Acceleration Techniques for Sparse Recovery Based Plane-wave Decomposition of a Sound Field

Plane-wave decomposition by sparse recovery is a reliable and accurate technique for plane-wave decomposition which can be used for source localization, beamforming, etc. In this work, we introduce techniques to accelerate the plane-wave decomposition by sparse recovery. The method consists of two main algorithms which are spherical Fourier transformation (SFT) and sparse recovery. Comparing the two algorithms, the sparse recovery is the most computationally intensive. We implement the SFT on an FPGA and the sparse recovery on a multithreaded computing platform. Then the multithreaded computing platform could be fully utilized for the sparse recovery. On the other hand, implementing the SFT on an FPGA helps to flexibly integrate the microphones and improve the portability of the microphone array. For implementing the SFT on an FPGA, we develop a scalable FPGA design model that enables the quick design of the SFT architecture on FPGAs. The model considers the number of microphones, the number of SFT channels and the cost of the FPGA and provides the design of a resource optimized and cost-effective FPGA architecture as the output. Then we investigate the performance of the sparse recovery algorithm executed on various multithreaded computing platforms (i.e., chip-multiprocessor, multiprocessor, GPU, manycore). Finally, we investigate the influence of modifying the dictionary size on the computational performance and the accuracy of the sparse recovery algorithms. We introduce novel sparse-recovery techniques which use non-uniform dictionaries to improve the performance of the sparse recovery on a parallel architecture

FPGA acceleration of sequence analysis tools in bioinformatics

Thesis (Ph.D.)--Boston UniversityWith advances in biotechnology and computing power, biological data are being produced at an exceptional rate. The purpose of this study is to analyze the application of FPGAs to accelerate high impact production biosequence analysis tools. Compared with other alternatives, FPGAs offer huge compute power, lower power consumption, and reasonable flexibility. BLAST has become the de facto standard in bioinformatic approximate string matching and so its acceleration is of fundamental importance. It is a complex highly-optimized system, consisting of tens of thousands of lines of code and a large number of heuristics. Our idea is to emulate the main phases of its algorithm on FPGA. Utilizing our FPGA engine, we quickly reduce the size of the database to a small fraction, and then use the original code to process the query. Using a standard FPGA-based system, we achieved 12x speedup over a highly optimized multithread reference code. Multiple Sequence Alignment (MSA)--the extension of pairwise Sequence Alignment to multiple Sequences--is critical to solve many biological problems. Previous attempts to accelerate Clustal-W, the most commonly used MSA code, have directly mapped a portion of the code to the FPGA. We use a new approach: we apply prefiltering of the kind commonly used in BLAST to perform the initial all-pairs alignments. This results in a speedup of from 8Ox to 190x over the CPU code (8 cores). The quality is comparable to the original according to a commonly used benchmark suite evaluated with respect to multiple distance metrics. The challenge in FPGA-based acceleration is finding a suitable application mapping. Unfortunately many software heuristics do not fall into this category and so other methods must be applied. One is restructuring: an entirely new algorithm is applied. Another is to analyze application utilization and develop accuracy/performance tradeoffs. Using our prefiltering approach and novel FPGA programming models we have achieved significant speedup over reference programs. We have applied approximation, seeding, and filtering to this end. The bulk of this study is to introduce the pros and cons of these acceleration models for biosequence analysis tools

Intelligent Management of Inter-Thread Synchronization Dependencies for Concurrent Programs.

Power dissipation limits and design complexity have made the microprocessor industry less successful in improving the performance of monolithic processors, even though semiconductor technology continues to scale. Consequently, chip multiprocessors (CMPs) have become a standard for all ranges of computing from cellular phones to high-performance servers. As sufficient thread level parallelism (TLP) is necessary to exploit the computational power provided by CMPs, most performance-aware programmers need to parallelize their programs. For shared memory multi-threaded programs, synchronization mechanisms such as mutexes, barriers, and condition variables, are used to enforce the threads to interact with each other in the way the programmers intended. However, employing synchronization operations in both correct and efficient way at the same time is extremely difficult, and there have been trade-offs between programmability and efficiency of using synchronizations. This thesis proposes a collection of works that increase the programmability and efficiency of concurrent programs by intelligently managing the synchronization operations. First, we focus on mutex locks and unlocks. Many concurrency bug detection tools and automated bug fixers rely on the precise identification of critical sections guarded by lock/unlock operations. We suggest a practical lock/unlock pairing mechanism that combines static analysis with dynamic instrumentation to identify critical sections in POSIX multi-threaded C/C++ programs. Second, we present Dynamic Core Boosting (DCB) to accelerate critical paths in multi-thread programs. Inter-thread dependencies through synchronizations form critical paths. These critical paths are major performance bottlenecks for concurrent programs, and they are exacerbated by workload imbalances in performance asymmetric CMPs. DCB coordinates its compiler, runtime subsystem, and architecture to mitigates such performance bottlenecks. Finally, we propose exploiting synchronization operations for better energy efficiency through dynamic power management.PhDComputer Science & EngineeringUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/108886/1/netforce_1.pd

Energy and Reliability in Future NOC Interconnected CMPS

In this dissertation, I explore energy and reliability in future NoC (Network-on-Chip) interconnected CMPs (chip multiprocessors) as they have become a first-order constraint in future CMP design. In the first part, we target the root cause of network energy consumption through techniques that reduce link and router-level switching activity. We specifically focus on memory subsystem traffic, as it comprises the bulk of NoC load in a CMP. By transmitting only the flits that contain words that we predicted would be useful using a novel spatial locality predictor, our scheme seeks to reduce network activity. We aim to further lower NoC energy consumption through microarchitectural mechanisms that inhibit datapath switching activity caused by unused words in individual flits. Using simulation-based performance studies and detailed energy models based on synthesized router designs and different link wire types, we show that (a) the pre- diction mechanism achieves very high accuracy, with an average rate of false-unused prediction of just 2.5%; (b) the combined NoC energy savings enabled by the predictor and microarchitectural support are 36% on average and up to 57% in the best case; and (c) there is no system performance penalty as a result of this technique. In the second part, we present a method for dynamic voltage/frequency scaling of networks-on-chip and last level caches in CMP designs, where the shared resources form a single voltage/frequency domain. We develop a new technique for monitoring and control and validate it by running PARSEC benchmarks through full system simulations. These techniques reduce energy-delay product by 46% compared to a state-of-the-art prior work. In the third part, we develop critical path models for HCI- and NBTI-induced wear assuming stress caused under realistic workload conditions, and apply them onto the interconnect microarchitecture. A key finding from this modeling is that, counter to prevailing wisdom, wearout in the CMP on-chip interconnect is correlated with a lack of load observed in the NoC routers, rather than high load. We then develop a novel wearout-decelerating scheme in which routers under low load have their wearout-sensitive components exercised without significantly impacting the router’s cycle time, pipeline depth, and area or power consumption. We subsequently show that the proposed design yields a 13.8∼65× increase in CMP lifetime

On the design of architecture-aware algorithms for emerging applications

This dissertation maps various kernels and applications to a spectrum of programming models and architectures and also presents architecture-aware algorithms for different systems. The kernels and applications discussed in this dissertation have widely varying computational characteristics. For example, we consider both dense numerical computations and sparse graph algorithms. This dissertation also covers emerging applications from image processing, complex network analysis, and computational biology. We map these problems to diverse multicore processors and manycore accelerators. We also use new programming models (such as Transactional Memory, MapReduce, and Intel TBB) to address the performance and productivity challenges in the problems. Our experiences highlight the importance of mapping applications to appropriate programming models and architectures. We also find several limitations of current system software and architectures and directions to improve those. The discussion focuses on system software and architectural support for nested irregular parallelism, Transactional Memory, and hybrid data transfer mechanisms. We believe that the complexity of parallel programming can be significantly reduced via collaborative efforts among researchers and practitioners from different domains. This dissertation participates in the efforts by providing benchmarks and suggestions to improve system software and architectures.Ph.D.Committee Chair: Bader, David; Committee Member: Hong, Bo; Committee Member: Riley, George; Committee Member: Vuduc, Richard; Committee Member: Wills, Scot

Doctor of Philosophy

dissertationWith the explosion of chip transistor counts, the semiconductor industry has struggled with ways to continue scaling computing performance in line with historical trends. In recent years, the de facto solution to utilize excess transistors has been to increase the size of the on-chip data cache, allowing fast access to an increased portion of main memory. These large caches allowed the continued scaling of single thread performance, which had not yet reached the limit of instruction level parallelism (ILP). As we approach the potential limits of parallelism within a single threaded application, new approaches such as chip multiprocessors (CMP) have become popular for scaling performance utilizing thread level parallelism (TLP). This dissertation identifies the operating system as a ubiquitous area where single threaded performance and multithreaded performance have often been ignored by computer architects. We propose that novel hardware and OS co-design has the potential to significantly improve current chip multiprocessor designs, enabling increased performance and improved power efficiency. We show that the operating system contributes a nontrivial overhead to even the most computationally intense workloads and that this OS contribution grows to a significant fraction of total instructions when executing several common applications found in the datacenter. We demonstrate that architectural improvements have had little to no effect on the performance of the OS over the last 15 years, leaving ample room for improvements. We specifically consider three potential solutions to improve OS execution on modern processors. First, we consider the potential of a separate operating system processor (OSP) operating concurrently with general purpose processors (GPP) in a chip multiprocessor organization, with several specialized structures acting as efficient conduits between these processors. Second, we consider the potential of segregating existing caching structures to decrease cache interference between the OS and application. Third, we propose that there are components within the OS itself that should be refactored to be both multithreaded and cache topology aware, which in turn, improves the performance and scalability of many-threaded applications