Computer expert seeks PC’s to research

Sean C. Morgan

Of The New Era

Local computer technician Garth Tomic is recruiting local residents to help fight Alzheimer’s – and a host of other maladies – with their computers.

Tomic is challenging residents of Sweet Home and other Linn County communities to contribute to research into Alzheimer’s disease and other projects by plugging in and letting Stanford University borrow their unused computer processing power. He says computers that sit idle could be put to better use.

Tomic, who owns and operates Santiam Computers in Sweet Home, says that even when in operation, a computer processor still spends much of its time idle, and that unused power could be applied to good causes.

He wants to see Sweet Home computer owners step up and join Team Sweet Home, Oregon to contribute their excess computer power to Stanford research programs. He would also like to see Lebanon, Albany and other communities do it too as a form of friendly competition based on per capita performance.

It’s a way for someone who can’t donate cash to contribute to the cause, he says, and it doesn’t limit the computer’s ability to function. Stanford University uses unused processor time, either on the “central processing unit” or the video card in personal computers in what is called “distributed computing.”

Computer owners, including Playstation 3, download and run software to help create one of the largest supercomputers in the world. Every computer takes the project, called Folding@home, closer to its goals using novel computational methods coupled with distributed computing to simulate problems millions of times more challenging than it had previously achieved.

Tomic joined the Folding@home project about six weeks ago.

“It was something other guys were doing on my adventure motorcycle forum,” Tomic said. “It struck a competitive chord for me.”

The forum has about 17 members who actively contribute to the Folding@home program, Tomic said. Overall, the project has approximately 250,000 actively participating CPUs.

He has since managed to move up into the top 10,000 for amount of work processed, he said. “But I’ve got some heavy-duty horsepower running here at no small expense, I might add. That competitive gene is expensive.”

He has tried several different video cards to find out which perform the best, he said. The program uses video card processors first, followed by the CPU if the video card isn’t appropriate.

Many video cards in the Nvidia 8000 and 9000 series are able to handle the software while older cards cannot.

“If I find a good cause and it includes competition, so much the better,” Tomic said.

In addition to his own computers, he is running satellite machines in Bend, Phoenix and Portland as well as some in the shop for service.

The project started in Dr. Vijay Pande’s lab in Stanford’s Department of Chemistry and Structural Biology. In 1999 Pande, an associate professor in physical and biophysical chemistry, wrote algorithms that would enable thousands of isolated computers to calculate tiny portions of a folding sequence and combine their solutions.

The software downloads work units from Stanford and then processes them in the background by simulating the folding of proteins.

Proteins are biology’s workhorse, but before they can perform their functions in the body’s cells, which include serving as antibodies, enzymes, messengers, structural components and transport/storage units, they must transform themselves from long chains of amino acids into three-dimensional structures, a process called “folding.” This folding process remains a mystery in many ways to scientists.

When proteins do not fold correctly, serious consequences can result, including many well-known diseases such as Alzheimer’s, mad cow, CJD, ALS, Huntington’s, Parkinson’s, many cancers and many cancer-related symptoms, according to the program’s Web site.

Pande’s program requires massive processing power to achieve simulations of the folding, and Folding@home received recognition for this in the 2007 Guinness Book of World Records for achieving the computing power of one petaflop or 1 quadrillion “floating point operations per second.”

The program has received a number of awards, including recognition for significant advances in simulating protein aggregation at the heart of Alzheimer’s disease.

The software can run on virtually any computer, although the output of older machines will be lower, Tomic said.

Even the lowliest laptop can help to some extent, he said. He has one laptop producing 67 points per day while one of his big desktop computers folds more than 2,000 points per day. Points are how Folding@home keeps track of how much has been processed.

The software uses 100 percent of the CPU’s or graphic card’s processing power, but that isn’t anything to worry about.

“If the machine was designed properly (and most are), it’s designed to run at 100 percent without any grief,” he said. “When running properly, this shouldn’t slow down anything in the foreground.”

The software does not prevent the use of other computer software, although Tomic suggests turning it off while playing graphically intense games. The software works in the background and backs off as other software is in use.

He does have one caution though, he said. “The interior of the machine needs to be clean because it’s going to run at 100 percent.”

Dust that coats heat sinks and electronic components can cause higher heat buildup, he said, and that could lead to problems.

He recommends removing the computer cover, blowing off the dust and looking for failed capacitors or obvious failures before running the software.

Tomic said he will inspect and clean towers for $20. He will send all of that cash to the program at Stanford University.

For those looking for further information or interested in donating to disease research this way, visit folding.stanford.edu on the Web, click on “Download Folding@home” and follow instructions. Tomic may be reached at 367-6660.

To join Team Sweet Home, Oregon, join team number 156891 inside the user account page.

For the sake of the friendly competition between nearby communities, Tomic is hoping Lebanon and Albany will create teams of their own, and he is planning to contact other computer technicians to join the cause and take the lead in those communities.

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