Parallelization of dynamic programming recurrences in computational biology

The rapid growth of biosequence databases over the last decade has led to a performance bottleneck in the applications analyzing them. In particular, over the last five years DNA sequencing capacity of next-generation sequencers has been doubling every six months as costs have plummeted. The data produced by these sequencers is overwhelming traditional compute systems. We believe that in the future compute performance, not sequencing, will become the bottleneck in advancing genome science. In this work, we investigate novel computing platforms to accelerate dynamic programming algorithms, which are popular in bioinformatics workloads. We study algorithm-specific hardware architectures that exploit fine-grained parallelism in dynamic programming kernels using field-programmable gate arrays: FPGAs). We advocate a high-level synthesis approach, using the recurrence equation abstraction to represent dynamic programming and polyhedral analysis to exploit parallelism. We suggest a novel technique within the polyhedral model to optimize for throughput by pipelining independent computations on an array. This design technique improves on the state of the art, which builds latency-optimal arrays. We also suggest a method to dynamically switch between a family of designs using FPGA reconfiguration to achieve a significant performance boost. We have used polyhedral methods to parallelize the Nussinov RNA folding algorithm to build a family of accelerators that can trade resources for parallelism and are between 15-130x faster than a modern dual core CPU implementation. A Zuker RNA folding accelerator we built on a single workstation with four Xilinx Virtex 4 FPGAs outperforms 198 3 GHz Intel Core 2 Duo processors. Furthermore, our design running on a single FPGA is an order of magnitude faster than competing implementations on similar-generation FPGAs and graphics processors. Our work is a step toward the goal of automated synthesis of hardware accelerators for dynamic programming algorithms

A functional approach to heterogeneous computing in embedded systems

Developing programs for embedded systems presents quite a challenge; not only should programs be resource efficient, as they operate under memory and timing constraints, but they should also take full advantage of the hardware to achieve maximum performance. Since performance is such a significant factor in the design of embedded systems, modern systems typically incorporate more than one kind of processing element to benefit from specialized processing capabilities. For such heterogeneous systems the challenge in developing programs is even greater.In this thesis we explore a functional approach to heterogeneous system development as a means to address many of the modularity problems that are typically found in the application of low-level imperative programming for embedded systems. In particular, we explore a staged hardware software co-design language that we name Co-Feldspar and embed in Haskell. The staged approach enables designers to build their applications from reusable components and skeletons while retaining control over much of the generated source code. Furthermore, by embedding the language in Haskell we can exploit its type classes to write not only hardware and software programs, but also generic programs with overloaded instructions and expressions. We demonstrate the usefulness of the functional approach for co-design on a cryptographic example and signal processing filters, and benchmark software and mixed hardware-software implementations. Co-Feldspar currently adopts a monadic interface, which provides an imperative functional programming style that is suitable for explicit memory management and algorithms that rely on a certain evaluation order. For algorithms that are better defined as pure functions operating on immutable values, we provide a signal and array library that extends a monadic language, like Co-Feldspar. These extensions permit a functional style of programming by composing high-level combinators. Our compiler transforms such high-level code into efficient programs with mutating code. In particular, we show how to execute an FFT safely in-place, and how to describe a FIR and IIR filter efficiently as streams. Co-Feldspar’s monadic interface is however quite invasive; not only is the burden of explicit memory management quite heavy on the user, it is also quite easy to shoot on eself in the foot. It is for these reasons that we also explore a dynamic memory management discipline that is based on regions but predictable enough to be of use for embedded systems. Specifically, this thesis introduces a program analysis which annotates values with dynamically allocated memory regions. By limiting our efforts to functional languages that target embedded software, we manage to define a region inference algorithm that is considerably simpler than traditional approaches

SEER: Super-Optimization Explorer for HLS using E-graph Rewriting with MLIR

High-level synthesis (HLS) is a process that automatically translates a software program in a high-level language into a low-level hardware description. However, the hardware designs produced by HLS tools still suffer from a significant performance gap compared to manual implementations. This is because the input HLS programs must still be written using hardware design principles. Existing techniques either leave the program source unchanged or perform a fixed sequence of source transformation passes, potentially missing opportunities to find the optimal design. We propose a super-optimization approach for HLS that automatically rewrites an arbitrary software program into efficient HLS code that can be used to generate an optimized hardware design. We developed a toolflow named SEER, based on the e-graph data structure, to efficiently explore equivalent implementations of a program at scale. SEER provides an extensible framework, orchestrating existing software compiler passes and hardware synthesis optimizers. Our work is the first attempt to exploit e-graph rewriting for large software compiler frameworks, such as MLIR. Across a set of open-source benchmarks, we show that SEER achieves up to 38x the performance within 1.4x the area of the original program. Via an Intel-provided case study, SEER demonstrates the potential to outperform manually optimized designs produced by hardware experts

Analytical cost metrics: days of future past

2019 Summer.Includes bibliographical references.Future exascale high-performance computing (HPC) systems are expected to be increasingly heterogeneous, consisting of several multi-core CPUs and a large number of accelerators, special-purpose hardware that will increase the computing power of the system in a very energy-efficient way. Specialized, energy-efficient accelerators are also an important component in many diverse systems beyond HPC: gaming machines, general purpose workstations, tablets, phones and other media devices. With Moore's law driving the evolution of hardware platforms towards exascale, the dominant performance metric (time efficiency) has now expanded to also incorporate power/energy efficiency. This work builds analytical cost models for cost metrics such as time, energy, memory access, and silicon area. These models are used to predict the performance of applications, for performance tuning, and chip design. The idea is to work with domain specific accelerators where analytical cost models can be accurately used for performance optimization. The performance optimization problems are formulated as mathematical optimization problems. This work explores the analytical cost modeling and mathematical optimization approach in a few ways. For stencil applications and GPU architectures, the analytical cost models are developed for execution time as well as energy. The models are used for performance tuning over existing architectures, and are coupled with silicon area models of GPU architectures to generate highly efficient architecture configurations. For matrix chain products, analytical closed form solutions for off-chip data movement are built and used to minimize the total data movement cost of a minimum op count tree

GPU Accelerated Approach to Numerical Linear Algebra and Matrix Analysis with CFD Applications

A GPU accelerated approach to numerical linear algebra and matrix analysis with CFD applications is presented. The works objectives are to (1) develop stable and efficient algorithms utilizing multiple NVIDIA GPUs with CUDA to accelerate common matrix computations, (2) optimize these algorithms through CPU/GPU memory allocation, GPU kernel development, CPU/GPU communication, data transfer and bandwidth control to (3) develop parallel CFD applications for Navier Stokes and Lattice Boltzmann analysis methods. Special consideration will be given to performing the linear algebra algorithms under certain matrix types (banded, dense, diagonal, sparse, symmetric and triangular). Benchmarks are performed for all analyses with baseline CPU times being determined to find speed-up factors and measure computational capability of the GPU accelerated algorithms. The GPU implemented algorithms used in this work along with the optimization techniques performed are measured against preexisting work and test matrices available in the NIST Matrix Market. CFD analysis looked to strengthen the assessment of this work by providing a direct engineering application to analysis that would benefit from matrix optimization techniques and accelerated algorithms. Overall, this work desired to develop optimization for selected linear algebra and matrix computations performed with modern GPU architectures and CUDA developer which were applied directly to mathematical and engineering applications through CFD analysis

Accelerating Halide on an FPGA by using CIRCT and Calyx as an intermediate step to go from a high-level and software-centric IRs down to RTL

Image processing and, more generally, array processing play an essential role in modern life: from applying filters to the images that we upload to social media to running object detection algorithms on self-driving cars. Optimizing these algorithms can be complex and often results in non-portable code. The Halide language provides a simple way to write image and array processing algorithms by separating the algorithm definition (what needs to be executed) from its execution schedule (how it is executed), delivering state-of-the-art performance that exceeds hand-tuned parallel and vectorized code. Due to the inherent parallel nature of these algorithms, FPGAs present an attractive acceleration platform. While previous work has added an RTL code generator to Halide, and utilized other heterogeneous computing languages as an intermediate step, these projects are no longer maintained. MLIR is an attractive solution, allowing the generation of code that can target multiple devices, such as parallelized and vectorized CPU code, OpenMP, and CUDA. CIRCT builds on top of MLIR to convert generic MLIR code to register transfer level (RTL) languages by using Calyx, a new intermediate language (IL) for compiling high-level programs into hardware designs. This thesis presents a novel flow that implements an MLIR code generator for Halide that generates RTL code, adding the necessary wrappers to execute that code on Xilinx FPGA devices. Additionally, it implements a Halide runtime using the Xilinx Runtime (XRT), enabling seamless execution of the generated Halide RTL kernels. While this thesis provides initial support for running Halide kernels and not all features and optimizations are supported, it also details the future work needed to improve the performance of the generated RTL kernels. The proposed flow serves as a foundation for further research and development in the field of hardware acceleration for image and array processing applications using Halide