Blue Gene genie

Toby Howard

This article first appeared in Personal Computer World magazine, July 2000.

The last time Futures looked at supercomputers, a then top-of-the-range home PC had a 200 MHz processor with 32Mb of memory and a 2Gb disk. Three years later, PCs have moved on a bit. And so has the supercomputer world.

It's a bit like trying to measure a piece of string, but according to a list of the world's top 500 fastest computers the current fastest machine is a monster called "ASCI Red". Part of the US Department of Energy's Accelerated Strategic Computing Initiative at the Sandia National Laboratories in Albuquerque Red is an Intel machine with over nine thousand processors. It performs at 2 teraflops – that's two million million arithmetic operations every second – and runs simulations of nuclear weapons.

Number two on the top-500 list is "ASCI Blue", an IBM machine at the Lawrence Livermore National Laboratory, with nearly 6000 processors. But IBM won't be in second place for long, with the announcement of their new supercomputing project. It's called "Blue Gene", and it'll be the most powerful computer ever, 500 times faster than ASCI Red.

IBM has a track record of building impressive machines. A couple of years ago their "Deep Blue" machine famously beat world chess champion Garry Kasparaov . Blue Gene will be 1000 times as powerful as Deep Blue, making it about 2 million times the power of today's top-spec PCs.

To build such a revolutionary machine, IBM researchers have devised a new computer achitecture, which they call "Simple, Many, and Self-Healing", or SMASH for short. SMASH relies on an established processor design called RS/6000, which uses a very small and simple RISC instruction set – there are only 57 different instructions the processor can run . Each Blue Gene chip will have 32 processors onboard, and there'll be 64 chips on each of the machine's two-foot square motherboards. Then, there'll be a stack of eight motherboards, in a vertical tower. And there'll be 64 towers. The figures, when you tot them up, are amazing: each motherboard hosts 2048 processors – making a total of over a million.

The operating system will be a flavour of Unix, and the machine will be able to support over 8 million separate simultaneously parallel "threads" of computation. The $100 million machine will occupy 160 square feet of floor space at IBM's Watson Laboratories in Yorktown Heights, New York. It should be ready by 2005.

But what's all the computing power for? Unlike many of the world's supercomputers, Blue Gene won't be for used military or intelligence purposes. Its first application will be molecular biology.

One of the Holy Grails of contemporary scientific research is to understand how the proteins in our cells fold up into complex three-dimensional shapes. A protein is a long linked chain of amino acid molecules, and the links allow the protein to adopt a shape which determines its function in the cell. A number of diseases, including cystic fibrosis and Alzheimer's, are known to have their origins in anomalously folded proteins. Improved knowledge of how proteins fold could lead to the development of new drugs, and a far better understanding of how diseases attack cells.

Dr Paul Horn, Senior Vice-President of IBM Research, has a grand vision of the ultimate application of Blue Gene's protein-folding simulations: "One day, you're going to walk into a doctor's office and have a computer analyse a tissue sample," he says, "and the machine will instantly prescribe a treatment best suited to your specific illness and genetic makeup".

Didn't Doctor McCoy have one of those?

Toby Howard teaches at the University of Manchester.