Acceleration of a bioinformatics application using high-level synthesis

• Main Author: Abbas, Naeem
• Language: ENG
• Published: École normale supérieure de Cachan - ENS Cachan 2012
• Subjects: [INFO:INFO_OH] Computer Science/Other; [INFO:INFO_OH] Informatique/Autre; Bioinformatics; FPGA; Hardware acceleration; High level synthesis
• Online Access: http://tel.archives-ouvertes.fr/tel-00847076; http://tel.archives-ouvertes.fr/docs/00/84/70/76/PDF/Abbas2012.pdf

The revolutionary advancements in the field of bioinformatics have opened new horizons in biological and pharmaceutical research. However, the existing bioinformatics tools are unable to meet the computational demands, due to the recent exponential growth in biological data. So there is a dire need to build future bioinformatics platforms incorporating modern parallel computation techniques. In this work, we investigate FPGA based acceleration of these applications, using High-Level Synthesis. High-Level Synthesis tools enable automatic translation of abstract specifications to the hardware design, considerably reducing the design efforts. However, the generation of an efficient hardware using these tools is often a challenge for the designers. Our research effort encompasses an exploration of the techniques and practices, that can lead to the generation of an efficient design from these high-level synthesis tools. We illustrate our methodology by accelerating a widely used application -- HMMER -- in bioinformatics community. HMMER is well-known for its compute-intensive kernels and data dependencies that lead to a sequential execution. We propose an original parallelization scheme based on rewriting of its mathematical formulation, followed by an in-depth exploration of hardware mapping techniques of these kernels, and finally show on-board acceleration results. Our research work demonstrates designing flexible hardware accelerators for bioinformatics applications, using design methodologies which are more efficient than the traditional ones, and where resulting designs are scalable enough to meet the future requirements.