Researchers are using IBM's Roadrunner to analyze tens of thousands of genetic sequences from individuals with HIV.
(Credit: Los Alamos National Laboratory)
Physicist Tanmoy Bhattacharya and HIV researcher Bette Korber are creating an evolutionary genetic family tree based on samples taken by the international Center for HIV/AIDS Vaccine Immunology consortium, in order to compare the evolutionary history of more than 10,000 sequences from more than 400 people with HIV.
If they can identify common features of the virus as it is transmitted, researchers might be able to create a vaccine that recognizes the virus before the body's immune system reacts to--and mutates--it.
What already sounds like a lot of data, however, could balloon further, hence the importance of Roadrunner. "We are at the cusp of being able to obtain more than 100,000 viral sequences from a single person," Korber said. "For this new kind data to be useful, computational advances will have to keep pace."
Roadrunner, developed by IBM for the Department of Energy (and occupying about 6,000 square feet at the Los Alamos National Laboratory in New Mexico), first broke the petaflop barrier (which means it performed more than one million billion calculations per second) in May 2008. It may soon be known for helping develop a "specially designed" HIV vaccine, Bhattacharya says:
The petascale supercomputer gives us the capacity to look for similarities across whole populations of acute patients. At this scale we can begin to figure out the relationships between chronic and acute infections using statistics to determine the interconnecting branches--and it is these interconnections where a specially-designed vaccine might be most effective.
In addition to helping map the HIV genetic tree, Roadrunner has also recently simulated the Big Bang in an attempt to better understand dark matter, calculating the physics behind 64 billion proto-galaxies, each about the size of a billion of our suns. Once it crunched those numbers (all in a day's work, right?), Roadrunner's results predicted five times more dark matter than astronomers have thus far observed.
Roadrunner maintains its lead as the fastest supercomputer in the world.
(Credit: IBM)Despite the Jaguar nipping at its heels, Roadrunner continues to speed past the supercomputing pack.
That's according to the twice yearly Top500 list of the fastest supercomputers in the world, which is to be announced Tuesday morning at the 2009 International Supercomputing Conference in Hamburg, Germany. The list is released in June and November every year.
The IBM supercomputer housed at the Department of Energy's Los Alamos National Laboratory, known as Roadrunner, maintains the lead it grabbed a year ago. The computer can process 1.105 petaflop/s, or quadrillions of floating point operations per second, according to the Top500 Linpack benchmark. Hot on its heels for the second year in a row is the Cray XT5 Jaguar system at the DOE's Oak Ridge National Laboratory, which clocked in at 1.059 petaflop/s.
Despite the consistency of those top two systems, there were some newcomers to the top 10 of the list of 500 this year, and not from within the U.S. The new IBM computer, known as JUGENE, installed at Forschungszentrum Juelich in Germany hit 825.5 teraflop/s, or trillions of floating point operations per second, which was good enough for third place on the list. Forschungszentrum Juelich also is home to the 10th place supercomputer, JUROPA, which is a combination of Bull Novascale and Sun Sunblade x6048 servers. It achieved 274.8 teraflop/s.
The rest of the top 10 fastest computers in the world are all housed in the U.S. But some notable international sites are demanding attention. An IBM BlueGene/P system at King Abdullah University of Science and Technology in Saudi Arabia took 14th place, while the Dawning 5000A at the Shanghai Supercomputer Center in China took 15th place.
The threshold to get on the Top500 list this year got increasingly tough. The slowest computer on the list hit 17.1 teraflop/s, when six months ago the slowest computer on the list achieved 12.64 teraflop/s. That also means the total combined power of the 500 supercomputers is faster than ever at 22.6 petaflop/s. Six months ago the top 500 hit 16.95 petaflop/s, and 11.7 petaflop/s a year ago.
Despite holding some of the top spots, IBM's overall dominance as the top supplier of servers for these supercomputers has been eclipsed by Hewlett-Packard. While IBM leads in overall installed performance, HP has the greater market share at 212 to IBM's 188.
Inside those servers, Intel has the lion's share of processors, with just under 80 percent, or 399 of the top 500. IBM Power processors are the second-most popular, and can be found in 55 of the systems.
The Top 10 List:
• Roadrunner, IBM, Los Alamos National Laboratory (1.105 petaflop/s)
• Jaguar, Cray, Oak Ridge National Laboratory (1.059 petaflop/s)
• JUGENE, IBM, Forschungszentrum Juelich (825.5 teraflop/s)
• Pleiades, SGI, NASA Ames Research Center (487.01 teraflop/s)
• BlueGeneL, IBM, Lawrence Livermore National Laboratory (478.2 teraflop/s)
• Kraken XT5, Cray, National Institute for Computational Sciences (463.3 teraflop/s)
• BlueGene/P, IBM, Argonne National Laboratory (458.61 teraflop/s)
• Ranger, Sun, Texas Advanced Computing Center (433.20 teraflop/s)
• Dawn, IBM, Lawrence Livermore National Laboratory (415.70 teraflop/s)
• JUROPA, Bull SA, Forschungszentrum Juelich (274.80 teraflop/s)
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