New IBM top supercomputer Blue Gene to study human body

 York Town Heights 06 Dec 99 A computer - nicknamed "Blue Gene" by IBM researchers who are developing it - will be capable of more than one quadrillion operations per second (one petaflop). This is 500 times faster than the world's current fastest supercomputer. Blue Gene's massive computing power will initially be used to model the folding of human proteins. This fundamental study of biology is one of the "grand challenge" applications. Learning more about how proteins fold is expected to give medical researchers better understanding of diseases, as well as potential cures.

"This is exactly what IBM Research does best -- continuously placing big, aggressive bets on technologies that change the future of computing", said Dr. Paul M. Horn, senior vice president of IBM Research. "If this computer unlocks the mystery of how proteins fold, it will be an important milestone in the future of medicine and health care."

IBM Research believes a radical new approach to computer design and architecture will allow Blue Gene to achieve petaflop-scale performance in about five years -- one-third of the close to 15 years it would normally take following Moore's Law. The two fastest computers in the world today are part of the ASCI programme run by the U.S. Department of Energy, and which were recently tested at about 2 teraflops -- two trillion operations per second each.

"We think a tremendous gain in performance will be made possible by the first major revolution in how computers are built since the mid-1980s", said Dr. Ambuj Goyal, IBM Research's vice president of computer science. "We call this new approach to computer architecture SMASH, which stands for Simple, Many and Self-Healing."

The SMASH architecture differs from existing approaches in three ways:

  • It dramatically simplifies the number of instructions carried out by each processor, allowing them to work faster and with significantly lower power and chip surface requirements (the traditional approach is to add complex features to gain performance);
  • It will facilitate a massively parallel system capable of more than 8 million simultaneous threads of computation (compared to the maximum of 5000 threads today);
  • It will make the computer self-stabilizing and self-healing -- automatically able to overcome failures of individual processors and computing threads.

    Blue Gene will consist of more than one million processors, each capable of one billion operations per second (1 gigaflop). Thirty-two of these ultra-fast processors will be placed on a single chip (32 gigaflops). A compact two-foot by two-foot board containing 64 of these chips will be capable of 2 teraflops, making it as powerful as the 8000-square foot ASCI computers.

    Eight of these boards will be placed in 6-foot-high racks (16 teraflops), and the final machine (less than 2000 sq. ft.) will consist of 64 racks linked together to achieve the one petaflop performance.

    Protein Folding Holds Key to Understanding Basics of Life

    The scientific community considers protein folding one of the most significant "grand challenges" -- a fundamental problem in science or engineering that has broad economic and scientific impact and whose solution can be advanced only by applying high-performance computing technologies.

    Proteins control all cellular processes in the human body. Comprising strings of amino acids that are joined like links of a chain, a protein folds into a highly complex, three-dimensional shape that determines its function. Any change in shape dramatically alters the function of a protein, and even the slightest change in the folding process can turn a desirable protein into a disease.

    Better understanding of how proteins fold will give scientists and doctors better insight into diseases and ways to combat them. Pharmaceutical companies could design high-tech prescription drugs customised to the specific needs of individual people. And doctors could respond more rapidly to changes in bacteria and viruses that cause them to become drug-resistant.

    "Breakthroughs in computers and information technology are now creating new frontiers in biology", said Horn. "One day, you're going to be able to walk into a doctor's office and have a computer analyse a tissue sample, identify the pathogen that ails you, and then instantly prescribe a treatment best suited to your specific illness and individual genetic makeup."

    About 50 scientists from IBM Research's Deep Computing Institute and Computational Biology Group will work on Blue Gene and the protein folding grand challenge. IBM Research is the world's largest research organisation dedicated to information technology, with eight labs around the world, including Austin, Beijing, Delhi, Haifa, Tokyo, San Jose, Yorktown Heights (New York), and Zurich. IBM Research works closely with the company's Life Sciences Unit, which was formed earlier this year to deliver information technology services and solutions to advance the pharmaceutical, biotechnology and agri-science industries.

     

    Ad Emmen

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