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Stokes supercomputer boosts Irish scientists' work
Sunday, March 01, 2009 By Emmet Cole
A supercomputer hosted by the Irish Centre for High-End Computing (ICHEC) is helping Irish scientists to participate in world-class research with a speed and efficiency beyond the wildest dreams of their predecessors.

Capable of performing 25.1 trillion calculations per second (25.1 teraflops), the Stokes supercomputer (named after George Gabriel Stokes, the Sligo-born mathematician and physicist) not only makes your desktop computer look like an abacus, but it also holds 117th place in the latest list of the world's Top 500 fastest computers. Purchased to replace ICHEC's Walton supercomputer (3.14 teraf lops), Stokes has been in operation since January 1 and is already bringing huge benefits to Irish researchers, said JC Desplat, Associate Director of ICHEC. A supercomputer hosted by the Irish Centre for High-End Computing (ICHEC) is helping Irish scientists to participate in world-class research with a speed and efficiency beyond the wildest dreams of their predecessors.“We're seeing considerable enthusiasm within the Irish scientific community. Stokes has given Irish scientific researchers new standards of versatility, speed and capability, greatly exceeding those of Walton,” said Desplat. Met Eireann has already migrated its day-to-day operational forecasts from Walton to Stokes, to better tackle the difficult problem of predicting Irish weather. Stokes also plays an important role in preparations for the forthcoming international IPCC AR-5 climate modelling report. Built by California based, supercomputer manufacturers, Silicon Graphics, Stokes is an SGI ICE 8200 parallel computer, offering 84 terabytes of storage, and 320 nodes, each containing two Intel Xeon &EURO;5462 quad-core processors and 16GB of RAM. This provides a total of 2,560 cores and 5,120GB of Ram.

The number of cores is important to scientific researchers, said Desplat, because supercomputers perform tasks differently to standard computers.

“Your desktop has one processor that does everything from managing your operating system to handling applications. When you use a supercomputer like Stokes, however, you assign specific processes to each processor,” explains Desplat.

More cores means more processes running concurrently, more efficient number-crunching and greatly reduced processing times.

“Processes that took a week on Walton can now be performed in a 24-hour period. We're also seeing a large increase in the number of jobs that we can perform concurrently,” explains Desplat.

Communications between the computer's nodes is handled by advanced Infiniband technology (many times faster than Walton's Gigabit Ethernet infrastructure).

With specs like these, Stokes is perfectly adapted to the competitive, data intensive world of life sciences research, said Simon Wong, support scientist at ICHEC, with genomics and phylogenetics - the study of the relationships between DNA sequences of different organisms - two areas likely to benefit most from access to the new machine.

“There's a lot of competition for quick turnaround and results in the life sciences and Stokes will really help Irish life sciences to be competitive on a global scale,” says Wong.

Stokes - which is estimated to have cost just under €2million - was financed mainly by e-INIS, a national project coordinated by the Dublin Institute for Advanced Studies and the Higher Education Authority, with contributions from University College Dublin (UCD) and the National University of Ireland, Maynooth. Stokes is located in UCD's Research IT Data Centre, on the Belfield campus.

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