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23
ExternalMemory Graph Algorithms
, 1995
"... We present a collection of new techniques for designing and analyzing efficient externalmemory algorithms for graph problems and illustrate how these techniques can be applied to a wide variety of specific problems. Our results include: ffl Proximateneighboring. We present a simple method for der ..."
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Cited by 174 (22 self)
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We present a collection of new techniques for designing and analyzing efficient externalmemory algorithms for graph problems and illustrate how these techniques can be applied to a wide variety of specific problems. Our results include: ffl Proximateneighboring. We present a simple method for deriving externalmemory lower bounds via reductions from a problem we call the "proximate neighbors" problem. We use this technique to derive nontrivial lower bounds for such problems as list ranking, expression tree evaluation, and connected components. ffl PRAM simulation. We give methods for efficiently simulating PRAM computations in external memory, even for some cases in which the PRAM algorithm is not workoptimal. We apply this to derive a number of optimal (and simple) externalmemory graph algorithms. ffl Timeforward processing. We present a general technique for evaluating circuits (or "circuitlike" computations) in external memory. We also use this in a deterministic list rank...
ExternalMemory Algorithms for Processing Line Segments in Geographic Information Systems
, 2007
"... In the design of algorithms for largescale applications it is essential to consider the problem of minimizing I/O communication. Geographical information systems (GIS) are good examples of such largescale applications as they frequently handle huge amounts of spatial data. In this paper we develop ..."
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Cited by 75 (30 self)
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In the design of algorithms for largescale applications it is essential to consider the problem of minimizing I/O communication. Geographical information systems (GIS) are good examples of such largescale applications as they frequently handle huge amounts of spatial data. In this paper we develop efficient externalmemory algorithms for a number of important problems involving line segments in the plane, including trapezoid decomposition, batched planar point location, triangulation, redâ€“blue line segment intersection reporting, and general line segment intersection reporting. In GIS systems the first three problems are useful for rendering and modeling, and the latter two are frequently used for overlaying maps and extracting information from them.
I/O Optimal Isosurface Extraction
, 1997
"... In this paper we give I/Ooptimal techniques for the extraction of isosurfaces from volumetric data, by a novel application of the I/Ooptimal interval tree of Arge and Vitter. The main idea is to preprocess the dataset once and for all to build an efficient search structure in disk, and then each ti ..."
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Cited by 73 (17 self)
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In this paper we give I/Ooptimal techniques for the extraction of isosurfaces from volumetric data, by a novel application of the I/Ooptimal interval tree of Arge and Vitter. The main idea is to preprocess the dataset once and for all to build an efficient search structure in disk, and then each time we want to extract an isosurface, we perform an outputsensitive query on the search structure to retrieve only those active cells that are intersected by the isosurface. During the query operation, only two blocks of main memory space are needed, and only those active cells are brought into the main memory, plus some negligible overhead of disk accesses. This implies that we can efficiently visualize very large datasets on workstations with just enough main memory to hold the isosurfaces themselves. The implementation is delicate but not complicated. We give the first implementation of the I/Ooptimal interval tree, and also implement our methods as an I/O filter for Vtk's isosurface ext...
Efficient External Memory Algorithms by Simulating CoarseGrained Parallel Algorithms
, 2003
"... External memory (EM) algorithms are designed for largescale computational problems in which the size of the internal memory of the computer is only a small fraction of the problem size. Typical EM algorithms are specially crafted for the EM situation. In the past, several attempts have been made to ..."
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Cited by 40 (10 self)
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External memory (EM) algorithms are designed for largescale computational problems in which the size of the internal memory of the computer is only a small fraction of the problem size. Typical EM algorithms are specially crafted for the EM situation. In the past, several attempts have been made to relate the large body of work on parallel algorithms to EM, but with limited success. The combination of EM computing, on multiple disks, with multiprocessor parallelism has been posted as a challenge by the ACMWorking Group on Storage I/O for LargeScale Computing.
Efficient ExternalMemory Data Structures and Applications
, 1996
"... In this thesis we study the Input/Output (I/O) complexity of largescale problems arising e.g. in the areas of database systems, geographic information systems, VLSI design systems and computer graphics, and design I/Oefficient algorithms for them. A general theme in our work is to design I/Oeffic ..."
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Cited by 38 (12 self)
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In this thesis we study the Input/Output (I/O) complexity of largescale problems arising e.g. in the areas of database systems, geographic information systems, VLSI design systems and computer graphics, and design I/Oefficient algorithms for them. A general theme in our work is to design I/Oefficient algorithms through the design of I/Oefficient data structures. One of our philosophies is to try to isolate all the I/O specific parts of an algorithm in the data structures, that is, to try to design I/O algorithms from internal memory algorithms by exchanging the data structures used in internal memory with their external memory counterparts. The results in the thesis include a technique for transforming an internal memory tree data structure into an external data structure which can be used in a batched dynamic setting, that is, a setting where we for example do not require that the result of a search operation is returned immediately. Using this technique we develop batched dynamic external versions of the (onedimensional) rangetree and the segmenttree and we develop an external priority queue. Following our general philosophy we show how these structures can be used in standard internal memory sorting algorithms
I/OEfficient Scientific Computation Using TPIE
 In Proceedings of the Goddard Conference on Mass Storage Systems and Technologies, NASA Conference Publication 3340, Volume II
, 1995
"... In recent years, I/Oefficient algorithms for a wide variety of problems have appeared in the literature. Thus far, however, systems specifically designed to assist programmers in implementing such algorithms have remained scarce. TPIE is a system designed to fill this void. It supports I/Oeff ..."
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Cited by 35 (10 self)
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In recent years, I/Oefficient algorithms for a wide variety of problems have appeared in the literature. Thus far, however, systems specifically designed to assist programmers in implementing such algorithms have remained scarce. TPIE is a system designed to fill this void. It supports I/Oefficient paradigms for problems from a variety of domains, including computational geometry, graph algorithms, and scientific computation. The TPIE interface frees programmers from having to deal not only of explicit read and write calls, but also the complex memory management that must be performed for I/Oefficient computation.
A Transparent Parallel I/O Environment
 In Proc. 1994 DAGS Symposium on Parallel Computation
, 1994
"... We describe TPIE, a Transparent Parallel I/O Environment. TPIE is a system designed to bridge the gap between current theoretical knowledge about the construction of I/Ooptimal algorithms on parallel disk systems and the design and implementation of parallel I/O systems. We discuss the design of ..."
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Cited by 34 (2 self)
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We describe TPIE, a Transparent Parallel I/O Environment. TPIE is a system designed to bridge the gap between current theoretical knowledge about the construction of I/Ooptimal algorithms on parallel disk systems and the design and implementation of parallel I/O systems. We discuss the design of TPIE and its interface, the structure of a typical implementation, applications of the system, our prototype, and future research directions. The initial goal of our work is a prototype system to demonstrate: 1) that optimal algorithms can be made to run efficiently on parallel I/O devices; and 2) that high level hardware independent interfaces to the I/O paradigms required to implement such algorithms can be provided to application programmers. The TPIE interface is designed to be portable across a variety of parallel hardware platforms; thus code that runs efficiently on one machine will run efficiently on others. Longer term goals for TPIE include extending the prototype in ways t...
The I/OComplexity of Ordered BinaryDecision Diagram Manipulation
 UNIVERSITY OF AARHUS
, 1995
"... Ordered BinaryDecision Diagrams (OBDD) are the stateoftheart data structure for boolean function manipulation and there exist several software packages for OBDD manipulation. OBDDs have been successfully used to solve problems in e.g. digitalsystems design, verification and testing, in math ..."
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Cited by 27 (17 self)
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Ordered BinaryDecision Diagrams (OBDD) are the stateoftheart data structure for boolean function manipulation and there exist several software packages for OBDD manipulation. OBDDs have been successfully used to solve problems in e.g. digitalsystems design, verification and testing, in mathematical logic, concurrent system design and in artificial intelligence. The OBDDs used in many of these applications quickly get larger than the avaliable main memory and it becomes essential to consider the problem of minimizing the Input/Output (I/O) communication. In this paper we analyze why existing OBDD manipulation algorithms perform poorly in an I/O environment and develop new I/Oefficient algorithms.
ExternalMemory Algorithms with Applications in Geographic Information Systems
 Algorithmic Foundations of GIS
, 1997
"... In the design of algorithms for largescale applications it is essential to consider the problem of minimizing Input/Output (I/O) communication. Geographical information systems (GIS) are good examples of such largescale applications as they frequently handle huge amounts of spatial data. In this n ..."
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Cited by 26 (9 self)
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In the design of algorithms for largescale applications it is essential to consider the problem of minimizing Input/Output (I/O) communication. Geographical information systems (GIS) are good examples of such largescale applications as they frequently handle huge amounts of spatial data. In this note we survey the recent developments in externalmemory algorithms with applications in GIS. First we discuss the AggarwalVitter I/Omodel and illustrate why normal internalmemory algorithms for even very simple problems can perform terribly in an I/Oenvironment. Then we describe the fundamental paradigms for designing I/Oefficient algorithms by using them to design efficient sorting algorithms. We then go on and survey externalmemory algorithms for computational geometry problems  with special emphasis on problems with applications in GIS  and techniques for designing such algorithms: Using the orthogonal line segment intersection problem we illustrate the distributionsweeping and ...
Experiments on the Practical I/O Efficiency of Geometric Algorithms: Distribution Sweep vs. Plane Sweep
, 1995
"... We present an extensive experimental study comparing the performance of four algorithms for the following orthogonal segment intersection problem: given a set of horizontal and vertical line segments in the plane, report all intersecting horizontalvertical pairs. The problem has important applicati ..."
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Cited by 26 (8 self)
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We present an extensive experimental study comparing the performance of four algorithms for the following orthogonal segment intersection problem: given a set of horizontal and vertical line segments in the plane, report all intersecting horizontalvertical pairs. The problem has important applications in VLSI layout and graphics, which are largescale in nature. The algorithms under evaluation are distribution sweep and three variations of plane sweep. Distribution sweep is specifically designed for the situations in which the problem is too large to be solved in internal memory, and theoretically has optimal I/O cost. Plane sweep is a wellknown and powerful technique in computational geometry, and is optimal for this particular problem in terms of internal computation. The three variations of plane sweep differ by the sorting methods (external vs. internal sorting) used in the preprocessing phase and the dynamic data structures (B tree vs. 234 tree) used in the sweeping ...