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Heterogeneous systems consisting of general-purpose processors and different types of hardware accelerators are becoming more and more common in HPC systems. Especially Field Programmable Gate Arrays (FPGAs) provide an energy-efficient way to achieve high performance. Numerous application areas, including bio- and neuroinformatics, require enormous processing capability and employ simple computation...
Heterogeneous systems consisting of general-purpose processors and different types of hardware accelerators are becoming more and more common in HPC systems. Especially Field Programmable Gate Arrays (FPGAs) provide an energy-efficient way to achieve high performance. Numerous application areas, including bio- and neuroinformatics, require enormous processing capabilities and employ simple computation...
Field-Programmable Gate Arrays, which are widely used as prototyping platforms, are intruding the domain of custom-specific high-performance hardware accelerators, which operate highly efficiently by exploiting bit- and word-level parallelism. One opportunity to feed these FPGA accelerators with Gbytes of data is the direct attachment of mass-storage devices through a Serial-ATA link. State-of-the-art...
The mapping of reads, i.e. short DNA base pair strings, to large genome databases has become a critical operation for genetic analysis and diagnosis. Although this mapping operation is a simple string search tolerant of some character mismatches, it is yet extremely challenging due to the tremendous size of the searched genome databases. It is the heavy use of search heuristics such as BLAST, Maq...
The mapping of DNA sequences to huge genome databases is an essential analysis task in modern molecular biology. Having linearized reference genomes available, the alignment of short DNA reads obtained from the sequencing of an individual genome against such a database provides a powerful diagnostic and analysis tool. In essence, this task amounts to a simple string search tolerating a certain number...
This work describes the carry-compact addition (CCA), a novel addition scheme that allows the acceleration of carry-chain computations on contemporary FPGA devices. While based on concepts known from the carry-look ahead addition and from parallel prefix adders, their adaptation by the CCA takes the context of an FPGA as implementation environment into account. These typically provide carry-chain...
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