match the structure of the computation, and an 

 FPGA-based computer can achieve supercom- 

 puter performance on a range of applications at a 

 fraction of the cost. Importantly, the reconfigu- 

 ration of the processor structure is done not by 

 designing new computer hardware but by pro- 

 gramming the FPGA-based computer in a stan- 

 dard high-level language. 



The Splash 1 and Splash 2 attached processor 

 systems, which were designed and built at the 

 Supercomputing Research Center (SRC) using 

 FPGAs from Xilinx. Inc.. are just this kind of 

 FPGA-based reconfigurable computer. Together 

 with the National Cancer Institute, the SRC is 

 writing software that will perform DNA and pro- 

 tein sequence comparisons and alignment on 

 existing databases at speeds equal to or greater 

 than those of supercomputers. Applications for 

 Splash 2 are written in VHDL (the DOD stan- 

 dard Very High Speed Integrated Circuit 

 Hardware Description Language). On applica- 

 tions running on Splash 2, performance equal to 

 or as much as 100 times that of some conven- 

 tional supercomputers has been achieved. 



replaced by Xilinx FPGAs. which can be pro- 

 grammed with the usual CM-2 languages and 

 utilities. It is common on multiprocessor 

 machines to find such floating point accelera- 

 tors; the use of FPGAs in their place allows 

 computationally intensive kernels of an applica- 

 tion to be executed on FPGA-based hardware 

 specifically configured for the application. On 

 complete applications programmed at the SRC, 

 the CM-2X has achieved three to four times the 

 performance of the CM-2. 



Similar approaches are being evaluated for other 

 architectures. For example, the CM-5, also built 

 by Thinking Machines, Inc., has from 32 to 

 1.024 network-connected nodes each consisting 

 of a high performance microprocessor and four 

 custom designed vector processors. Embedding 

 FPGAs into its nodes and network offers the 

 potential for producing dramatic improvement 

 on specific applications and, by altering the 

 FPGA programming, observation of internal sys- 

 tem states to assist in program tuning and debug- 

 ging. 



The CM-2X. built by Thinking Machines, Inc., 

 for the SRC. is a CM-2 in which the Weitek 

 floating point accelerator chips have been 



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