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With the advent of several accurate and sophisticated statistical algorithms and pipelines for DNA sequence analysis, it is becoming increasingly possible to translate raw sequencing data into biologically meaningful information for further clinical analysis and processing. However, given the large volume of the data involved, even modestly complex algorithms would require a prohibitively long time to complete. Hence it is urgent to explore non-conventional implementation platforms to accelerate genomics research.In this thesis, we present a Field-Programmable Gate Array (FPGA) accelerated implementation of the Pair Hidden Markov Model (Pair HMM) forward algorithm, the performance bottleneck in the HaplotypeCaller, a critical function in the popular Genome Analysis Toolkit (GATK) variant calling tool. We introduce the PE ring structure which, thanks to the finegrained parallelism allowed by the FPGA, can be built into various configurations striking a trade-off between Instruction-Level Parallelism (ILP) and data parallelism. We investigate the resource utilization and performance of different configurations. Our solution can achieve a speed-up of up to 487× compared to the C++ baseline implementation on CPU and 1.56× compared to the previous best hardware implementation.ii To my parents, for their love and support.iii ACKNOWLEDGMENTS

High level synthesis (HLS) is an important enabling technology for the adoption of hardware accelerator technologies. It promises the performance and energy efficiency of hardware designs with a lower barrier to entry in design expertise, and shorter design time. State-of-the-art high level synthesis now includes a wide variety of powerful optimizations that implement efficient hardware. These optimizations can implement some of the most important features generally performed in manual designs including parallel hardware units, pipelining of execution both within a hardware unit and between units, and fine-grained data communication. We may generally classify the optimizations as those that optimize hardware implementation within a code block (intra-block) and those that optimize communication and pipelining between code blocks (interblock). However, both optimizations are in practice difficult to apply. Real-world applications contain data-dependent blocks of code and communicate through complex data access patterns. Existing high level synthesis tools cannot apply these powerful optimizations unless the code is inherently compatible, severely limiting the optimization opportunity.In this paper we present an integrated framework to model and enable both intra-and inter-block optimizations. This integrated technique substantially improves the opportunity to use the powerful HLS optimizations that implement parallelism, pipelining, and fine-grained communication. Our polyhedral model-based technique systematically defines a set of data access patterns, identifies effective data access patterns, and performs the loop transformations to enable the intra-and inter-block optimizations. Our framework automatically explores transformation options, performs code transformations, and inserts the appropriate HLS directives to implement the HLS optimizations. Furthermore, our framework can automatically generate the optimized communication blocks for fine-grained communication between hardware blocks. Experimen- * Corresponding Author Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. To copy otherwise, to republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. FPGA '13, February 11-13, 2013, Monterey, California, USA. Copyright 2013 ACM 978-1-4503-1887 tal evaluation demonstrates that we can achieve an average of 6.04X speedup over the high level synthesis solution without our transformations to enable intra-and inter-block optimizations.

FPGAs are an attractive platform for applications with high computation demand and low energy consumption requirements. However, design effort for FPGA implementations remains high—often an order of magnitude larger than design effort using high-level languages. Instead of this time-consuming process, high-level synthesis (HLS) tools generate hardware implementations from algorithm descriptions in languages such as C/C++ and SystemC. Such tools reduce design effort: high-level descriptions are more compact and less error prone. HLS tools promise hardware development abstracted from software designer knowledge of the implementation platform. In this paper, we present an unbiased study of the performance, usability and productivity of HLS using AutoPilot (a state-of-the-art HLS tool). In particular, we first evaluate AutoPilot using the popular embedded benchmark kernels. Then, to evaluate the suitability of HLS on real-world applications, we perform a case study of stereo matching, an active area of computer vision research that uses techniques also common for image denoising, image retrieval, feature matching, and face recognition. Based on our study, we provide insights on current limitations of mapping general-purpose software to hardware using HLS and some future directions for HLS tool development. We also offer several guidelines for hardware-friendly software design. For popular embedded benchmark kernels, the designs produced by HLS achieve 4X to 126X speedup over the software version. The stereo matching algorithms achieve between 3.5X and 67.9X speedup over software (but still less than manual RTL design) with a fivefold reduction in design effort versus manual RTL design.

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