A Year 1988 Sixty-Processor Parallel Life Science Computer
In 1988 Klaus Schulten urgently needed a few million dollars for his research. He wanted to simulate a biological membrane, as no other method existed to characterize this crucial part of a biological cell in atomic detail. The required computation was too large for any computer at that time, but a Cray 1 supercomputer, but that machine cost millions and Schulten needed it all to himself.
Schulten and two brilliant students, Helmut Grubmueller and Helmut Heller, decided to build a computer as powerful as a Cray 1, for just $30,000! They thought this feasible with a new chip, the Transputer, that promised to make building one’s own parallel supercomputer like child's play. That's what the manufacturer claimed, but it was not as simple as promised.
The three biophysicists designed their computer and all ten group members soldered boards with 6 Transputer processors each. The machine, with altogether 60 Transputers, was named T60. After the job, each group member proudly signed his name on the front of his board, still visible today. The group built a case and the boards went in. When operated, the machine gave a nice warm breeze of air, the temperature reflecting the kind of computing actually happening at any moment in the machine.
The computer came in on budget, but then the most difficult work started - the programming of a multi-processor computer, one of the first of its kind. The machine connected the sixty processors like pearls on two communication strings to exchange data when simulating the biological membrane. The program, named Ego, grew every day, until finally it orchestrated all processors for the simulation task. Ego ran on T60 day and night for a year to accomplish the largest biomolecular simulation ever, that of a membrane with 200 lipids and water, altogether 30,000 atoms.
T60 and Ego proved that computational biology could be done effectively on parallel computers and started one of the most successful developments in the history of computational science, funded by the National Institutes of Health and by the National Science Foundation. Since 1988, the computers used have grown in size to almost one hundred thousand processors today (2010). The simulation and analysis programs of the Schulten group, operating on these supercomputers, laptops, and everything in-between, have been adopted by over 160,000 registered users world-wide, busying computers around the world every minute of the day. As a result, biomolecular simulations on parallel computers have revealed how human kidneys function, how the brain generates electrical signals, how drugs attack viruses, and how plants harvest sunlight to power life on earth.
Click here for a publication reporting simulation of a biological membrane using the T60.
