A Framework For Parallelizing Sampling-Based Motion Planning Algorithms

Motion planning is the problem of finding a valid path for a robot from a start position to a goal position. It has many uses such as protein folding and animation. However, motion planning can be slow and take a long time in difficult environments. Parallelization can be used to speed up this process. This research focused on the implementation of a framework for the implementation and testing of Parallel Motion Planning algorithms. Additionally, two methods were implemented to test this framework. The results showed a reasonable amount of speed-up and coverage and connectivity similar to sequential methods

A scalable method for parallelizing sampling-based motion planning algorithms

Abstract—This paper describes a scalable method for paral-lelizing sampling-based motion planning algorithms. It subdi-vides configuration space (C-space) into (possibly overlapping) regions and independently, in parallel, uses standard (sequen-tial) sampling-based planners to construct roadmaps in each region. Next, in parallel, regional roadmaps in adjacent regions are connected to form a global roadmap. By subdividing the space and restricting the locality of connection attempts, we reduce the work and inter-processor communication associated with nearest neighbor calculation, a critical bottleneck for scalability in existing parallel motion planning methods. We show that our method is general enough to handle a variety of planning schemes, including the widely used Probabilistic Roadmap (PRM) and Rapidly-exploring Random Trees (RRT) algorithms. We compare our approach to two other existing parallel algorithms and demonstrate that our approach achieves better and more scalable performance. Our approach achieves almost linear scalability on a 2400 core LINUX cluster and on a 153,216 core Cray XE6 petascale machine. I

A Framework For Parallelizing Sampling-Based Motion Planning Algorithms

Motion planning is the problem of finding a valid path for a robot from a start position to a goal position. It has many uses such as protein folding and animation. However, motion planning can be slow and take a long time in difficult environments. Parallelization can be used to speed up this process. This research focused on the implementation of a framework for the implementation and testing of Parallel Motion Planning algorithms. Additionally, two methods were implemented to test this framework. The results showed a reasonable amount of speed-up and coverage and connectivity similar to sequential methods

A Scalable Framework for Parallelizing Sampling-Based Motion Planning Algorithms

Motion planning is defined as the problem of finding a valid path taking a robot (or any movable object) from a given start configuration to a goal configuration in an environment. While motion planning has its roots in robotics, it now finds application in many other areas of scientific computing such as protein folding, drug design, virtual prototyping, computer-aided design (CAD), and computer animation. These new areas test the limits of the best sequential planners available, motivating the need for methods that can exploit parallel processing. This dissertation focuses on the design and implementation of a generic and scalable framework for parallelizing motion planning algorithms. In particular, we focus on sampling-based motion planning algorithms which are considered to be the state-of-the-art. Our work covers the two broad classes of sampling-based motion planning algorithms--the graph-based and the tree-based methods. Central to our approach is the subdivision of the planning space into regions. These regions represent sub- problems that can be processed in parallel. Solutions to the sub-problems are later combined to form a solution to the entire problem. By subdividing the planning space and restricting the locality of connection attempts to adjacent regions, we reduce the work and inter-processor communication associated with nearest neighbor calculation, a critical bottleneck for scalability in existing parallel motion planning methods. We also describe how load balancing strategies can be applied in complex environments. We present experimental results that scale to thousands of processors on different massively parallel machines for a range of motion planning problems

Algorithm-Level Optimizations for Scalable Parallel Graph Processing

Efficiently processing large graphs is challenging, since parallel graph algorithms suffer from poor scalability and performance due to many factors, including heavy communication and load-imbalance. Furthermore, it is difficult to express graph algorithms, as users need to understand and effectively utilize the underlying execution of the algorithm on the distributed system. The performance of graph algorithms depends not only on the characteristics of the system (such as latency, available RAM, etc.), but also on the characteristics of the input graph (small-world scalefree, mesh, long-diameter, etc.), and characteristics of the algorithm (sparse computation vs. dense communication). The best execution strategy, therefore, often heavily depends on the combination of input graph, system and algorithm. Fine-grained expression exposes maximum parallelism in the algorithm and allows the user to concentrate on a single vertex, making it easier to express parallel graph algorithms. However, this often loses information about the machine, making it difficult to extract performance and scalability from fine-grained algorithms. To address these issues, we present a model for expressing parallel graph algorithms using a fine-grained expression. Our model decouples the algorithm-writer from the underlying details of the system, graph, and execution and tuning of the algorithm. We also present various graph paradigms that optimize the execution of graph algorithms for various types of input graphs and systems. We show our model is general enough to allow graph algorithms to use the various graph paradigms for the best/fastest execution, and demonstrate good performance and scalability for various different graphs, algorithms, and systems to 100,000+ cores

Improved Connected-Component Expansion Strategies for Sampling-Based Motion Planning

Motion planning is the problem of computing valid paths through an environment. Since computing exact solutions is intractable, sampling-based algorithms, such as Probabilistic RoadMaps (PRMs), have gained popularity. PRMs compute an approximate mapping of the planning space by sacrificing completeness in favor of efficiency. However, these algorithms have certain bottlenecks that hinder performance, causing difficulty mapping narrow or crowded regions, with the asymptotic bottleneck of these algorithms being the nearest-neighbor queries required to connect the roadmap. Thus, roadmaps may fail to efficiently capture the connectivity of the planning space. In this thesis, we present a set of connected component (CC) expansion algorithms, each with different biases (random expand, expand to the nearest CC, expand away from the host CC, and expand along the medial-axis) and expansion node selection policies (random, farthest from CC's centroid, and difficult nodes), that create a linked-chain of configurations designed to enable efficient connection of CCs. Given an a priori roadmap quality requirement in terms of roadmap connectivity, we show that when our expansion methods augment PRMs, we reach the required roadmap connectivity in less time

The STAPL Parallel Container Framework

The Standard Template Adaptive Parallel Library (STAPL) is a parallel programming infrastructure that extends C with support for parallelism. STAPL provides a run-time system, a collection of distributed data structures (pContainers) and parallel algorithms (pAlgorithms), and a generic methodology for extending them to provide customized functionality. Parallel containers are data structures addressing issues related to data partitioning, distribution, communication, synchronization, load balancing, and thread safety. This dissertation presents the STAPL Parallel Container Framework (PCF), which is designed to facilitate the development of generic parallel containers. We introduce a set of concepts and a methodology for assembling a pContainer from existing sequential or parallel containers without requiring the programmer to deal with concurrency or data distribution issues. The STAPL PCF provides a large number of basic data parallel structures (e.g., pArray, pList, pVector, pMatrix, pGraph, pMap, pSet). The STAPL PCF is distinguished from existing work by offering a class hierarchy and a composition mechanism which allows users to extend and customize the current container base for improved application expressivity and performance. We evaluate the performance of the STAPL pContainers on various parallel machines including a massively parallel CRAY XT4 system and an IBM P5-575 cluster. We show that the pContainer methods, generic pAlgorithms, and different applications, all provide good scalability on more than 10^4 processors

Doctor of Philosophy

dissertationThe development of systematic evolution of ligands by exponential enrichment, or SELEX, in 1990 propelled interest in nucleic acid engineering. The ability of nucleic acids to undergo directed evolution has resulted in the widespread interest in the development of aptamers, or single stranded nucleic acids that possess affinity to a specific target molecule. Aptamers exist to diverse classes of molecules, and because of their versatility are being regarded as robust recognition elements for a variety of biotechnology applications. Further, the small-molecule harnessing potential of aptamers has shown great promise for the development of biosensors. Importantly, traditional selection methods can be expanded upon to enable the generation of functional nucleic acids which are optimized for biosensing platforms. Novel SELEX methods are a powerful tool to develop innovative technologies for detection and imaging using aptamer-based biosensors. Our lab has contributed to a variety of areas within this field including the use of ribozymes as a tag for intracellular imaging of RNA. We have designed a novel IP-SELEX method which allows for the generation of ribozymes that are capable of performing a reaction to covalently attach a small-molecule fluorophore to itself (Chapter 2). We show that this ribozyme can label in cellular conditions and hold great promise as a genetically encodable tag for live cell labeling of mRNA. We have also developed a new class of small-molecule sensors through the evolution of nucleic acids with noncanonical backbone structures, or xeno nucleic acids (XNA). XNA molecules have many advantageous properties because of their noncanonical structures, notably nuclease resistance. Using our unique method, optimized by the use of an XNA primer, we were able generate the first artificial genetic polymers capable of small-molecule recognition (Chapter 3). We discovered threose nucleic acid (TNA) aptamers with affinity for a small-molecule mycotoxin (OTA). We show that these aptamers have outstanding biostability in the presence of nucleases and retain the ability to bind the target in these environments. We acknowledge the potential for structure-switching (SS) aptamer biosensors as a privileged architecture for small-molecule detection and the development of fluorescence assays. We propose an innovative technique for the direct selection of SS biosensors, in which we take advantage of both restriction digests and polymerase chain reaction (PCR) as key steps to eliminate nonfunctional sequences. Importantly, because amplification simultaneously serves as the selection step there is no requirement for a solid support. We anticipate this will overcome the limitations of bead-based selection methods and enable for efficient and effective generation of SS biosensors