Noah Johnson
Folding Proteins at Home
But How Valid?
To test the validity of the simulation, Pande and his team asked Folding@home volunteers to calculate the rate of folding in a well-understood protein known as BBA-5.
Then they compared the computer findings with physical tests on the same protein. Folding@home computers modeled the protein snapping into shape in 6 thousandths of a second — the same amount of time protein takes to form and fold in the lab.
Every day, Folding@home parcels out computational tasks among 43,000 desktop computers, demonstrating that distributed computing can be applied not only to mathematics, but also to problems scientists confront in their laboratories.
Friendly Competition
Protein folding isn’t exactly sexy, so Pande nurtured volunteers’ interest by setting up a competition for those donating the most computer time.
It worked.
Since the project began, volunteers have organized themselves into thousands of teams — with names such as Dutch Power Cows, Overclockers Australia and Alliance Francophone. Some teams have just two people; others, thousands of members, all linked by the Internet.
Johnson is the point man for the Mac OS X team, which is comprised of about 1,000 volunteers, all running Mac OS X.
“People are starting to bring G5s online. People with G5s are flying by everyone. We just passed a German team and we’ll be passing other teams as well.”
Extreme Overclockers
Johnson hosts a web page on his Mac so new members can download the software and current members can check their progress, which is measured in points based on how many chunks of data a computer processes.
“I provide a place for the team to get together to discuss problems they’re having, ways to improve folding and so on,” Johnson says. “When the new Folding@home application came out for the Power Mac G5, we provided information on the team forum to help people use it.
The site also posts individual, team and overall project statistics so Mac OS X team members can see how they’re doing against other teams. “In just the last two months,” he says, “we moved from 30th to 24th place out of 2,000 teams worldwide in terms of our work unit production.”
Bringing G5s Online
“And people are starting to bring G5s online,” Johnson adds. “Before, on earlier Macs, they’d stay in one place in the stats; nobody would pass them and they wouldn’t pass anybody. But people with G5s are flying by everyone. We just passed a German team and we’ll be passing other teams as well.”
Because of the way the software is written, Folding@home doesn’t interfere with Johnson’s normal use of his Mac. “When you’re not using the computer,” he explains, “the project will use everything you’ve got — all of the processor 100% of the time.
“But if you want to use the computer,” he points out, “the project will scale back and you won’t see a hit in performance. When you’re done, it goes back to 100%.”
“Every day, Folding@home parcels out computational tasks among 43,000 desktop computers, demonstrating that distributed computing can be applied to problems scientists confront in their laboratories.”
Folding on the Mac
“The reason I fold on a Mac,” Johnson confides, “is that I work 40 hours a week at a Windows shop. I got tired of fixing computers all day long and then coming home and fixing computers. So I converted to Mac for sanity’s sake.
“The Mac has been just head and shoulders over Windows as far as ease of use and not having to fix it all the time,” Johnson says. “And the operating system is fun to use; with Windows, you have to be tinkering all the time and fixing registry entries. I didn’t want to come home and do my job at home.”
Also, Johnson says, performance is a factor. “Beberg originally ported the Linux version of Folding@home to the Mac,” he says, “but he also optimized the software for the Power Mac G4, G5 and even the G3. We saw 200 and 300% speed increases with the new software,” says Johnson.
Power Mac G5 Performance
“Let’s say you have a 1GHz processor for your Pentium 4 and a 1GHz G5. Obviously the G5 runs faster than that, but they are baselined at 1GHz apiece. Because the software is optimized for the G5, it will get more work done than a Pentium. It actually manages to squeeze more out of the processor on a megahertz-to-megahertz basis.
“Now,” Johnson says, “we can compete with AMD and Intel processors head to head. Since we launched the new core, we’ve seen an increase in points very clearly. Which means we’re handling larger work units more quickly.”