FPGA and Rapid Prototyping Technology Use
in a Special Purpose Computer for Molecular Genetics
J. Gill Watt*
Thayer School of Engineering, Dartmouth College Hanover, NH 03755
*currently with Digital Equipment Corporation, Hudson MA
It has long been known that for certain narrowly defined problems, special-purpose processors can achieve significant cost/performance gains over general purpose machines. We describe one such processor here: a custom accelerator for gene sequence analysis,.
The use of rapid prototyping technology was crucial in our efforts to produce a working system in a short amount of time. Field programmable gate arrays and in-house PCB prototyping were of special importance. We discuss how these technologies were used in our system, and offer price-performance comparisons of our processor with other machines. The processor is completely functional, and yields a 15x performance improvement over an unassisted host.
Recent advances in molecular biology have made computational accelerators for gene sequence comparison of growing importance. Biologists will soon be capable of sequencing the entire human genome, producing billions of bytes of information and demanding large amounts of computing power.
Unfortunately, computer architects have not matched this demand for increased computing power with improved architectures. Biologists must content themselves with personal computers, which offer low cost and low performance, or supercomputers, which perform well but are extremely expensive. There is little middle ground.
To address this problem, we have constructed a machine that costs as much as a personal computer but offers an order of magnitude improvement in performance. This machine, the Gene Sequence Processor, attaches to a host computer and can compare gene sequences 15x faster than the host alone, for a cost of around $2,000. Our machine is also "alignment-preserving"; it permits the user to see how sequences are related to one another in addition to computing a numerical similarity metric. We will explain this in more detail shortly.
2.0 Previous Work
The past few years have seen a dramatic increase in the efforts of biologists to use computers for gene sequencing. The Journal of Nucleic Acids Research produces a special issue every two years devoted exclusively to computer related research. There is now a special journal for the applications of computers in biology , as well as books devoted to computers and gene sequence analysis .
Virtually all this work is concerned with software and algorithms. Research in the area of architecture has been less active, probably due to the relative inaccessibility of architectural ideas to biologists. One of the first attempts was made by Collins and Coulson , who suggest using the DAP SIMD machine, for sequence processing. Mukherjee  discusses efficient hardware algorithms for finding the longest common subsequence of two strings, although no performance results are reported. Many supercomputers have received careful attention from researchers, including the Hitachi S810-20 , and the iPSC/1 and the CM-1 . Lopresti discusses the performance of the Multiflow Trace, Convex C1, Cray-2, and CM-2 on gene sequence comparison problems in . We shall have more to say about these results in later sections.
Perhaps the most successful effort in the area of special purpose processing is the Splash highly parallel programmable logic array, developed by Lopresti and colleagues at the Supercomputing Research Center . This machine evolved out of the Princeton Nucleic Acid Comparator, or P-NAC, developed by Lopresti and Lipton . Both of these machines use a systolic array architecture to calculate the diagonal values of the dynamic programming array in parallel. Both Splash and P-NAC were prototyped successfully, although neither machine is alignment-preserving. We will compare their price and performance with the Gene Sequence Processor shortly.
3.0 The Gene Sequence Processor
The Gene Sequence Processor was designed and built at the Thayer Rapid Prototyping Facility, a laboratory dedicated to the rapid production and evaluation of digital systems. This laboratory has been involved in several successful experiments in rapid digital system design. In addition to the Gene Sequence Processor, other projects include a completely functional DLX microprocessor, an FHT transform engine, and a real-time data processor for rocket telemetry. For further information on the RPF and these projects, the reader is referred to , , and .
The GSP consists of five basic subsystems: DRAM, SRAM, a counter/comparator, the host interface, and the Gene ALU. It implements a dynamic programming algorithm to compute the minimum cost sequence of insertions, deletions, and substitutions necessary to transform one nucleotide sequence into another, based on a set of cost functions supplied by the user. The total cost of this sequence of operations is referred to as the edit distance between A and B. For more information on sequence comparison algorithms, the reader is referred to  and .
The GSP contains 8 megabytes of DRAM, organized as a 4M x 16-bit words, limiting the product of the lengths of the sequences to be compared to 222. The DRAM holds the dynamic programming array. Each byte of a DRAM word is broken into 6 bits of data and a 2 bit field called a back pointer. Back pointers are used to reconstruct the minimum cost sequence of operations necessary to transform one sequence into another. For more information on back pointers the reader is referred to .
Back pointer information was made identical in each byte to simplify the design of the processor, leaving 12 bits of data in each array entry. Thus the maximum edit distance the GSP can compute is 212 = 4096. Currently, cost function values are constrained to be integers. This has not proven to be a limiting factor in our experiments.
The sequences to be compared, cost function values, and sequence lengths are downloaded into a 4k x 8 SRAM. The counter/comparator is used to generate DRAM addresses for the dynamic programming calculation, and to halt the computation when the last entry in the dynamic programming array has been calculated (the location of the last entry varies with the size of the sequences to be compared). The processor interface is responsible for all interaction with the host.
The Gene ALU is an optimized computational element tailored to the basic operations of the comparison algorithm. The relevant cost coefficients and DP array values are added in parallel, and sent to a 3-way comparator that determines the minimum value. This value is then written back into the DRAM dynamic programming array.
The Gene ALU is bit-sliced into upper and lower bytes, with each slice implemented on a field programmable gate array, or FPGA. FPGA's have proven extremely valuable in our design; we anticipate these devices to play a major role in microsystem prototyping over the next few years. Accordingly, we discuss their use in the next section. Readers unfamiliar with FPGAs are referred to  and .
4.0 FPGA Usage in the Gene Sequence Processor
The Gene Sequence Processor uses 5 Actel FPGA's: 3 ACT1020's, 1 68-pin ACT1010, and 1 44-pin ACT1010. (Actel's antifuse-based architecture is described by El Gamal and El-Ayat in  and ). FPGA utilization in the GSP is as follows:
Gene ALU: 2 ACT1020's, used for adder (3), latches, and a 3-way comparator. 1 FPGA for each byte.
Counter/Comparator: ACT1020 (1), used for 16-bit counter (2), 16-bit comparator (2), register.
SRAM interface: ACT1010-68, SRAM selector & latch, 16-bit 2-1 mux & latch.
DRAM RAS/CAS mux: ACT1010-48, 10-bit 2-1 mux
We observed the following benefits from using FPGAs in the GSP:
1) Reduced board area. Our design was constrained at the outset to fit on two boards of fixed size. Implementing the random logic of the Gene ALU alone, using discrete components, would have exceeded these constraints.
2) Reduced chip count. The 5 FPGAs listed above replaced approximately 50 TTL components. This reduced design complexity and bringup time (see #5).
3) Reduced power consumption. The FPGAs consume substantially less power than the components they replace.
4) Increased flexibility in design partitioning. FPGAs in a design can be viewed as boxes whose contents can change as the design evolves. It was common in the design of the GSP to migrate various pieces of the design on and off FPGAs as the design changed.
5) Reduced bringup time. All our FPGAs worked correctly the 1st time they were programmed. The reliability of the devices eliminates many sources of errors during system bringup. The use of FPGAs to replace large numbers of discrete components means fewer connections, fewer nets, and easier debugging.
For a more detailed discussion of the advantages and disadvantages of using FPGAs in digital designs, the reader is referred to , , and .
5.0 Rapid PCB Prototyping Technology
The RPF is perhaps unique as an academic laboratory in that it has the capability of producing printed circuit boards on site, in the same room in which systems are designed. The RPF employs a PCB prototyping system developed by Direct Imaging Incorporated, in which a resistive ink is sprayed on copper sheets and then etched with sodium persulfate. The ink is then scrubbed off, the sheets tin plated and automatically drilled, and then assembled into a finished prototype.
The GSP consists of two boards, both made completely in-house at the RPF. No external fabrication was required. Netlists of the simulated design are input to a PCB layout program, which produces a Gerber file. This file is then input to the PCB prototyping system, running on an IBM PC. The system uses a special printer to spray ink onto a copper sheet. This sheet is then rinsed with sodium persulfate, etching the copper away where the ink does not protect it. After the etching process, the ink is scrubbed away with steel wool, and the sheets immersed in a tin solution to plate the traces.
Once the sheets are dry, they are lined up and drilled. Drilling takes place on an NC drilling machine supplied with the PCB prototyper. The drilling process is completely automatic, under control of the PC. User intervention is required only to mount new sheets and change drill bits. When the sheets are drilled, they are lined up using an optical punch and laminated. Pins are inserted into the appropriate holes, sockets are soldered onto the board, and the system is ready for IC's and testing.
The existence of in-house PCB prototyping technology makes rapid prototyping feasible for research facilities that do not have access to on-site VLSI fabrication. The turnaround time for boards becomes hours instead of weeks, a considerable improvement over using remote facilities for system development.
6.0 Performance Results
The current implementation of GSP consists of two boards that plug in to the NuBus slots of a Mac II f/x personal computer. The performance of these boards is shown in Figure 1, in which the sequence comparison time of the GSP is compared with that of the unaided host. Host execution times were measured running a C implementation of the dynamic programming algorithm. We deliberately made this program as fast as possible, to avoid biasing the results in favor of the GSP. Execution time is shown on the vertical axis, plotted against the number of nucleotides. For these measurements, both sequences are the same length.
Figure 1 shows an average performance improvement of about 15x. Note that despite the appearance of the graph, GSP performance scales quadratically. As expected, using special purpose hardware to solve a problem while leaving the algorithm unchanged improves performance by a constant factor.
The GSP board is clocked at 10 MHz, and requires 6 clock ticks = 600ns to calculate each entry in the dynamic programming array. The resulting execution times are thus very close to 600(n+1)2/109, as the time to initialize the system and retrieve the alignment using the back pointers is negligible.
The cost-performance plane for gene sequence comparison is shown in Figure 2. These numbers are taken from  and , with the points for the GSP and the unassisted Mac II added by the authors. Performance/cost ratios for the machines in Figure 2 are shown in Table 1. In both Figure 2 and Table 1, performance is taken to be the reciprocal of execution time. Note that both axes in Figure 2 are logarithmic.
Figure 1: GSP Performance
Figure 2: Cost-Performance Plane
Table 1: Performance/Cost Ratios
Machine est. Cost ($) Performance (1/sec) (Perf/Cost)*103
SPLASH 10000 5000 500
GSP 2000 100 50
P-NAC 4000 110 27.5
Mac II fx 2000 9 4.5
Sun 4 25000 17 .68
Sun 3 10000 2 .2
Convex C1 250000 11 .044
Multiflow Trace 750000 27 .036
VAX 11/785 100000 2 .020
CM-2 10000000 21 .002
Cray-2 10000000 15 .001
We see that for gene sequence comparison, the GSP has the most favorable performance/cost ratio of all machines but Splash. The performance improvement of Splash is quite significant, due its use of a systolic array architecture to exploit parallelism. It is unlikely that the GSP could achieve comparable performance without a significant increase in cost. Unlike Splash, however, the GSP is alignment-preserving, and while it appears that Splash can be modified to produce alignments , no performance results have been reported as yet. The GSP can also be programmed by a novice, using the Macintosh user interface. Finally, the GSP project was completed in a single man-year, with the actual design and debugging of the board requiring only three months. This suggests that future versions, for which more time and resources will be available, can achieve even better results.
7.0 Conclusions and Future Work
The initial goal of this project was to construct an attached processor for gene sequence analysis that would offer an order of magnitude improvement in performance over personal computers without any increase in cost. Our efforts were successful: the Gene Sequence Processor has met or exceeded design specifications. We were also able to advance our work in rapid prototyping, in particular with regard to FPGA's and PCB fabrication, using the environment of the Rapid Prototyping Facility.
We believe our emphasis on building working hardware has paid off. Results obtained from functioning machines are inherently more credible than simulation studies, and are more likely to be reproduced elsewhere. Our efforts in this area indicate that technological advances are making the production of working hardware feasible in environments where formerly simulation was all that could be attempted. We expect this trend to continue, bringing with it an increased rigor and credibility to computer architecture as an intellectual discipline.
Much remains to be done with the Gene Sequence Processor. Our next goal is to add another order of magnitude of performance to GSP without a corresponding increase in cost. We hope to achieve this in several ways. The current GSP exploits none of the parallelism inherent in dynamic programming algorithms, a significant source of performance for Splash. Future implementations of GSP will attempt to utilize more parallelism, within existing cost constraints. Other possibilities include adding an SRAM cache to exploit the highly regular memory reference pattern of the dynamic programming algorithm, using a faster clock, and incorporating pipelining into the design.
The authors gratefully acknowledge the assistance of the Whitaker Foundation, whose generosity made the construction of the GSP possible. Support for the Rapid Prototyping Facility was provided by a variety of sources, including Actel, Altera, Xilinx, Sun Microsystems, Viewlogic, National Semiconductor, and Direct Imaging Incorporated. Additional support was provided by the Thayer School of Engineering, and the National Science Foundation, award #CDA-8921062.
The first author can be reached electronically
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