SC Conference - Activity Details

HPC Fellowship: Automatic Parallelization of Dynamic Programming Recurrences in Computational Biology

Arpith Chacko Jacob  (Washington University in St. Louis)
Doctoral Research Showcase Session
Wednesday,  04:30PM - 05:00PM
Room 17A/17B
The rapid growth of sequence databases over the last decade has lead to a performance bottleneck in the applications analyzing them. Special-purpose hardware is becoming increasingly popular to accelerate algorithms in computational biology, realizing significant speedup. Unfortunately, a major impediment has been the high development cost as compared to a general-purpose processor. The goal of our research is to provide high level abstractions and tools for the automated synthesis of FPGA accelerators. We focus on dynamic programming recurrences which encompass a large set of problems in computational biology. We describe a high-level domain specific language and report on our efforts to automatically synthesize parallel arrays from this description given certain resource constraints. We also describe the process of partitioning an oversized input to perform the computation in small chunks that can be placed on limited logic resources available on an FPGA device.
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