Amdahl's law for predicting the future of multicores considered harmful

Several recent works predict the future of multicore systems or identify scalability bottlenecks based on Amdahl's law. Amdahl's law implicitly assumes, however, that the problem size stays constant, but in most cases more cores are used to solve larger and more complex problems. There is a related law known as Gustafson's law which assumes that runtime, not the problem size, is constant. In other words, it is assumed that the runtime on p cores is the same as the runtime on 1 core and that the parallel part of an application scales linearly with the number of cores. We apply Gustafson's law to symmetric, asymmetric, and dynamic multicores and show that this leads to fundamentally different results than when Amdahl's law is applied. We also generalize Amdahl's and Gustafson's law and study how this quantitatively effects the dimensioning of future multicore systems

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

Memory-Aware Scheduling for Fixed Priority Hard Real-Time Computing Systems

As a major component of a computing system, memory has been a key performance and power consumption bottleneck in computer system design. While processor speeds have been kept rising dramatically, the overall computing performance improvement of the entire system is limited by how fast the memory can feed instructions/data to processing units (i.e. so-called memory wall problem). The increasing transistor density and surging access demands from a rapidly growing number of processing cores also significantly elevated the power consumption of the memory system. In addition, the interference of memory access from different applications and processing cores significantly degrade the computation predictability, which is essential to ensure timing specifications in real-time system design. The recent IC technologies (such as 3D-IC technology) and emerging data-intensive real-time applications (such as Virtual Reality/Augmented Reality, Artificial Intelligence, Internet of Things) further amplify these challenges. We believe that it is not simply desirable but necessary to adopt a joint CPU/Memory resource management framework to deal with these grave challenges. In this dissertation, we focus on studying how to schedule fixed-priority hard real-time tasks with memory impacts taken into considerations. We target on the fixed-priority real-time scheduling scheme since this is one of the most commonly used strategies for practical real-time applications. Specifically, we first develop an approach that takes into consideration not only the execution time variations with cache allocations but also the task period relationship, showing a significant improvement in the feasibility of the system. We further study the problem of how to guarantee timing constraints for hard real-time systems under CPU and memory thermal constraints. We first study the problem under an architecture model with a single core and its main memory individually packaged. We develop a thermal model that can capture the thermal interaction between the processor and memory, and incorporate the periodic resource sever model into our scheduling framework to guarantee both the timing and thermal constraints. We further extend our research to the multi-core architectures with processing cores and memory devices integrated into a single 3D platform. To our best knowledge, this is the first research that can guarantee hard deadline constraints for real-time tasks under temperature constraints for both processing cores and memory devices. Extensive simulation results demonstrate that our proposed scheduling can improve significantly the feasibility of hard real-time systems under thermal constraints

Proceedings, MSVSCC 2018

Proceedings of the 12th Annual Modeling, Simulation & Visualization Student Capstone Conference held on April 19, 2018 at VMASC in Suffolk, Virginia. 155 pp

Compiler techniques for scalable performance of stream programs on multicore architectures

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2010.Cataloged from PDF version of thesis.Includes bibliographical references (p. 211-222).Given the ubiquity of multicore processors, there is an acute need to enable the development of scalable parallel applications without unduly burdening programmers. Currently, programmers are asked not only to explicitly expose parallelism but also concern themselves with issues of granularity, load-balancing, synchronization, and communication. This thesis demonstrates that when algorithmic parallelism is expressed in the form of a stream program, a compiler can effectively and automatically manage the parallelism. Our compiler assumes responsibility for low-level architectural details, transforming implicit algorithmic parallelism into a mapping that achieves scalable parallel performance for a given multicore target. Stream programming is characterized by regular processing of sequences of data, and it is a natural expression of algorithms in the areas of audio, video, digital signal processing, networking, and encryption. Streaming computation is represented as a graph of independent computation nodes that communicate explicitly over data channels. Our techniques operate on contiguous regions of the stream graph where the input and output rates of the nodes are statically determinable. Within a static region, the compiler first automatically adjusts the granularity and then exploits data, task, and pipeline parallelism in a holistic fashion. We introduce techniques that data-parallelize nodes that operate on overlapping sliding windows of their input, translating serializing state into minimal and parametrized inter-core communication. Finally, for nodes that cannot be data-parallelized due to state, we are the first to automatically apply software-pipelining techniques at a coarse granularity to exploit pipeline parallelism between stateful nodes. Our framework is evaluated in the context of the StreamIt programming language. StreamIt is a high-level stream programming language that has been shown to improve programmer productivity in implementing streaming algorithms. We employ the StreamIt Core benchmark suite of 12 real-world applications to demonstrate the effectiveness of our techniques for varying multicore architectures. For a 16-core distributed memory multicore, we achieve a 14.9x mean speedup. For benchmarks that include sliding-window computation, our sliding-window data-parallelization techniques are required to enable scalable performance for a 16-core SMP multicore (14x mean speedup) and a 64-core distributed shared memory multicore (52x mean speedup).by Michael I. Gordon.Ph.D