Time-Optimal Algorithms on Meshes With Multiple Broadcasting

The mesh-connected computer architecture has emerged as a natural choice for solving a large number of computational tasks in image processing, computational geometry, and computer vision. However, due to its large communication diameter, the mesh tends to be slow when it comes to handling data transfer operations over long distances. In an attempt to overcome this problem, mesh-connected computers have recently been augmented by the addition of various types of bus systems. One such system known as the mesh with multiple broadcasting involves enhancing the mesh architecture by the addition of row and column buses. The mesh with multiple broadcasting has proven to be feasible to implement in VLSI, and is used in the DAP family of computers. In recent years, efficient algorithms to solve a number of computational problems on meshes with multiple broadcasting have been proposed in the literature. The problems considered in this thesis are semigroup computations, sorting, multiple search, various convexity-related problems, and some tree problems. Based on the size of the input data for the problem under consideration, existing results can be broadly classified into sparse and dense. Specifically, for a given √n x √n mesh with multiple broadcasting, we refer to problems involving $m \in O(\sqrt{n}$) items as sparse, while the case £ O(n) will be referred to as dense. Finally, the case corresponding to 2 ≤ m ≤ n is be termed general. The motivation behind the current work is twofold. First, time-optimal solutions are proposed for the problems listed above. Secondly, an attempt is made to remove the artificial limitation of problems studied to sparse and dense cases. To establish the time-optimality of the algorithms presented in this work, we use some existing lower bound techniques along with new ones that we develop. We solve the semigroup computation problem for the general case and present a novel lower bound argument. We solve the multiple search problem in the general case and present some surprising applications to computational geometry. In the case of sorting, the general case is defined to be slightly different. For the specified range of the size of input, we present a time and VLSI-optimal algorithm. We also present time lower bound results and matching algorithms for a number of convexity related and tree problems in the sparse case

Visibility-Related Problems on Parallel Computational Models

Visibility-related problems find applications in seemingly unrelated and diverse fields such as computer graphics, scene analysis, robotics and VLSI design. While there are common threads running through these problems, most existing solutions do not exploit these commonalities. With this in mind, this thesis identifies these common threads and provides a unified approach to solve these problems and develops solutions that can be viewed as template algorithms for an abstract computational model. A template algorithm provides an architecture independent solution for a problem, from which solutions can be generated for diverse computational models. In particular, the template algorithms presented in this work lead to optimal solutions to various visibility-related problems on fine-grain mesh connected computers such as meshes with multiple broadcasting and reconfigurable meshes, and also on coarse-grain multicomputers. Visibility-related problems studied in this thesis can be broadly classified into Object Visibility and Triangulation problems. To demonstrate the practical relevance of these algorithms, two of the fundamental template algorithms identified as powerful tools in almost every algorithm designed in this work were implemented on an IBM-SP2. The code was developed in the C language, using MPI, and can easily be ported to many commercially available parallel computers

A Computational Paradigm on Network-Based Models of Computation

The maturation of computer science has strengthened the need to consolidate isolated algorithms and techniques into general computational paradigms. The main goal of this dissertation is to provide a unifying framework which captures the essence of a number of problems in seemingly unrelated contexts in database design, pattern recognition, image processing, VLSI design, computer vision, and robot navigation. The main contribution of this work is to provide a computational paradigm which involves the unifying framework, referred to as the multiple Query problem, along with a generic solution to the Multiple Query problem. To demonstrate the applicability of the paradigm, a number of problems from different areas of computer science are solved by formulating them in this framework. Also, to show practical relevance, two fundamental problems were implemented in the C language using MPI. The code can be ported onto many commercially available parallel computers; in particular, the code was tested on an IBM-SP2 and on a network of workstations

Geometric modeling for computer aided design

The primary goal of this grant has been the design and implementation of software to be used in the conceptual design of aerospace vehicles particularly focused on the elements of geometric design, graphical user interfaces, and the interaction of the multitude of software typically used in this engineering environment. This has resulted in the development of several analysis packages and design studies. These include two major software systems currently used in the conceptual level design of aerospace vehicles. These tools are SMART, the Solid Modeling Aerospace Research Tool, and EASIE, the Environment for Software Integration and Execution. Additional software tools were designed and implemented to address the needs of the engineer working in the conceptual design environment. SMART provides conceptual designers with a rapid prototyping capability and several engineering analysis capabilities. In addition, SMART has a carefully engineered user interface that makes it easy to learn and use. Finally, a number of specialty characteristics have been built into SMART which allow it to be used efficiently as a front end geometry processor for other analysis packages. EASIE provides a set of interactive utilities that simplify the task of building and executing computer aided design systems consisting of diverse, stand-alone, analysis codes. Resulting in a streamlining of the exchange of data between programs reducing errors and improving the efficiency. EASIE provides both a methodology and a collection of software tools to ease the task of coordinating engineering design and analysis codes

Rapid model-guided design of organ-scale synthetic vasculature for biomanufacturing

Our ability to produce human-scale bio-manufactured organs is critically limited by the need for vascularization and perfusion. For tissues of variable size and shape, including arbitrarily complex geometries, designing and printing vasculature capable of adequate perfusion has posed a major hurdle. Here, we introduce a model-driven design pipeline combining accelerated optimization methods for fast synthetic vascular tree generation and computational hemodynamics models. We demonstrate rapid generation, simulation, and 3D printing of synthetic vasculature in complex geometries, from small tissue constructs to organ scale networks. We introduce key algorithmic advances that all together accelerate synthetic vascular generation by more than 230-fold compared to standard methods and enable their use in arbitrarily complex shapes through localized implicit functions. Furthermore, we provide techniques for joining vascular trees into watertight networks suitable for hemodynamic CFD and 3D fabrication. We demonstrate that organ-scale vascular network models can be generated in silico within minutes and can be used to perfuse engineered and anatomic models including a bioreactor, annulus, bi-ventricular heart, and gyrus. We further show that this flexible pipeline can be applied to two common modes of bioprinting with free-form reversible embedding of suspended hydrogels and writing into soft matter. Our synthetic vascular tree generation pipeline enables rapid, scalable vascular model generation and fluid analysis for bio-manufactured tissues necessary for future scale up and production.Comment: 58 pages (19 main and 39 supplement pages), 4 main figures, 9 supplement figure

A fast adaptive convex hull algorithm on two-dimensional processor arrays with a reconfigurable BUS system

A bus system that can change dynamically to suit computational needs is referred to as reconfigurable. We present a fast adaptive convex hull algorithm on a two-dimensional processor array with a reconfigurable bus system (2-D PARBS, for short). Specifically, we show that computing the convex hull of a planar set of n points taken O(log n/log m) time on a 2-D PARBS of size mn x n with 3 less than or equal to m less than or equal to n. Our result implies that the convex hull of n points in the plane can be computed in O(1) time in a 2-D PARBS of size n(exp 1.5) x n

Algorithmic Motion Planning and Related Geometric Problems on Parallel Machines (Dissertation Proposal)

The problem of algorithmic motion planning is one that has received considerable attention in recent years. The automatic planning of motion for a mobile object moving amongst obstacles is a fundamentally important problem with numerous applications in computer graphics and robotics. Numerous approximate techniques (AI-based, heuristics-based, potential field methods, for example) for motion planning have long been in existence, and have resulted in the design of experimental systems that work reasonably well under various special conditions [7, 29, 30]. Our interest in this problem, however, is in the use of algorithmic techniques for motion planning, with provable worst case performance guarantees. The study of algorithmic motion planning has been spurred by recent research that has established the mathematical depth of motion planning. Classical geometry, algebra, algebraic geometry and combinatorics are some of the fields of mathematics that have been used to prove various results that have provided better insight into the issues involved in motion planning [49]. In particular, the design and analysis of geometric algorithms has proved to be very useful for numerous important special cases. In the remainder of this proposal we will substitute the more precise term of algorithmic motion planning by just motion planning

Supporting divide-and-conquer algorithms for image processing

Divide-and-conquer is an important algorithm strategy, but it is not widely used in image processing. For higher-level, symbolic operations it should often be the strategy of choice for parallel computers. It is natural for a machine with a regular interconnection scheme such as a mesh, mesh with broadcasting, tree, pyramid, mesh-of-trees, PRAM, or hypercube, and can be used either on a machine with a pixel per processor or on one with many pixels per processor. However, divide-and-conquer algorithms use parallel computers in a different manner than, say, local edge detection, so machines optimized for local neighborhood algorithms may be poor for divide-and-conquer algorithms. Some characteristics of divide-and-conquer algorithms are examined, along with some of their implications for the design of machines and languages which can support the efficient programming and execution of divide-and-conquer algorithms.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/26821/1/0000380.pd

Efficient Molecular Dynamics Simulation on Reconfigurable Models with MultiGrid Method

In the field of biology, MD simulations are continuously used to investigate biological studies. A Molecular Dynamics (MD) system is defined by the position and momentum of particles and their interactions. The dynamics of a system can be evaluated by an N-body problem and the simulation is continued until the energy reaches equilibrium. Thus, solving the dynamics numerically and evaluating the interaction is computationally expensive even for a small number of particles in the system. We are focusing on long-ranged interactions, since the calculation time is O(N^2) for an N particle system. In this dissertation, we are proposing two research directions for the MD simulation. First, we design a new variation of Multigrid (MG) algorithm called Multi-level charge assignment (MCA) that requires O(N) time for accurate and efficient calculation of the electrostatic forces. We apply MCA and back interpolation based on the structure of molecules to enhance the accuracy of the simulation. Our second research utilizes reconfigurable models to achieve fast calculation time. We have been working on exploiting two reconfigurable models. We design FPGA-based MD simulator implementing MCA method for Xilinx Virtex-IV. It performs about 10 to 100 times faster than software implementation depending on the simulation accuracy desired. We also design fast and scalable Reconfigurable mesh (R-Mesh) algorithms for MD simulations. This work demonstrates that the large scale biological studies can be simulated in close to real time. The R-Mesh algorithms we design highlight the feasibility of these models to evaluate potentials with faster calculation times. Specifically, we develop R-Mesh algorithms for both Direct method and Multigrid method. The Direct method evaluates exact potentials and forces, but requires O(N^2) calculation time for evaluating electrostatic forces on a general purpose processor. The MG method adopts an interpolation technique to reduce calculation time to O(N) for a given accuracy. However, our R-Mesh algorithms require only O(N) or O(logN) time complexity for the Direct method on N linear R-Mesh and N¡¿N R-Mesh, respectively and O(r)+O(logM) time complexity for the Multigrid method on an X¡¿Y¡¿Z R-Mesh. r is N/M and M = X¡¿Y¡¿Z is the number of finest grid points