-Design verification via simulation is an important component in the development of digital systems. However, with continuing increases in the capabilities of VLSI systems, the simulation task has become a significant bottleneck in the design process. As a result, researchers are attempting to exploit parallel processing techniques to improve the performance of VLSI logic simulation. This tutorial describes the current state-of-the-art in parallel logic simulation, including parallel simulation techniques, factors that impact simulation performance, performance results to date, and the directions currently being pursued by the research community.

No abstract

No abstract

Biosequence similarity search is an important application in modern molecular biology. Search algorithms aim to identify sets of sequences whose extensional similarity suggests a common evolutionary origin or function. The most widely used similarity search tool for biosequences is BLAST, a program designed to compare query sequences to a database. Here, we present the design of BLASTN, the version of BLAST that searches DNA sequences, on the Mercury system, an architecture that supports high-volume, high-throughput data movement off a data store and into reconfigurable hardware. An important component of application deployment on the Mercury system is the functional decomposition of the application onto both the reconfigurable hardware and the traditional processor. Both the Mercury BLASTN application design and its performance analysis are described. 1: IntroductionComputational search through large databases of DNA and protein sequence is a fundamental tool of modern molecular biology. Rapid advances in the speed and cost-effectiveness of DNA sequencing have led to an explosion in the rate at which new sequences, including entire mammalian genomes [35], are being generated. To understand the function and evolutionary history of an organism, biologists now seek to identify discrete biologically meaningful features in its genome sequence. A powerful approach to identify such features is comparative annotation, in which a query sequence, such as new genome, is compared to a large database of known biosequences. Database sequences exhibiting high similarity to the query, as measured by string edit distance [31], are hypothesized to derive from the same ancestral sequence as the query and in many cases to have the same biological function.BLAST, the Basic Local Alignment Search Tool [1], is the most widely used software for rapidly comparing a query sequence to a biosequence database. Although BLAST's algorithms are highly optimized for efficient similarity search, growth in the databases it uses is outpacing speed improvements in general-purpose computing hardware. For example, the National Center for Biological Information (NCBI) Genbank database grew exponentially between 1992 and 2003 with a doubling time of 12-16 months [24]. The problem is particularly acute for BLASTN, the BLAST variant used to compare DNA sequences, because each new genome sequenced from animals or higher plants produces between 10 8 and 10 10 bytes of new DNA sequence.One response to runaway growth in biosequence databases has been to distribute BLAST searches across multiple computers, each responsible for searching only part of a database. This approach requires both a substantial hardware investment and the ability to coordinate a {praveenk, jbuhler, roger, jbf, kg2, jarpith, jmlancas}@cse.wustl.edu. NIH-PA Author ManuscriptNIH-PA Author Manuscript NIH-PA Author Manuscript search across processors. An alternate approach that makes more parsimonious use of hardware is to build a specialized BLAST accelerator. By using an applic...

We present the initial results from the FHPCA Supercomputer project at the University of Edinburgh. The project has successfully built a general-purpose 64 FPGA computer and ported to it three demonstration applications from the oil, medical and finance sectors. This paper describes in brief the machine itselfMaxwell -its hardware and software environment and presents very early benchmark results from runs of the demonstrators.