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

The modern science of networks has brought significant advances to our understanding of complex systems. One of the most relevant features of graphs representing real systems is community structure, or clustering, i. e. the organization of vertices in clusters, with many edges joining vertices of the same cluster and comparatively few edges joining vertices of different clusters. Such clusters, or communities, can be considered as fairly independent compartments of a graph, playing a similar role like, e. g., the tissues or the organs in the human body. Detecting communities is of great importance in sociology, biology and computer science, disciplines where systems are often represented as graphs. This problem is very hard and not yet satisfactorily solved, despite the huge effort of a large interdisciplinary community of scientists working on it over the past few years. We will attempt a thorough exposition of the topic, from the definition of the main elements of the problem, to the presentation of most methods developed, with a special focus on techniques designed by statistical physicists, from the discussion of crucial issues like the significance of clustering and how methods should be tested and compared against each other, to the description of applications to real networks.

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Community detection in graphs

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

Many applications in computer graphics require complex, highly detailed models. However, the level of detail actually necessary may vary considerably. To control processing time, it is often desirable to use approximations in place of excessively detailed models. We have developed a surface simplification algorithm which can rapidly produce high quality approximations of polygonal models. The algorithm uses iterative contractions of vertex pairs to simplify models and maintains surface error approximations using quadric matrices. By contracting arbitrary vertex pairs (not just edges), our algorithm is able to join unconnected regions of models. This can facilitate much better approximations, both visually and with respect to geometric error. In order to allow topological joining, our system also supports non-manifold surface models. CR Categories: I.3.5 [Computer Graphics]: Computational Geometry and Object Modeling—surface and object representations

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Surface simplification using quadric error metrics

Several algorithms for approximating terrains and other height fields using polygonal meshes are described, compared, and optimized. These algorithms take a height field as input, typically a rectangular grid of elevation data H(x, y), and approximate it with a mesh of triangles, also known as a triangulated irregular network, or TIN. The algorithms attempt to minimize both the error and the number of triangles in the approximation. Applications include fast rendering of terrain data for flight simulation and fitting of surfaces to range data in computer vision. The methods can also be used to simplify multi-channel height fields such as textured terrains or planar color images. The most successful method we examine is the greedy insertion algorithm. It begins with a simple triangulation of the domain and, on each pass, finds the input point with highest error in the current approximation and inserts it as a vertex in the triangulation. The mesh is updated either with Delaunay triangulation or with data-dependent triangulation. Most previously published variants of this algorithm had expected time cost of O(mn) or O(n logm+m), where n is the number of points in the input height field and m is the number of vertices in the triangulation. Our optimized algorithm is faster, with an expected cost of O((m+n) logm). On current workstations, this allows one million point terrains to be simplified quite accurately in less than a minute. We are releasing a C++ implementation of our algorithm.

/pdf/fast-polygonal-approximation-of-terrains-and-height-fields-2mp2yluyy2.pdf

Fast Polygonal Approximation of Terrains and Height Fields

Many applications in computer graphics and related fields can benefit from automatic simplification of complex polygonal surface models. Applications are often confronted with either very densely over-sampled surfaces or models too complex for the limited available hardware capacity. An effective algorithm for rapidly producing high-quality approximations of the original model is a valuable tool for managing data complexity. 
In this dissertation, I present my simplification algorithm, based on iterative vertex pair contraction. This technique provides an effective compromise between the fastest algorithms, which often produce poor quality results, and the highest-quality algorithms, which are generally very slow. For example, a 1000 face approximation of a 100,000 face model can be produced in about 10 seconds on a PentiumPro 200. The algorithm can simplify both the geometry and topology of manifold as well as non-manifold surfaces. In addition to producing single approximations, my algorithm can also be used to generate multiresolution representations such as progressive meshes and vertex hierarchies for view-dependent refinement. 
The foundation of my simplification algorithm, is the quadric error metric which I have developed. It provides a useful and economical characterization of local surface shape, and I have proven a direct mathematical connection between the quadric metric and surface curvature. A generalized form of this metric can accommodate surfaces with material properties, such as RGB color or texture coordinates. 
I have also developed a closely related technique for constructing a hierarchy of well-defined surface regions composed of disjoint sets of faces. This algorithm involves applying a dual form of my simplification algorithm to the dual graph of the input surface. The resulting structure is a hierarchy of face clusters which is an effective multiresolution representation for applications such as radiosity.

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Quadric-based polygonal surface simplification

Modern parallel microprocessors deliver high performance on applications that expose substantial fine-grained data parallelism. Although data parallelism is widely available in many computations, implementing data parallel algorithms in low-level languages is often an unnecessarily difficult task. The characteristics of parallel microprocessors and the limitations of current programming methodologies motivate our design of Copperhead, a high-level data parallel language embedded in Python. The Copperhead programmer describes parallel computations via composition of familiar data parallel primitives supporting both flat and nested data parallel computation on arrays of data. Copperhead programs are expressed in a subset of the widely used Python programming language and interoperate with standard Python modules, including libraries for numeric computation, data visualization, and analysis. In this paper, we discuss the language, compiler, and runtime features that enable Copperhead to efficiently execute data parallel code. We define the restricted subset of Python which Copperhead supports and introduce the program analysis techniques necessary for compiling Copperhead code into efficient low-level implementations. We also outline the runtime support by which Copperhead programs interoperate with standard Python modules. We demonstrate the effectiveness of our techniques with several examples targeting the CUDA platform for parallel programming on GPUs. Copperhead code is concise, on average requiring 3.6 times fewer lines of code than CUDA, and the compiler generates efficient code, yielding 45-100% of the performance of hand-crafted, well optimized CUDA code.

/pdf/copperhead-compiling-an-embedded-data-parallel-language-2dk0ppe0k5.pdf

Copperhead: compiling an embedded data parallel language

Many algorithms for reducing the number of triangles in a surface model have been proposed, but to date there has been little theoretical analysis of the approximations they produce. Previously we described an algorithm that simplifies polygonal models using a quadric error metric. This method is fast and produces high quality approximations in practice. Here we provide some theory to explain why the algorithm works as well as it does. Using methods from differential geometry and approximation theory, we show that in the limit as triangle area goes to zero on a differentiable surface, the quadric error is directly related to surface curvature. Also, in this limit, a triangulation that minimizes the quadric error metric achieves the optimal triangle aspect ratio in that it minimizes theL2 geometric error. This work represents a new theoretical approach for the analysis of simplification algorithms. © 1999 Elsevier Science B.V. All rights reserved.

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Optimal triangulation and quadric-based surface simplification

Morse theory reveals the topological structure of a shape based on the critical points of a real function over the shape. A poor choice of this real function can lead to a complex configuration of an unnecessarily high number of critical points. This paper solves a relaxed form of Laplace's equation to find a "fair" Morse function with a user-controlled number and configuration of critical points. When the number is minimal, the resulting Morse complex cuts the shape into a disk. Specifying additional critical points at surface features yields a base domain that better represents the geometry and shares the same topology as the original mesh, and can also cluster a mesh into approximately developable patches. We make Morse theory on meshes more robust with teflon saddles and flat edge collapses, and devise a new "intermediate value propagation" multigrid solver for finding fair Morse functions that runs in provably linear time.

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Michael Garland

Papers

Fast Polygonal Approximation of Terrains and Height Fields

Quadric-based polygonal surface simplification

Copperhead: compiling an embedded data parallel language

Optimal triangulation and quadric-based surface simplification

Fair morse functions for extracting the topological structure of a surface mesh