Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Fast parallel algorithms for short-range molecular dynamics

Machine Learning is the study of methods for programming computers to learn. Computers are applied to a wide range of tasks, and for most of these it is relatively easy for programmers to design and implement the necessary software. However, there are many tasks for which this is difficult or impossible. These can be divided into four general categories. First, there are problems for which there exist no human experts. For example, in modern automated manufacturing facilities, there is a need to predict machine failures before they occur by analyzing sensor readings. Because the machines are new, there are no human experts who can be interviewed by a programmer to provide the knowledge necessary to build a computer system. A machine learning system can study recorded data and subsequent machine failures and learn prediction rules. Second, there are problems where human experts exist, but where they are unable to explain their expertise. This is the case in many perceptual tasks, such as speech recognition, hand-writing recognition, and natural language understanding. Virtually all humans exhibit expert-level abilities on these tasks, but none of them can describe the detailed steps that they follow as they perform them. Fortunately, humans can provide machines with examples of the inputs and correct outputs for these tasks, so machine learning algorithms can learn to map the inputs to the outputs. Third, there are problems where phenomena are changing rapidly. In finance, for example, people would like to predict the future behavior of the stock market, of consumer purchases, or of exchange rates. These behaviors change frequently, so that even if a programmer could construct a good predictive computer program, it would need to be rewritten frequently. A learning program can relieve the programmer of this burden by constantly modifying and tuning a set of learned prediction rules. Fourth, there are applications that need to be customized for each computer user separately. Consider, for example, a program to filter unwanted electronic mail messages. Different users will need different filters. It is unreasonable to expect each user to program his or her own rules, and it is infeasible to provide every user with a software engineer to keep the rules up-to-date. A machine learning system can learn which mail messages the user rejects and maintain the filtering rules automatically. Machine learning addresses many of the same research questions as the fields of statistics, data mining, and psychology, but with differences of emphasis. Statistics focuses on understanding the phenomena that have generated the data, often with the goal of testing different hypotheses about those phenomena. Data mining seeks to find patterns in the data that are understandable by people. Psychological studies of human learning aspire to understand the mechanisms underlying the various learning behaviors exhibited by people (concept learning, skill acquisition, strategy change, etc.).

Machine learning

Deposits of clastic carbonate-dominated (calciclastic) sedimentary slope systems in the rock record have been identified mostly as linearly-consistent carbonate apron deposits, even though most ancient clastic carbonate slope deposits fit the submarine fan systems better. Calciclastic submarine fans are consequently rarely described and are poorly understood. Subsequently, very little is known especially in mud-dominated calciclastic submarine fan systems. Presented in this study are a sedimentological core and petrographic characterisation of samples from eleven boreholes from the Lower Carboniferous of Bowland Basin (Northwest England) that reveals a >250 m thick calciturbidite complex deposited in a calciclastic submarine fan setting. Seven facies are recognised from core and thin section characterisation and are grouped into three carbonate turbidite sequences. They include: 1) Calciturbidites, comprising mostly of highto low-density, wavy-laminated bioclast-rich facies; 2) low-density densite mudstones which are characterised by planar laminated and unlaminated muddominated facies; and 3) Calcidebrites which are muddy or hyper-concentrated debrisflow deposits occurring as poorly-sorted, chaotic, mud-supported floatstones. These

Phd by thesis

We will review some of the major results in random graphs and some of the more challenging open problems. We will cover algorithmic and structural questions. We will touch on newer models, including those related to the WWW.

Random graphs

Planning algorithms are impacting technical disciplines and industries around the world, including robotics, computer-aided design, manufacturing, computer graphics, aerospace applications, drug design, and protein folding. This coherent and comprehensive book unifies material from several sources, including robotics, control theory, artificial intelligence, and algorithms. The treatment is centered on robot motion planning but integrates material on planning in discrete spaces. A major part of the book is devoted to planning under uncertainty, including decision theory, Markov decision processes, and information spaces, which are the “configuration spaces” of all sensor-based planning problems. The last part of the book delves into planning under differential constraints that arise when automating the motions of virtually any mechanical system. Developed from courses taught by the author, the book is intended for students, engineers, and researchers in robotics, artificial intelligence, and control theory as well as computer graphics, algorithms, and computational biology.

Planning Algorithms: Introductory Material

Although there are many motion planning techniques, there is no method that outperforms all others for all problem instances. Rather, each technique has different strengths and weaknesses which makes it best-suited for certain types of problems. Moreover, since an environment can contain vastly different regions, there may not be a single planner that will perform well in all its regions. Ideally, one would use a suite of planners in concert and would solve the problem by applying the best-suited planner in each region. In this paper, we propose an automated framework for feature-sensitive motion planning. We use a machine learning approach to characterize and partition C-space into regions that are well suited to one of the methods in our library of roadmapbased motion planners. After the best-suited method is applied in each region, the resulting region roadmaps are combined to form a roadmap of the entire planning space. Over a range of problems, we demonstrate that our simple prototype system reliably outperforms any of the planners on their own.

A Machine Learning Approach for Feature-Sensitive Motion Planning.

While many methods to simulate flocking behaviors have been proposed, these techniques usually only provide simplistic navigation and planning capabilities because each flock member's behavior depends only on its local environment. In this work, we investigate how the addition of global information in the form of a roadmap of the environment enables more sophisticated flocking behaviors and supports global navigation and planning. In this paper, we propose new techniques for four distinct group behaviors: homing, goal searching, traversing narrow areas and shepherding. Extending ideas from cognitive modeling, we embed behavior rules in individual flock members and in the roadmap. These embedded behaviors enable the creatures to modify their actions based on their current location and state. For example, the flock might move as an unordered group in open regions and in a follow-the-leader fashion through narrow passages. These behaviors exploit global knowledge of the environment and utilize information gathered by all flock members which is communicated by allowing individual flock members to dynamically update the shared roadmap to reflect (un)desirable routes or regions. We present experimental results showing how the judicious use of simple roadmaps of the environment enables complex behaviors to be obtained at minimal cost. Animations can be viewed at http://parasol.tamu.edu.

/pdf/better-group-behaviors-in-complex-environments-using-global-4o9oln8un5.pdf

Better group behaviors in complex environments using global roadmaps

We give fast randomized and deterministic parallel methods for constructing convex hulls in R/sup d/, for any fixed d. Our methods are for the weakest shared-memory model, the EREW PRAM, and have optimal work bounds (with high probability for the randomized methods). In particular, we show that the convex hull of n points in R/sup d/ can be constructed in O(log n) time using O(n log n+n/sup [d/2]/) work, with high probability. We also show that it can be constructed deterministically in O(log/sup 2/ n) time using O(n log n) work for d=3 and in O(log n) time using O(n/sup [d/2]/ log/sup c([d/2]-[d/2]/) n) work for d/spl ges/4, where c>0 is a constant which is optimal for even d/spl ges/4. We also show how to make our 3-dimensional methods output-sensitive with only a small increase in running time. These methods can be applied to other problems as well. >

Parallel algorithms for higher-dimensional convex hulls

The problem we address is the distributed reconfiguration of a planar metamorphic robotic system composed of any number of hexagonal modules. After presenting a framework for classifying motion planning algorithms for metamorphic robotic systems, we describe distributed algorithms for reconfiguring a straight chain of hexagonal modules to any intersecting straight chain configuration. We prove our algorithms are correct, and show that they are either optimal or asymptotically optimal in the number of moves and asymptotically optimal in the time required for parallel reconfiguration.

/pdf/distributed-reconfiguration-of-metamorphic-robot-chains-18o20nug7p.pdf

Distributed reconfiguration of metamorphic robot chains

In this paper we give a new run–time technique for finding an optimal parallel execution schedule for a partially parallel loop, i.e., a loop whose parallelization requires synchronization to ensure that the iterations are executed in the correct order. Given the original loop, the compiler generates inspector code that performs run–time preprocessing of the loop’s access pattern, and scheduler code that schedules (and executes) the loop iterations. The inspector is fully parallel, uses no synchronization, and can be applied to any loop. In addition, it can implement at run–time the two most effective transformations for increasing the amount of parallelism in a loop: array privatization and reduction parallelization (element–wise). We also describe a new scheme for constructing an optimal parallel execution schedule for the iterations of the loop.

/pdf/run-time-methods-for-parallelizing-partially-parallel-loops-3tmi7t4tay.pdf

Nancy M. Amato

Papers

A Machine Learning Approach for Feature-Sensitive Motion Planning.

Better group behaviors in complex environments using global roadmaps

Parallel algorithms for higher-dimensional convex hulls

Distributed reconfiguration of metamorphic robot chains

Run-time methods for parallelizing partially parallel loops