Solving hard subgraph problems in parallel

This thesis improves the state of the art in exact, practical algorithms for finding subgraphs. We study maximum clique, subgraph isomorphism, and maximum common subgraph problems. These are widely applicable: within computing science, subgraph problems arise in document clustering, computer vision, the design of communication protocols, model checking, compiler code generation, malware detection, cryptography, and robotics; beyond, applications occur in biochemistry, electrical engineering, mathematics, law enforcement, fraud detection, fault diagnosis, manufacturing, and sociology. We therefore consider both the ``pure'' forms of these problems, and variants with labels and other domain-specific constraints. Although subgraph-finding should theoretically be hard, the constraint-based search algorithms we discuss can easily solve real-world instances involving graphs with thousands of vertices, and millions of edges. We therefore ask: is it possible to generate ``really hard'' instances for these problems, and if so, what can we learn? By extending research into combinatorial phase transition phenomena, we develop a better understanding of branching heuristics, as well as highlighting a serious flaw in the design of graph database systems. This thesis also demonstrates how to exploit two of the kinds of parallelism offered by current computer hardware. Bit parallelism allows us to carry out operations on whole sets of vertices in a single instruction---this is largely routine. Thread parallelism, to make use of the multiple cores offered by all modern processors, is more complex. We suggest three desirable performance characteristics that we would like when introducing thread parallelism: lack of risk (parallel cannot be exponentially slower than sequential), scalability (adding more processing cores cannot make runtimes worse), and reproducibility (the same instance on the same hardware will take roughly the same time every time it is run). We then detail the difficulties in guaranteeing these characteristics when using modern algorithmic techniques. Besides ensuring that parallelism cannot make things worse, we also increase the likelihood of it making things better. We compare randomised work stealing to new tailored strategies, and perform experiments to identify the factors contributing to good speedups. We show that whilst load balancing is difficult, the primary factor influencing the results is the interaction between branching heuristics and parallelism. By using parallelism to explicitly offset the commitment made to weak early branching choices, we obtain parallel subgraph solvers which are substantially and consistently better than the best sequential algorithms

Efficient implementation of resource-constrained cyber-physical systems using multi-core parallelism

The quest for more performance of applications and systems became more challenging in the recent years. Especially in the cyber-physical and mobile domain, the performance requirements increased significantly. Applications, previously found in the high-performance domain, emerge in the area of resource-constrained domain. Modern heterogeneous high-performance MPSoCs provide a solid foundation to satisfy the high demand. Such systems combine general processors with specialized accelerators ranging from GPUs to machine learning chips. On the other side of the performance spectrum, the demand for small energy efficient systems exposed by modern IoT applications increased vastly. Developing efficient software for such resource-constrained multi-core systems is an error-prone, time-consuming and challenging task. This thesis provides with PA4RES a holistic semiautomatic approach to parallelize and implement applications for such platforms efficiently. Our solution supports the developer to find good trade-offs to tackle the requirements exposed by modern applications and systems. With PICO, we propose a comprehensive approach to express parallelism in sequential applications. PICO detects data dependencies and implements required synchronization automatically. Using a genetic algorithm, PICO optimizes the data synchronization. The evolutionary algorithm considers channel capacity, memory mapping, channel merging and flexibility offered by the channel implementation with respect to execution time, energy consumption and memory footprint. PICO's communication optimization phase was able to generate a speedup almost 2 or an energy improvement of 30% for certain benchmarks. The PAMONO sensor approach enables a fast detection of biological viruses using optical methods. With a sophisticated virus detection software, a real-time virus detection running on stationary computers was achieved. Within this thesis, we were able to derive a soft real-time capable virus detection running on a high-performance embedded system, commonly found in today's smart phones. This was accomplished with smart DSE algorithm which optimizes for execution time, energy consumption and detection quality. Compared to a baseline implementation, our solution achieved a speedup of 4.1 and 87\% energy savings and satisfied the soft real-time requirements. Accepting a degradation of the detection quality, which still is usable in medical context, led to a speedup of 11.1. This work provides the fundamentals for a truly mobile real-time virus detection solution. The growing demand for processing power can no longer satisfied following well-known approaches like higher frequencies. These so-called performance walls expose a serious challenge for the growing performance demand. Approximate computing is a promising approach to overcome or at least shift the performance walls by accepting a degradation in the output quality to gain improvements in other objectives. Especially for a safe integration of approximation into existing application or during the development of new approximation techniques, a method to assess the impact on the output quality is essential. With QCAPES, we provide a multi-metric assessment framework to analyze the impact of approximation. Furthermore, QCAPES provides useful insights on the impact of approximation on execution time and energy consumption. With ApproxPICO we propose an extension to PICO to consider approximate computing during the parallelization of sequential applications