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SC Conference - Activity Details
HPC Fellowship: Automatic Parallelization of Dynamic Programming Recurrences in Computational Biology
Presenter:
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Arpith Chacko Jacob
(Washington University in St. Louis)
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Doctoral Research Showcase Session
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Wednesday, 04:30PM - 05:00PM
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Room 17A/17B
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Abstract:
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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