next up previous
Next: About this document

High-Performance Special-Purpose Computers in Science

Toshiyuki Fukushige
Piet Hut
Junichiro Makino
Department of Systems Sciences, College of Arts and Sciences,
University of Tokyo
+Institute for Advanced Study


The next decade will be an exciting time for computational physicists. After 50 years of being forced to use standardized commercial equipment, it will finally become relatively straightforward to adapt one's computing tools to one's own needs. The breakthrough that opens this new era is the now wide-spread availability of programmable chips that allow virtually every computational scientist to design his or her own special-purpose computer.

Towards Real Numerical Laboratories

Unlike real laboratories, numerical laboratories have been constructed almost exclusively from commercial products, which gave little flexibility. Starting in the late seventies, after the first microchips became available, there have been some exceptions. However, only the bravest souls dared to design their own equipment (Bakker and Bruin 1988).

In those days, speeding up the most compute-intensive few lines of FORTRAN code, in a large-scale simulation project, required building a bulky piece of electronic hardware consisting of tens of large circuit boards. By the late eighties, things looked a lot better already, since it had become possible to integrate such circuits into a single custom chip. However, the barrier, real or perceived, against building your own hardware was still substantial.

By now, after another ten years, the barrier has almost disappeared. With programmable chips, the question is not so much whether to make one's hands dirty building a machine, but rather how to program: whether to program the existing central processing unit of a commercial machine, or whether to program a more generic set of distributed processing units. In both cases, the trick is to find the best map between the scientific problem and the layout of the computational hardware. What favors the programmable option over the use of standard CPUs are the facts that: 1) supercomputers, optimized for scientific calculations, are rapidly disappearing, leaving us with less-than-optimal vanilla-flavored computers; 2) generic CPU chips are now becoming so complex that the overwhelming fraction of silicon real estate is dedicated to the electronic equivalent of bureaucracy rather than raw computing.

Of course, there is still one major drawback to the use of programmable chips in computational science: habit. It takes a while for scientists to switch their approach to a problem, even when more efficient methods have become available. Therefore, in order to prepare for the future, it is useful to look back at the past, to see what has already been accomplished during the last ten years, using special-purpose computers. Anything that has been done in this area, relying on specially designed chips, can in principle be done now with programmable chips, at only a fraction of the effort involved. Let us focus on a specific case.

A Case Study: The GRAPE Project

Our GRAPE project, started 10 years ago, is one example in which computational physicists developed special-purpose computers successfully. Here, success means that the developed machine made it possible to solve problems which were impossible to solve on general-purpose computers.

One of these projects has resulted in the GRAPE (short for GRAvity PipE) family of special-purpose hardware, designed and built by a small group of astrophysicists at the University of Tokyo (Makino and Taiji 1998). Like a graphics accelerator speeding up graphics calculations on a workstation, without changing the software running on that workstation, the GRAPE acts as a Newtonian force accelerator, in the form of an attached piece of hardware. In a large-scale gravitational N-body calculation, almost all instructions of the corresponding computer program are thus performed on a standard work station, while only the gravitational force calculations, in innermost loop, are replaced by a function call to the special-purpose hardware.

The GRAPE-4, which was completed in 1995 for the total budget of 240 M JYE (around 2 M dollars), offered a peak speed of 1.08 Tflops. On practical problems, a significant fraction of this speed can be actually used. For example, the Grape-4 developers have won the Gordon Bell prize for high-performance computing for two years in a row. In 1995, the prize was awarded to Junichiro Makino and Makoto Taiji for a sustained speed of 112 Gflops, achieved using one-sixth of the full machine on a 128k particle simulation of the evolution of a double black-hole system in the core of a galaxy. The 1996 prize was awarded to Toshiyuki Fukushige and Junichiro Makino for a 332 Gflops simulation of the formation of a cold dark matter halo around a galaxy, modeled using 768k particles on three-quarters of the full machine. The first general-purpose computer to offer a similar level of the performance is the 9000-processor ASCI Red machine, with a price tag around 50 M dollars, completed in late 1997.

In addition, more than 40 copies of small (5-30 Gflops) GRAPE-3 and GRAPE-4 versions are now being used in a major astrophysical institutes in many different countries.

In a year from now, the GRAPE-6 will become available, at a speed that will be at least 100 times faster than that of the GRAPE-4. In addition, single board versions will become available (the `GRAPE-6 junior'), that can be purchased by individual astrophysicists, to run at a speed of 500 Gflops, coupled to a normal workstation as a front-end. Such a single board will thus provide a speed-up of well over a factor 1,000 for a price comparable to that of the workstation.

What is the main reason behind the success of the GRAPE? From a technological point of view, it is not overly difficult to design a special-purpose computer with a cost-performance better than that of commercially available general-purpose computers. The reason is simply that an ever diminishing fraction of the available transistors in the present-day microprocessors are actually used in arithmetic operations. In contrast, in GRAPE systems essentially all available transistors in a processor chip are used to implement arithmetic units.

This main reason behind the optimal usage of silicon real estate in the GRAPE is that the data flow in a GRAPE chip is fixed, while most of the transistors in present-day microprocessors are utilize to provide flexible data flow. In other words, the key trick to outperform general-purpose machines is to build a hardware accelerator for a specialized function, and not to build a programmable computer. To design a programmable computer is a difficult task, and you have a very little chance (unless you are a Seymour Cray) to outwit competent designers in large companies. However, designing a specialized piece of hardware for a single function is not something computer architects do. So there is essentially no competition.

Having it all

The interesting shift, alluded to in our opening statement, is that it is no longer necessary to choose between programming a computer and building a special-purpose computer. With the availability of increasingly efficient programmable chips, one can program an off-the-shelf chip, such as a FPGA (Field-Programmable Gate Array) chip, to emulate a special-purpose chip. It is like having your cake and eating it: you can emulate a fixed date flow. Before you program the chip, it is far more flexible than a standard CPU, in the sense that you are not bound by a given instruction set, providing all instructions yourself, from the bottom up. And after having programmed the chip, it has turned into a data flow machine, without any need to decode additional information on the fly.

Figure 1: Relation between programmable microprocessors (MPU), FPGA, and custom LSIs. Future FPGA will offer more flexibility and higher performance.

Of course, there is a drawback to any new development. With current FPGAs, flexibility comes with a cost: more than 90% of the silicon resource is used to provide programmability. Even so, custom computing machines based on FPGA have become a viable alternative for both general-purpose computers and specialized hardwares, given the fact that standard CPUs tend to have lower and lower efficiency as well, while their complexity keeps increasing.

We have developed a small system with two FPGA chips to evaluate the potential of FPGA technology. The current FPGAs turned out to be large enough to house a complete GRAPE-3 chip (110K transistors). The chips available in next year will be large enough to house a GRAPE-4 chip and the effective performance would exceed 1 Gflops per chip.


To summarize, FPGAs offer the possibility of combining the flexibility of conventional programmable computer and the high throughput of special-purpose hardware. To play the devil's advocate, one might argue that FPGAs could combine the difficulty of design of special-purpose hardware and the low efficiency of the programmable computer. To be honest, at present there still is that danger. To continue the devil's advocate argument: implementing a function onto an FPGA is analogous to programming a universal Turing machine, in the sense that it offers the maximum flexibility at the lowest level. Clearly, a more sensible design methodology is necessary. On the bright side, rapid advances are being made in the development of higher level tools for implementing algorithms on FPGAs. And the more the parallelization bottleneck, using general-purpose computers, will be felt, the larger the incentive will become to switch to a use of programmable chips.

Thus FPGAs are not a universal solution for all problems in computational physics. A full-custom chip offers clear advantages when its high initial development cost can be amortized by mass production. General-purpose computers are still better in developing sophisticated algorithms, and experimenting with them. But the use of FPGAs can be expected to increase rapidly, in computational science, for a wide range of problems, that are too complex to `put in stone' in the form of a special-purpose chip, but not too complex to program onto a FPGA. In that way, problems which cannot be solved in a practical time on programmable computers, do not have to be shelved until commercial computers catch up and deliver the required speed. As the example of the GRAPE has shown us, even a small group of computational scientists can solve their particular computational problems years ahead of (the commercial) schedule.


Bakker A. F. and Bruin C. (1988) Design and implementation of the Delft molecular-dynamics processor. In Alder B. J. (ed) Special Purpose Computers, pages 183--232. (Academic Press, San Diego)

Makino J. and Taiji M. (1998) Special Purpose Computers for Scientific Simulations -- The GRAPE systems. (John Wiley and Sons, Chichester)

next up previous
Next: About this document

Jun Makino
Thu Nov 26 22:23:29 JST 1998