIDIA GeForce 8800 GTX graphical processing unit (GPU) for PCs, which was released in November 2006. The GPU has 128 processors – compared to the Cell’s eight – and when slotted into a PC, helps turn it into a high-quality gaming engine. To start with, these cards were hard to program, just like the PS2 without the Linux add-on, but NVIDIA soon cottoned on to the sales opportunities that scientists like Martínez could offer for its product. In February 2007 it released the Compute Unified Device Architecture, a software package that allows the C programming language to be used to program the GPUs.

The results were staggering. When Martínez used it to simulate the repulsion between two electrons in an atom, he found that the calculation ran 130 times faster than it did on an ordinary desktop computer (Journal of Chemical Theory and Computation, DOI: 10.1021/ct700268q). He is now calculating the energy of the electrons in 1000 atoms, which add up to the size of a small protein. “We can now do the things we were killing ourselves to do,” he says.

Martínez predicts that it will soon be possible to use the GPU to predict more accurately which drug molecules will most strongly interact with a protein and how they will react, which could revolutionise pharmaceutical research. Similarly, Koji Yasuda at Nagoya University in Japan reported in a paper published this month (Journal of Computational Chemistry, vol 29, p 334) that he used the same GPU to map the electron energies in two molecules: the anti-cancer drug paclitaxel and the cyclic peptide valinomycin.

Games hardware still isn’t perfect for science. The Cell’s eight processors and the NVIDIA GPUs are forced to round decimal numbers to seven decimal places. As numbers are repeatedly multiplied together, this small error becomes magnified. In a game, the result might be nothing more serious than a car appearing slightly closer to a wall than it should, but in research such inaccuracies can be show-stoppers.

It’s not just the chips that researchers can usefully borrow from gaming hardware. Take the Wii’s hand-held remote control, which contains an accelerometer that can sense in which direction it is being moved, and how vigorously. It transmits this information via a Bluetooth link to the console, where it is used to adjust the graphics to respond to the player’s movements in real time.
Monitoring Parkinson’s

The device recently grabbed attention as a tool for surgeons to improve their technique (New Scientist, 19 January, p 24). Meanwhile, neurologist Thomas Davis at the Vanderbilt Medical Center in Nashville, Tennessee, is using it to measure movement deficiencies in Parkinson’s patients. By attaching up to four Wii remotes to different limbs, Davis captures data for tremor, speed and smoothness of movement, and gait. This data is then sent via the Bluetooth link to a laptop running software that allows Davis to assess quantitatively how well a patient can move. Davis hopes this can be used in clinical trials for Parkinson’s drugs to replace the scoring scales now used, which are based on a doctor observing a patient’s condition.

Others are using the console to assess the progress of patients who have had a stroke or a head injury by monitoring their performance as they play Wii games. Johnny Chung Lee at Carnegie Mellon University in Pittsburgh, Pennsylvania, is using the Wii remote as a virtual reality research tool. As the wearer’s head moves, the Wii tracks it and displays images dependent on where the wearer is looking. Meanwhile, a team at the University of Valladolid in Spain hopes to use the Wii remote to rotate and manipulate ultrasound images more intuitively.

Computer gamers have always hankered after the latest console or PC hardware to run ever more realistic-looking games. Now scientists are lining up right beside them.

From issue 2643 of New Scientist magazine, 16 February 2008, page 26-27

And not an xbox360 in sight….


Two Long Sleepless Nights

September 28, 2007

So baby CJ is settling well here at home though she hasn’t settled during the night. Both me and Olly are quite tired but we may have found the solution.

I bottle fed her some expressed milk for the first time today and she has settled like magic. We have one content baby. It’s the first time she has been fed by bottle and the first time I have fed her. What a magical experience. We’ll see if a bottle settles her tonight at bed time.

On a more serious note:

Nutrient pollution from farms and livestock hurts amphibians

Remember the uproar in 1995 when school kids in Minnesota began finding frogs with extra limbs? The mutated amphibians looked like props in some sci-fi movie, and scientists quickly began searching for the culprit behind the deformities. Speculation centered on pesticides, increased UV radiation, and infection from parasites—which ultimately turned out to be the “villain.”

But the question remained: why were these parasites—called trematodes—increasing in number and preying on frogs? According to a study published earlier this week in the Proceedings of the National Academy of Sciences, the leading cause of the problem is the runoff of phosphorous and nitrogen fertilizer, originating from agriculture (likely the monoculture corn and soybean farms of the Midwest), cattle grazing, and domestic runoff.

What’s the connection? Through a process called eutrophication, the excess nutrients from animal manure and fertilizers cause more algae to grow in surface waters, like the pond where the kids first found the mutated frogs. The extra algae helps increase populations of snails (which feed on algae), as well as populations of the microscopic parasites (trematodes), which the snails eat and release into ponds. The trematodes form cysts on developing tadpoles, which can cause frogs to develop missing, or in some cases multiple, limbs. The frog’s predators then eat the frogs and the parasites, spreading the trematodes back into the ecosystem and relaunching the cycle.

But don’t think you’re safe from the effects of this pollution just because you’re not an amphibian. “Since most human diseases involve multiple hosts, understanding how increased nutrient pollution affects freshwater and marine food webs to influence disease is an emerging frontier in ecological research,” says Pieter Johnson, a water scientist at the University of Colorado at Boulder and the lead author of the study.

Organic farming is the way forward as I have said many times, along with getting rid of farmed animals totally.

Arctic thaw may be at “tipping point”

Fri Sep 28, 2007 9:24am EDT

 

By Alister Doyle, Environment Correspondent

OSLO (Reuters) – A record melt of Arctic summer sea ice this month may be a sign that global warming is reaching a critical trigger point that could accelerate the northern thaw, some scientists say.

“The reason so much (of the Arctic ice) went suddenly is that it is hitting a tipping point that we have been warning about for the past few years,” James Hansen, director of NASA’s Goddard Institute for Space Studies, told Reuters.

The Arctic summer sea ice shrank by more than 20 percent below the previous 2005 record low in mid-September to 4.13 million sq km (1.6 million sq miles), according to a 30-year satellite record. It has now frozen out to 4.2 million sq km.

The idea of climate tipping points — like a see-saw that suddenly flips over when enough weight gets onto one side — is controversial because it is little understood and dismissed by some as scaremongering about runaway effects.

The polar thaw may herald a self-sustaining acceleration that could threaten indigenous peoples and creatures such as polar bears — as Arctic sea ice shrinks, the darker ocean soaks up ever more heat than reflective snow and ice.

In Germany, the Potsdam Institute for Climate Impact Research says Arctic sea ice has “already tipped.”

Among potential “tipping elements” that are still stable, it lists on its Web site a melt of Siberian permafrost, a slowdown of the Gulf Stream and disruptions to the Indian monsoon.

“I’d say we are reaching a tipping point or are past it for the ice. This is a strong indication that there is an amplifying mechanism here,” said Paal Prestrud of the Center for International Climate and Environmental Research in Oslo.
“But that’s more or less speculation. There isn’t scientific documentation other than the observations,” he said.

SHIPPING, POLAR BEARS

Many experts now reckon Arctic ice may disappear in summer before mid-century, decades before earlier forecasts. The thaw would open the region to oil and gas exploration or shipping.

Reuters will host a summit of leading newsmakers on Oct 1-3 to review the state of the environment. Speakers will include Rajendra Pachauri, the head of the U.N. Climate Panel and Michael Morris, chief executive of American Electric Power.

“All models seem to underestimate the speed at which the ice is melting,” said Anders Levermann, a Potsdam professor.

“I do not believe that this is alarmist… not all tipping points are irreversible,” he said. And societies can weigh up remote risks, such as planes crashing or nuclear meltdowns.

Hansen said he is seeking more study of causes of the melt, widely blamed on greenhouse gases from burning fossil fuels but perhaps slightly stoked by soot from forest fires or industries in Russia and China. Ice darkened by soot melts faster.

“It is a very good lesson, because the ice sheets (on Greenland and Antarctica) have their own tipping points, somewhat harder to get started but far more dangerous for humanity around the globe,” he said.

A melt of floating Arctic sea ice does not affect sea levels but Greenland has enough ice to raise oceans by 7 meters and Antarctica by about 57 meters, according to U.N. estimates.
Pachauri’s authoritative climate panel, in a summary report due for release in November, does not use the phrase “tipping point” but does say: “Climate change could lead to abrupt or irreversible climate changes and impacts.”

It says, for instance, that it is “very unlikely” that the Gulf Stream bringing warm water north to Europe will switch off this century. That could bring a big regional cooling.

And it says that a melt of ice sheets could lead to big sea level rises over thousands of years. “Rapid sea level rise on century time scales cannot be excluded,” it adds.

From the bits and pieces I have read it is going to take a long while for us to notice a difference in Global Warming even if we were to stop polluting now, maybe up to 10 to 20 years. That doesn’t mean we shouldn’t stop, because the longer we continue the worse it is going to get. Fact. Hopefully the summit happening shortly will come up with some strong concrete goals and objectives that will be kept rather than spotlighted for a short period of time and then brushed under the carpet. A certain North American country and a treaty beginning with K springs to mind.