Memory management and parallelization of data intensive all-to-all comparison in shared-memory systems

This thesis presents a novel program parallelization technique incorporating with dynamic and static scheduling. It utilizes a problem specific pattern developed from the prior knowledge of the targeted problem abstraction. Suitable for solving complex parallelization problems such as data intensive all-to-all comparison constrained by memory, the technique delivers more robust and faster task scheduling compared to the state-of-the art techniques. Good performance is achieved from the technique in data intensive bioinformatics applications.

Using Ownership to Reason About Inherent Parallelism in Object-Oriented Programs

With the emergence of multi-cores into the mainstream, there is a growing need for systems to allow programmers and automated systems to reason about data dependencies and inherent parallelismin imperative object-oriented languages. In this paper we exploit the structure of object-oriented programs to abstract computational side-effects. We capture and validate these effects using a static type system. We use these as the basis of sufficient conditions for several different data and task parallelism patterns. We compliment our static type system with a lightweight runtime system to allow for parallelization in the presence of complex data flows. We have a functioning compiler and worked examples to demonstrate the practicality of our solution.

A framework for reasoning about inherent parallelism in modern object-oriented languages

With the emergence of multi-core processors into the mainstream, parallel programming is no longer the specialized domain it once was. There is a growing need for systems to allow programmers to more easily reason about data dependencies and inherent parallelism in general purpose programs. Many of these programs are written in popular imperative programming languages like Java and C]. In this thesis I present a system for reasoning about side-effects of evaluation in an abstract and composable manner that is suitable for use by both programmers and automated tools such as compilers. The goal of developing such a system is to both facilitate the automatic exploitation of the inherent parallelism present in imperative programs and to allow programmers to reason about dependencies which may be limiting the parallelism available for exploitation in their applications. Previous work on languages and type systems for parallel computing has tended to focus on providing the programmer with tools to facilitate the manual parallelization of programs; programmers must decide when and where it is safe to employ parallelism without the assistance of the compiler or other automated tools. None of the existing systems combine abstraction and composition with parallelization and correctness checking to produce a framework which helps both programmers and automated tools to reason about inherent parallelism. In this work I present a system for abstractly reasoning about side-effects and data dependencies in modern, imperative, object-oriented languages using a type and effect system based on ideas from Ownership Types. I have developed sufficient conditions for the safe, automated detection and exploitation of a number task, data and loop parallelism patterns in terms of ownership relationships. To validate my work, I have applied my ideas to the C] version 3.0 language to produce a language extension called Zal. I have implemented a compiler for the Zal language as an extension of the GPC] research compiler as a proof of concept of my system. I have used it to parallelize a number of real-world applications to demonstrate the feasibility of my proposed approach. In addition to this empirical validation, I present an argument for the correctness of the type system and language semantics I have proposed as well as sketches of proofs for the correctness of the sufficient conditions for parallelization proposed.

Improved estimates of percolation and anisotropic permeability from 3-D X-ray microtomography using stochastic analyses and visualization

X-ray microtomography (micro-CT) with micron resolution enables new ways of characterizing microstructures and opens pathways for forward calculations of multiscale rock properties. A quantitative characterization of the microstructure is the first step in this challenge. We developed a new approach to extract scale-dependent characteristics of porosity, percolation, and anisotropic permeability from 3-D microstructural models of rocks. The Hoshen-Kopelman algorithm of percolation theory is employed for a standard percolation analysis. The anisotropy of permeability is calculated by means of the star volume distribution approach. The local porosity distribution and local percolation probability are obtained by using the local porosity theory. Additionally, the local anisotropy distribution is defined and analyzed through two empirical probability density functions, the isotropy index and the elongation index. For such a high-resolution data set, the typical data sizes of the CT images are on the order of gigabytes to tens of gigabytes; thus an extremely large number of calculations are required. To resolve this large memory problem parallelization in OpenMP was used to optimally harness the shared memory infrastructure on cache coherent Non-Uniform Memory Access architecture machines such as the iVEC SGI Altix 3700Bx2 Supercomputer. We see adequate visualization of the results as an important element in this first pioneering study.

Parallel authentication and public-key encryption

A parallel authentication and public-key encryption is introduced and exemplified on joint encryption and signing which compares favorably with sequential Encrypt-then-Sign (ɛtS) or Sign-then-Encrypt (Stɛ) schemes as far as both efficiency and security are concerned. A security model for signcryption, and thus joint encryption and signing, has been recently defined which considers possible attacks and security goals. Such a scheme is considered secure if the encryption part guarantees indistinguishability and the signature part prevents existential forgeries, for outsider but also insider adversaries. We propose two schemes of parallel signcryption, which are efficient alternative to Commit-then-Sign-and- Encrypt (Ct&G3&S). They are both provably secure in the random oracle model. The first one, called generic parallel encrypt and sign, is secure if the encryption scheme is semantically secure against chosen-ciphertext attacks and the signature scheme prevents existential forgeries against random-message attacks. The second scheme, called optimal parallel encrypt. and sign, applies random oracles similar to the OAEP technique in order to achieve security using encryption and signature components with very weak security requirements — encryption is expected to be one-way under chosen-plaintext attacks while signature needs to be secure against universal forgeries under random-plaintext attack, that is actually the case for both the plain-RSA encryption and signature under the usual RSA assumption. Both proposals are generic in the sense that any suitable encryption and signature schemes (i.e. which simply achieve required security) can be used. Furthermore they allow both parallel encryption and signing, as well as parallel decryption and verification. Properties of parallel encrypt and sign schemes are considered and a new security standard for parallel signcryption is proposed.

Evolutionary optimization and game strategies for advanced multi-disciplinary design : applications to aeronautics and UAV design

Many complex aeronautical design problems can be formulated with efficient multi-objective evolutionary optimization methods and game strategies. This book describes the role of advanced innovative evolution tools in the solution, or the set of solutions of single or multi disciplinary optimization. These tools use the concept of multi-population, asynchronous parallelization and hierarchical topology which allows different models including precise, intermediate and approximate models with each node belonging to the different hierarchical layer handled by a different Evolutionary Algorithm. The efficiency of evolutionary algorithms for both single and multi-objective optimization problems are significantly improved by the coupling of EAs with games and in particular by a new dynamic methodology named “Hybridized Nash-Pareto games”. Multi objective Optimization techniques and robust design problems taking into account uncertainties are introduced and explained in detail. Several applications dealing with civil aircraft and UAV, UCAV systems are implemented numerically and discussed. Applications of increasing optimization complexity are presented as well as two hands-on test cases problems. These examples focus on aeronautical applications and will be useful to the practitioner in the laboratory or in industrial design environments. The evolutionary methods coupled with games presented in this volume can be applied to other areas including surface and marine transport, structures, biomedical engineering, renewable energy and environmental problems.