Blue Gene/L was top of the biannually produced list because in June 2005 it set a new world record performance of 280.6 trillion calculations per second.
It is installed at the Lawrence Livermore National Laboratory in California and the other Blue Gene machine is at IBM's Thomas J Watson research lab in New York state.
The Blue Gene/L machine has doubled in size since the last list was compiled and now harnesses the computational power of more than 130,000 processors.
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