Abstract
As FPGA devices become larger, more coarse-grain modules coupled with large scale reconfigurable fabric become available, thus enabling new classes of applications to run efficiently, as compared to a general-purpose computer. This paper presents an architecture that benefits from the large number of DSP modules in Xilinx technology to implement massive floating point arithmetic. Our architecture computes the Phylogenetic Likelihood Function (PLF) which accounts for approximately 95% of total execution time in all state-of-the-art Maximum Likelihood (ML) based programs for reconstruction of evolutionary relationships. We validate and assess performance of our architecture against a highly optimized and parallelized software implementation of the PLF that is based on RAxML, which is considered to be one of the fastest and most accurate programs for phylogenetic inference. Both software and hardware implementations use double precision floating point arithmetic. The new architecture achieves speedups ranging from 1.6 up to 7.2 compared to a high-end 8-way dual-core general-purpose computer running the aforementioned highly optimized OpenMP-based multi-threaded version of the PLF.
Original language | English |
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Title of host publication | 2009 International Conference on Field Programmable Logic and Applications, FPL 2009 |
Place of Publication | Piscataway, NJ |
Publisher | IEEE |
Pages | 674-678 |
Number of pages | 5 |
ISBN (Electronic) | 978-1-4244-3892-1 |
DOIs | |
Publication status | Published - 2009 |
Externally published | Yes |
Event | 19th International Conference on Field Programmable Logic and Applications, FPL 2009 - Prague, Czech Republic Duration: 31 Aug 2009 → 2 Sept 2009 Conference number: 19 |
Publication series
Name | International Conference on Field Programmable Logic and Applications (FPL) |
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Publisher | IEEE |
Volume | 2009 |
ISSN (Print) | 1946-147X |
ISSN (Electronic) | 1946-1488 |
Conference
Conference | 19th International Conference on Field Programmable Logic and Applications, FPL 2009 |
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Abbreviated title | FPL |
Country/Territory | Czech Republic |
City | Prague |
Period | 31/08/09 → 2/09/09 |