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13
Radix Sort For Vector Multiprocessors
 In Proceedings Supercomputing '91
, 1991
"... We have designed a radix sort algorithm for vector multiprocessors and have implemented the algorithm on the CRAY YMP. On one processor of the YMP, our sort is over 5 times faster on large sorting problems than the optimized library sort provided by CRAY Research. On eight processors we achieve a ..."
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Cited by 44 (6 self)
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We have designed a radix sort algorithm for vector multiprocessors and have implemented the algorithm on the CRAY YMP. On one processor of the YMP, our sort is over 5 times faster on large sorting problems than the optimized library sort provided by CRAY Research. On eight processors we achieve an additional speedup of almost 5, yielding a routine over 25 times faster than the library sort. Using this multiprocessor version, we can sort at a rate of 15 million 64bit keys per second. Our sorting algorithm is adapted from a dataparallel algorithm previously designed for a highly parallel Single Instruction Multiple Data (SIMD) computer, the Connection Machine CM2. To develop our version we introduce three general techniques for mapping dataparallel algorithms ontovector multiprocessors. These techniques allow us to fully vectorize and parallelize the algorithm. The paper also derives equations that model the performance of our algorithm on the YMP. These equations are then used t...
An Empirical Assessment of Algorithms for Constructing a Minimum Spanning Tree
, 1994
"... We address the question of theoretical vs. practical behavior of algorithms for the minimum spanning tree problem. We review the factors that influence the actual running time of an algorithm, from choice of language, machine, and compiler, through lowlevel implementation choices, to purely algorit ..."
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Cited by 41 (4 self)
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We address the question of theoretical vs. practical behavior of algorithms for the minimum spanning tree problem. We review the factors that influence the actual running time of an algorithm, from choice of language, machine, and compiler, through lowlevel implementation choices, to purely algorithmic issues. We discuss how to design a careful experimental comparison between various alternatives. Finally, we present the results from a study in which we used: multiple languages, compilers, and machines; all the major variants of the comparisonbased algorithms; and eight varieties of graphs in five families, with sizes of up to 0.5 million vertices (in sparse graphs) or 1.3 million edges (in dense graphs).
HighPerformance Algorithm Engineering for Computational Phylogenetics
 J. Supercomputing
, 2002
"... A phylogeny is the evolutionary history of a group of organisms; systematists (and other biologists) attempt to reconstruct this history from various forms of data about contemporary organisms. Phylogeny reconstruction is a crucial step in the understanding of evolution as well as an important tool ..."
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Cited by 24 (7 self)
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A phylogeny is the evolutionary history of a group of organisms; systematists (and other biologists) attempt to reconstruct this history from various forms of data about contemporary organisms. Phylogeny reconstruction is a crucial step in the understanding of evolution as well as an important tool in biological, pharmaceutical, and medical research. Phylogeny reconstruction from molecular data is very difficult: almost all optimization models give rise to NPhard (and thus computationally intractable) problems. Yet approximations must be of very high quality in order to avoid outright biological nonsense. Thus many biologists have been willing to run farms of processors for many months in order to analyze just one dataset. Highperformance algorithm engineering offers a battery of tools that can reduce, sometimes spectacularly, the running time of existing phylogenetic algorithms, as well as help designers produce better algorithms. We present an overview of algorithm engineering techniques, illustrating them with an application to the "breakpoint analysis" method of Sankoff et al., which resulted in the GRAPPA software suite. GRAPPA demonstrated a speedup in running time by over eight orders of magnitude over the original implementation on a variety of real and simulated datasets. We show how these algorithmic engineering techniques are directly applicable to a large variety of challenging combinatorial problems in computational biology.
An Empirical Analysis of Algorithms for Constructing a Minimum Spanning Tree
 DIMACS Series in Discrete Mathematics and Theoretical Computer Science
, 1991
"... We compare algorithms for the construction of a minimum spanning tree through largescale experimentation on randomly generated graphs of different structures and different densities. In order to extrapolate with confidence, we use graphs with up to 130,000 nodes (sparse) or 750,000 edges (dense). A ..."
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Cited by 21 (1 self)
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We compare algorithms for the construction of a minimum spanning tree through largescale experimentation on randomly generated graphs of different structures and different densities. In order to extrapolate with confidence, we use graphs with up to 130,000 nodes (sparse) or 750,000 edges (dense). Algorithms included in our experiments are Prim's algorithm (implemented with a variety of priority queues), Kruskal's algorithm (using presorting or demand sorting), Cheriton and Tarjan's algorithm, and Fredman and Tarjan 's algorithm. We also ran a large variety of tests to investigate lowlevel implementation decisions for the data structures, as well as to enable us to eliminate the effect of compilers and architectures. Within the range of sizes used, Prim's algorithm, using pairing heaps or sometimes binary heaps, is clearly preferable. While versions of Prim's algorithm using efficient implementations of Fibonacci heaps or rankrelaxed heaps often approach and (on the densest graphs) so...
How to Find a Minimum Spanning Tree in Practice
 results and New Trends in Computer Science, volume 555 of Lecture Notes in Computer Science
, 1991
"... We address the question of theoretical vs. practical behavior of algorithms for the minimum spanning tree problem. We review the factors that influence the actual running time of an algorithm, from choice of language, machine, and compiler, through lowlevel implementation choices, to purely algor ..."
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Cited by 3 (0 self)
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We address the question of theoretical vs. practical behavior of algorithms for the minimum spanning tree problem. We review the factors that influence the actual running time of an algorithm, from choice of language, machine, and compiler, through lowlevel implementation choices, to purely algorithmic issues. We discuss how to design a careful experimental comparison between various alternatives. Finally, we present some results from an ongoing study in which we are using: multiple languages, compilers, and machines; all the major variants of the comparisonbased algorithms; and eight varieties of graphs with sizes of up to 130,000 vertices (in sparse graphs) or 750,000 edges (in dense graphs). 1 Introduction Finding spanning trees of minimum weight (minimum spanning trees or MSTs) is one of the best known graph problems; algorithms for this problem have a long history, for which see the article of Graham and Hell [6]. The best comparisonbased algorithm to date, due to Gabow...
clauses and featurestructure logic: Principles and unification algorithms, LLI
, 1993
"... The desirability of Horn clauses in logical deductive systems has long been recognized. The reasons are at least threefold. Firstly, while inference algorithms for full logics of any reasonable extent are typically intractable, for systems restricted to Horn clauses the picture is much better. (For ..."
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Cited by 1 (1 self)
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The desirability of Horn clauses in logical deductive systems has long been recognized. The reasons are at least threefold. Firstly, while inference algorithms for full logics of any reasonable extent are typically intractable, for systems restricted to Horn clauses the picture is much better. (For example, in ordinary propositional logic, while the full satisfiability problem is NPcomplete, a lineartime algorithm exists for Horn clauses.) Secondly, the knowledgerepresentation capabilities of Horn clauses, while weaker than those of the full logic, remain remarkably rich; indeed, far richer than that of simple conjunctive logic alone. Thirdly, Horn clauses define the maximal subset of a full logic which has the property of admitting generic models, which roughly means that for any set of Horn clauses, there is a least model of the clauses in that set. It is the purpose of this paper to initiate an investigation of Horn clause logic for an extended class of feature structures. After laying the groundwork for this context, we provide two key results. In the first, we show how the property of admitting
Modular Computer Aided Field Modeling Of Spatial Power Combining Systems
, 1997
"... PATWARDHAN, JAEE. Modular Computer Aided Field Modeling of Spatial Power Combining Systems. (Under the direction of Michael B. Steer.) In this thesis a electromagnetic simulator program is further enhanced and made suitable for a user friendly environment. This electromagnetic simulator tool is cap ..."
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PATWARDHAN, JAEE. Modular Computer Aided Field Modeling of Spatial Power Combining Systems. (Under the direction of Michael B. Steer.) In this thesis a electromagnetic simulator program is further enhanced and made suitable for a user friendly environment. This electromagnetic simulator tool is capable of analyzing any user drawn structures in CIF format. It uses the Galerkin moment method technique with subdomain sinusoidal basis functions for modeling electromagnetic structures. This tool basically consists of three main modules, the C shell which is the main controlling module and which interfaces with all the other modules of the simulator and which is the main focus of this thesis. This is the geometry interface of the simulator capable of interpreting geometric information from the CIF translator and passing it to the FORTRAN field simulator. The FORTRAN module which actually performs the moment method analysis was also developed at the Electronic Research Laboratory. The final...
MC Slicing for Volume Rendering Applications
"... Abstract. Recent developments in volume visualization using standard graphics hardware provide an effective and interactive way to understand and interpret the data. Mainly based on 3d texture mapping, these hardwareaccelerated visualization systems often use a cellprojection method based on a tet ..."
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Abstract. Recent developments in volume visualization using standard graphics hardware provide an effective and interactive way to understand and interpret the data. Mainly based on 3d texture mapping, these hardwareaccelerated visualization systems often use a cellprojection method based on a tetrahedral decomposition of volumes usually sampled as a regular lattice. On the contrary, the method we address in this paper considers the slicing problem as a restricted solution of the marching cubes algorithm [1, 2]. Our solution is thus simple, elegant and fast. The nature of the intersection polygons provides us with the opportunity to retain only 4 of the 15 canonical configurations defined by Lorensen and Cline and to propose a special lookup table. 1
Pacific Symposium on Biocomputing 6:583594 (2001) A New Implementation and Detailed Study of Breakpoint Analysis
"... Phylogenies derived from gene order data may prove crucial in answering some fundamental open questions in biomolecular evolution. Yet very few techniques are available for such phylogenetic reconstructions. One method is breakpoint analysis, developed by Blanchette and Sankoff for solving the “brea ..."
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Phylogenies derived from gene order data may prove crucial in answering some fundamental open questions in biomolecular evolution. Yet very few techniques are available for such phylogenetic reconstructions. One method is breakpoint analysis, developed by Blanchette and Sankoff for solving the “breakpoint phylogeny. ” Our earlier studies �� � confirmed the usefulness of this approach, but also found that BPAnalysis, the implementation developed by Sankoff and Blanchette, was too slow to use on all but very small datasets. We report here on a reimplementation ofBPAnalysis using the principles of algorithmic engineering. Our faster (by 2 to 3 orders of magnitude) and flexible implementation allowed us to conduct studies on the characteristics of breakpoint analysis, in terms of running time, quality, and robustness, as well as to analyze datasets that had so far been considered out of reach. We report on these findings and also discuss future directions for our new implementation. 1