Media Processing Applications on the Imagine Stream Processor
ICCD '02 Proceedings of the 2002 IEEE International Conference on Computer Design: VLSI in Computers and Processors (ICCD'02)
Brook for GPUs: stream computing on graphics hardware
ACM SIGGRAPH 2004 Papers
The UCSC Kestrel Parallel Processor
IEEE Transactions on Parallel and Distributed Systems
Multiple Sequence Alignment on an FPGA
ICPADS '05 Proceedings of the 11th International Conference on Parallel and Distributed Systems - Workshops - Volume 02
Heterogeneous Chip Multiprocessors
Computer
Single Pass, BLAST-Like, Approximate String Matching on FPGAs
FCCM '06 Proceedings of the 14th Annual IEEE Symposium on Field-Programmable Custom Computing Machines
ParTriCluster: A Scalable Parallel Algorithm for Gene Expression Analysis
SBAC-PAD '06 Proceedings of the 18th International Symposium on Computer Architecture and High Performance Computing
Conjoining soft-core FPGA processors
Proceedings of the 2006 IEEE/ACM international conference on Computer-aided design
Streaming Algorithms for Biological Sequence Alignment on GPUs
IEEE Transactions on Parallel and Distributed Systems
Hardware acceleration for thermodynamic constrained DNA code generation
DNA13'07 Proceedings of the 13th international conference on DNA computing
A multi-threaded DNA tag/anti-tag library generator for multi-core platforms
CIBCB'09 Proceedings of the 6th Annual IEEE conference on Computational Intelligence in Bioinformatics and Computational Biology
Reconfigurable multiprocessor systems: a review
International Journal of Reconfigurable Computing - Special issue on selected papers from ReconFig 2009 International conference on reconfigurable computing and FPGAs (ReconFig 2009)
Hi-index | 0.00 |
Bioinformatics applications such as gene and protein sequence matching algorithms are characterized by the need to process large amounts of data. While uni-processor performance growth is slowing due to an increasing gap between processor and memory speeds and a saturation of processor clock frequencies, Genbank data is doubling every 15 months. With the advent of chip multiprocessor systems, great improvements in processor performance could potentially be achieved by taking advantage of the high interprocessor communication bandwidth and new models of programming. We propose a stream chip multiprocessor micro- architecture customized for bioinformatics applications that takes advantage of the memory bandwidth available in chip multiprocessors by exploiting the data parallelism available in bioinformatics applications. The proposed stream chip multiprocessor micro architecture, on a Xilinx Virtex-5 FPGA with 60 customized MicroBlaze soft processor cores running at 80 MHz with a PCI- bus limited main memory bandwidth of 0.12 GB/s, would achieve a speed-up of 68% for the Smith-Waterman sequence matching algorithm compared to a 2.4 GHz AMD Opteron 250. An extrapolated 60 long stream CMP running at 1 GHz with a memory access rate of 2.7 GB/s would run 41.7 times faster than the 1.2 GHz Sun Niagara processor, 16.5 times faster than the 2.4 GHz AMD Opteron 250 and 12.3 times faster than the 2.4 GHz Intel Xeon processor.