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In a standard benchmark test, the computer achieved a rating of 35.6 teraflops (one trillion floating point operations per second).
"If we look at the previous Top 500 list that was published in November, the Earth Simulator is faster than the sum of the first 18 machines," said Dongarra in an e-mail response to a reporter's questions.
The computer was jointly developed by NEC and a team of engineers from the National Space Development Agency of Japan (NASDA), the Japan Atomic Energy Research Institute and Japan Marine Science and Technology Centre, at a price of around ¥50bn (£265m) as part of a project that began in 1997.
It was delivered to the Yokohama Institute for Earth Sciences in March and is used to create computer models for climate change simulations. A virtual planet earth exists within the system and data is transferred from satellites, buoys and other weather and climate data sources to help monitor global warming, atmospheric and marine pollution and torrential rainfall.