Shared Memory Parallel Subgraph Enumeration

The subgraph enumeration problem asks us to find all subgraphs of a target graph that are isomorphic to a given pattern graph. Determining whether even one such isomorphic subgraph exists is NP-complete---and therefore finding all such subgraphs (if they exist) is a time-consuming task. Subgraph enumeration has applications in many fields, including biochemistry and social networks, and interestingly the fastest algorithms for solving the problem for biochemical inputs are sequential. Since they depend on depth-first tree traversal, an efficient parallelization is far from trivial. Nevertheless, since important applications produce data sets with increasing difficulty, parallelism seems beneficial. We thus present here a shared-memory parallelization of the state-of-the-art subgraph enumeration algorithms RI and RI-DS (a variant of RI for dense graphs) by Bonnici et al. [BMC Bioinformatics, 2013]. Our strategy uses work stealing and our implementation demonstrates a significant speedup on real-world biochemical data---despite a highly irregular data access pattern. We also improve RI-DS by pruning the search space better; this further improves the empirical running times compared to the already highly tuned RI-DS.Comment: 18 pages, 12 figures, To appear at the 7th IEEE Workshop on Parallel / Distributed Computing and Optimization (PDCO 2017

Task allocation in a distributed computing system

A conceptual framework is examined for task allocation in distributed systems. Application and computing system parameters critical to task allocation decision processes are discussed. Task allocation techniques are addressed which focus on achieving a balance in the load distribution among the system's processors. Equalization of computing load among the processing elements is the goal. Examples of system performance are presented for specific applications. Both static and dynamic allocation of tasks are considered and system performance is evaluated using different task allocation methodologies

Overfitting in Synthesis: Theory and Practice (Extended Version)

In syntax-guided synthesis (SyGuS), a synthesizer's goal is to automatically generate a program belonging to a grammar of possible implementations that meets a logical specification. We investigate a common limitation across state-of-the-art SyGuS tools that perform counterexample-guided inductive synthesis (CEGIS). We empirically observe that as the expressiveness of the provided grammar increases, the performance of these tools degrades significantly. We claim that this degradation is not only due to a larger search space, but also due to overfitting. We formally define this phenomenon and prove no-free-lunch theorems for SyGuS, which reveal a fundamental tradeoff between synthesizer performance and grammar expressiveness. A standard approach to mitigate overfitting in machine learning is to run multiple learners with varying expressiveness in parallel. We demonstrate that this insight can immediately benefit existing SyGuS tools. We also propose a novel single-threaded technique called hybrid enumeration that interleaves different grammars and outperforms the winner of the 2018 SyGuS competition (Inv track), solving more problems and achieving a $5\times$ mean speedup.Comment: 24 pages (5 pages of appendices), 7 figures, includes proofs of theorem

Dynamic Scale Genetic Algorithm: An Enhanced Genetic Search for Discrete Optimization

The minimization of operations and support resources of reusable launch vehicles is a complex task, involving discrete optimization and the simulation domain. Genetic algorithms, offering a robust search strategy suitable for integer variables and the simulation domain, can be applied to minimize these resources. This research developed an enhanced genetic algorithm for problems with a linear objective function, the most common class of discrete optimization problems. The dynamic scale genetic algorithm developed here incorporates concepts of implicit enumeration to enhance search. This is achieved by utilizing problem specific information to refine the solution space over successive generations. The utility of the proposed algorithm was demonstrated by comparing its performance, in terms of quality of solutions produced, to that of the simple genetic algorithm. For all test problems, the dynamic scale genetic algorithm consistently produced better solutions in fewer generations. The proposed algorithm was successfully applied to optimize the operation and support resources of reusable launch vehicles, through a discrete event simulation model. The least cost solution so obtained represents an improvement over both the simple genetic algorithm, and the previous manual approach of minimizing operation and support resources

Algorithms for massively parallel generic hp-adaptive finite element methods

Efficient algorithms for the numerical solution of partial differential equations are required to solve problems on an economically viable timescale. In general, this is achieved by adapting the resolution of the discretization to the investigated problem, as well as exploiting hardware specifications. For the latter category, parallelization plays a major role for modern multi-core and multi-node architectures, especially in the context of high-performance computing. Using finite element methods, solutions are approximated by discretizing the function space of the problem with piecewise polynomials. With hp-adaptive methods, the polynomial degrees of these basis functions may vary on locally refined meshes. We present algorithms and data structures required for generic hp-adaptive finite element software applicable for both continuous and discontinuous Galerkin methods on distributed memory systems. Both function space and mesh may be adapted dynamically during the solution process. We cover details concerning the unique enumeration of degrees of freedom with continuous Galerkin methods, the communication of variable size data, and load balancing. Furthermore, we present strategies to determine the type of adaptation based on error estimation and prediction as well as smoothness estimation via the decay rate of coefficients of Fourier and Legendre series expansions. Both refinement and coarsening are considered. A reference implementation in the open-source library deal.II is provided and applied to the Laplace problem on a domain with a reentrant corner which invokes a singularity. With this example, we demonstrate the benefits of the hp-adaptive methods in terms of error convergence and show that our algorithm scales up to 49,152 MPI processes.Für die numerische Lösung partieller Differentialgleichungen sind effiziente Algorithmen erforderlich, um Probleme auf einer wirtschaftlich tragbaren Zeitskala zu lösen. Im Allgemeinen ist dies durch die Anpassung der Diskretisierungsauflösung an das untersuchte Problem sowie durch die Ausnutzung der Hardwarespezifikationen möglich. Für die letztere Kategorie spielt die Parallelisierung eine große Rolle für moderne Mehrkern- und Mehrknotenarchitekturen, insbesondere im Kontext des Hochleistungsrechnens. Mit Hilfe von Finite-Elemente-Methoden werden Lösungen durch Diskretisierung des assoziierten Funktionsraums mit stückweisen Polynomen approximiert. Bei hp-adaptiven Verfahren können die Polynomgrade dieser Basisfunktionen auf lokal verfeinerten Gittern variieren. In dieser Dissertation werden Algorithmen und Datenstrukturen vorgestellt, die für generische hp-adaptive Finite-Elemente-Software benötigt werden und sowohl für kontinuierliche als auch diskontinuierliche Galerkin-Verfahren auf Systemen mit verteiltem Speicher anwendbar sind. Sowohl der Funktionsraum als auch das Gitter können während des Lösungsprozesses dynamisch angepasst werden. Im Besonderen erläutert werden die eindeutige Nummerierung von Freiheitsgraden mit kontinuierlichen Galerkin-Verfahren, die Kommunikation von Daten variabler Größe und die Lastenverteilung. Außerdem werden Strategien zur Bestimmung des Adaptierungstyps auf der Grundlage von Fehlerschätzungen und -prognosen sowie Glattheitsschätzungen vorgestellt, die über die Zerfallsrate von Koeffizienten aus Reihenentwicklungen nach Fourier und Legendre bestimmt werden. Dabei werden sowohl Verfeinerung als auch Vergröberung berücksichtigt. Eine Referenzimplementierung erfolgt in der Open-Source-Bibliothek deal.II und wird auf das Laplace-Problem auf einem Gebiet mit einer einschneidenden Ecke angewandt, die eine Singularität aufweist. Anhand dieses Beispiels werden die Vorteile der hp-adaptiven Methoden hinsichtlich der Fehlerkonvergenz und die Skalierbarkeit der präsentierten Algorithmen auf bis zu 49.152 MPI-Prozessen demonstriert