A study of simulation performance based on event orderings

Master'sMASTER OF SCIENC

Novel Parallelization Techniques for Computer Graphics Applications

Increasingly complex and data-intensive algorithms in computer graphics applications require software engineers to find ways of improving performance and scalability to satisfy the requirements of customers and users. Parallelizing and tailoring each algorithm of each specific application is a time-consuming task and its implementation is domain-specific because it can not be reused outside the specific problem in which the algorithm is defined. Identifying reusable parallelization patterns that can be extrapolated and applied to other different algorithms is an essential task needed in order to provide consistent parallelization improvements and reduce the development time of evolving a sequential algorithm into a parallel one. This thesis focuses on defining general and efficient parallelization techniques and approaches that can be followed in order to parallelize complex 3D graphic algorithms. These parallelization patterns can be easily applied in order to convert most kinds of sequential complex and data-intensive algorithms to parallel ones obtaining consistent optimization results. The main idea in the thesis is to use multi-threading techniques to improve the parallelization and core utilization of 3D algorithms. Most of the 3D algorithms apply similar repetitive independent operations on a vast amount of 3D data. These application characteristics bring the opportunity of applying multi-thread parallelization techniques on such applications. The efficiency of the proposed idea is tested on two common computer graphics algorithms: hidden-line removal and collision detection. Both algorithms are data-intensive algorithms, whose conversions from a sequential to a multithread implementation introduce challenges, due to their complexities and the fact that elements in their data have different sizes and complexities, producing work-load imbalances and asymmetries between processing elements. The results show that the proposed principles and patterns can be easily applied to both algorithms, transforming their sequential to multithread implementations, obtaining consistent optimization results proportional to the number of processing elements. From the work done in this thesis, it is concluded that the suggested parallelization warrants further study and development in order to extend its usage to heterogeneous platforms such as a Graphical Processing Unit (GPU). OpenCL is the most feasible framework to explore in the future due to its interoperability among different platforms

Multi-core processors and the future of parallelism in software

The purpose of this thesis is to examine multi-core technology. Multi-core architecture provides benefits such as less power consumption, scalability, and improved application performance enabled by thread-level parallelism

Focus: A Graph Approach for Data-Mining and Domain-Specific Assembly of Next Generation Sequencing Data

Next Generation Sequencing (NGS) has emerged as a key technology leading to revolutionary breakthroughs in numerous biomedical research areas. These technologies produce millions to billions of short DNA reads that represent a small fraction of the original target DNA sequence. These short reads contain little information individually but are produced at a high coverage of the original sequence such that many reads overlap. Overlap relationships allow for the reads to be linearly ordered and merged by computational programs called assemblers into long stretches of contiguous sequence called contigs that can be used for research applications. Although the assembly of the reads produced by NGS remains a difficult task, it is the process of extracting useful knowledge from these relatively short sequences that has become one of the most exciting and challenging problems in Bioinformatics. The assembly of short reads is an aggregative process where critical information is lost as reads are merged into contigs. In addition, the assembly process is treated as a black box, with generic assembler tools that do not adapt to input data set characteristics. Finally, as NGS data throughput continues to increase, there is an increasing need for smart parallel assembler implementations. In this dissertation, a new assembly approach called Focus is proposed. Unlike previous assemblers, Focus relies on a novel hybrid graph constructed from multiple graphs at different levels of granularity to represent the assembly problem, facilitating information capture and dynamic adjustment to input data set characteristics. This work is composed of four specific aims: 1) The implementation of a robust assembly and analysis tool built on the hybrid graph platform 2) The development and application of graph mining to extract biologically relevant features in NGS data sets 3) The integration of domain specific knowledge to improve the assembly and analysis process. 4) The construction of smart parallel computing approaches, including the application of energy-aware computing for NGS assembly and knowledge integration to improve algorithm performance. In conclusion, this dissertation presents a complete parallel assembler called Focus that is capable of extracting biologically relevant features directly from its hybrid assembly graph

Network Partitioning in Distributed Agent-Based Models

Agent-Based Models (ABMs) are an emerging simulation paradigm for modeling complex systems, comprised of autonomous, possibly heterogeneous, interacting agents. The utility of ABMs lies in their ability to represent such complex systems as self-organizing networks of agents. Modeling and understanding the behavior of complex systems usually occurs at large and representative scales, and often obtaining and visualizing of simulation results in real-time is critical. The real-time requirement necessitates the use of in-memory computing, as it is difficult and challenging to handle the latency and unpredictability of disk accesses. Combining this observation with the scale requirement emphasizes the need to use parallel and distributed computing platforms, such as MPI-enabled CPU clusters. Consequently, the agent population must be partitioned across different CPUs in a cluster. Further, the typically high volume of interactions among agents can quickly become a significant bottleneck for real-time or large-scale simulations. The problem is exacerbated if the underlying ABM network is dynamic and the inter-process communication evolves over the course of the simulation. Therefore, it is critical to develop topology-aware partitioning mechanisms to support such large simulations. In this dissertation, we demonstrate that distributed agent-based model simulations benefit from the use of graph partitioning algorithms that involve a local, neighborhood-based perspective. Such methods do not rely on global accesses to the network and thus are more scalable. In addition, we propose two partitioning schemes that consider the bottom-up individual-centric nature of agent-based modeling. The First technique utilizes label-propagation community detection to partition the dynamic agent network of an ABM. We propose a latency-hiding, seamless integration of community detection in the dynamics of a distributed ABM. To achieve this integration, we exploit the similarity in the process flow patterns of a label-propagation community-detection algorithm and self-organizing ABMs. In the second partitioning scheme, we apply a combination of the Guided Local Search (GLS) and Fast Local Search (FLS) metaheuristics in the context of graph partitioning. The main driving principle of GLS is the dynamic modi?cation of the objective function to escape local optima. The algorithm augments the objective of a local search, thereby transforming the landscape structure and escaping a local optimum. FLS is a local search heuristic algorithm that is aimed at reducing the search space of the main search algorithm. It breaks down the space into sub-neighborhoods such that inactive sub-neighborhoods are removed from the search process. The combination of GLS and FLS allowed us to design a graph partitioning algorithm that is both scalable and sensitive to the inherent modularity of real-world networks

Performance modelling for system-level design

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Famtile: An Algorithm For Learning High-level Tactical Behavior From Observation

This research focuses on the learning of a class of behaviors defined as high-level behaviors. High-level behaviors are defined here as behaviors that can be executed using a sequence of identifiable behaviors. Represented by low-level contexts, these behaviors are known a priori to learning and can be modeled separately by a knowledge engineer. The learning task, which is achieved by observing an expert within simulation, then becomes the identification and representation of the low-level context sequence executed by the expert. To learn this sequence, this research proposes FAMTILE - the Fuzzy ARTMAP / Template-Based Interpretation Learning Engine. This algorithm attempts to achieve this learning task by constructing rules that govern the low-level context transitions made by the expert. By combining these rules with models for these low-level context behaviors, it is hypothesized that an intelligent model for the expert can be created that can adequately model his behavior. To evaluate FAMTILE, four testing scenarios were developed that attempt to achieve three distinct evaluation goals: assessing the learning capabilities of Fuzzy ARTMAP, evaluating the ability of FAMTILE to correctly predict expert actions and context choices given an observation, and creating a model of the expert\u27s behavior that can perform the high-level task at a comparable level of proficiency

Assessment of Next Generation Sequencing Technologies for \u3ci\u3eDe novo\u3c/i\u3e and Hybrid Assemblies of Challenging Bacterial Genomes

In past decade, tremendous progress has been made in DNA sequencing methodologies in terms of throughput, speed, read-lengths, along with a sharp decrease in per base cost. These technologies, commonly referred to as next-generation sequencing (NGS) are complimented by the development of hybrid assembly approaches which can utilize multiple NGS platforms. In the first part of my dissertation I performed systematic evaluations and optimizations of nine de novo and hybrid assembly protocols across four novel microbial genomes. While each had strengths and weaknesses, via optimization using multiple strategies I obtained dramatic improvements in overall assembly size and quality. To select the best assembly, I also proposed the novel rDNA operon validation approach to evaluate assembly accuracy. Additionally, I investigated the ability of third-generation PacBio sequencing platform and achieved automated finishing of Clostridium autoethanogenum without any accessory data. These complete genome sequences facilitated comparisons which revealed rDNA operons as a major limitation for short read technologies, and also enabled comparative and functional genomics analysis. To facilitate future assessment and algorithms developments of NGS technologies we publically released the sequence datasets for C. autoethanogenum which span three generations of sequencing technologies, containing six types of data from four NGS platforms. To assess limitations of NGS technologies, assessment of unassembled regions within Illumina and PacBio assemblies was performed using eight microbial genomes. This analysis confirmed rDNA operons as major breakpoints within Illumina assembly while gaps within PacBio assembly appears to be an unaccounted for event and assembly quality is cumulative effect of read-depth, read-quality, sample DNA quality and presence of phage DNA or mobile genetic elements. In a final collaborative study an enrichment protocol was applied for isolation of live endophytic bacteria from roots of the tree Populus deltoides. This protocol achieved a significant reduction in contaminating plant DNA and enabled use these samples for single-cell genomics analysis for the first time. Whole genome sequencing of selected single-cell genomes was performed, assembly and contamination removal optimized, and followed by the bioinformatics, phylogenetic and comparative genomics analyses to identify unique characteristics of these uncultured microorganisms

A Framework and Taxonomy of Videogame Playing Preferences

© Owners/Authors, 2017. This is the author's version of the work. It is posted here for your personal use. Not for redistribution. The definitive Version of Record was published in CHI PLAY '17 - Proceedings of the Annual Symposium on Computer-Human Interaction in Play.Player preferences for different gaming styles or game elements has been a topic of interest in human-computer interaction for over a decade. However, current models suggested by the extant literature are generally based on classifying abstract gaming motivations or player archetypes. These concepts do not directly map onto the building blocks of games, taking away from the utility of the findings. To address this issue, we propose a conceptual framework of player preferences based on two dimensions: game elements and game playing styles. To investigate these two concepts, we conducted an exploratory empirical investigation of player preferences, which allowed us to create a taxonomy of nine groups of game elements and five groups of game playing styles. These two concepts are foundational to games, which means that our model can be used by designers to create games that are tailored to their target audience. In addition, we demonstrate that there are significant effects of gender and age on participants’ preferences and discuss the implications of these findings.NSERC || RGPIN-418622-2012 SSHRC || 895-2011-1014, IMMERSe CFI || 35819 Mitacs || IT07255 SWaGUR CNPq, Brazi