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184
Cacheoblivious priority queue and graph algorithm applications
 In Proc. 34th Annual ACM Symposium on Theory of Computing
, 2002
"... In this paper we develop an optimal cacheoblivious priority queue data structure, supporting insertion, deletion, and deletemin operations in O ( 1 B logM/B N) amortized memory B transfers, where M and B are the memory and block transfer sizes of any two consecutive levels of a multilevel memory hi ..."
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Cited by 68 (9 self)
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In this paper we develop an optimal cacheoblivious priority queue data structure, supporting insertion, deletion, and deletemin operations in O ( 1 B logM/B N) amortized memory B transfers, where M and B are the memory and block transfer sizes of any two consecutive levels of a multilevel memory hierarchy. In a cacheoblivious data structure, M and B are not used in the description of the structure. The bounds match the bounds of several previously developed externalmemory (cacheaware) priority queue data structures, which all rely crucially on knowledge about M and B. Priority queues are a critical component in many of the best known externalmemory graph algorithms, and using our cacheoblivious priority queue we develop several cacheoblivious graph algorithms.
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 67 (25 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, red–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.
On External Memory Graph Traversal
 IN PROC. ACMSIAM SYMP. ON DISCRETE ALGORITHMS
, 2000
"... We describe a new external memory data structure, the buffered repository tree, and use it to provide the first nontrivial external memory algorithm for directed breadthfirst search (BFS) and an improved external algorithm for directed depthfirst search. We also demonstrate the equivalence of var ..."
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Cited by 62 (1 self)
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We describe a new external memory data structure, the buffered repository tree, and use it to provide the first nontrivial external memory algorithm for directed breadthfirst search (BFS) and an improved external algorithm for directed depthfirst search. We also demonstrate the equivalence of various formulations of external undirected BFS, and we use these to give the first I/Ooptimal BFS algorithm for undirected trees.
Outofcore algorithms for scientific visualization and computer graphics
 In Visualization’02 Course Notes
, 2002
"... Recently, several external memory techniques have been developed for a wide variety of graphics and visualization problems, including surface simplification, volume rendering, isosurface generation, ray tracing, surface reconstruction, and so on. This work has had significant impact given that in re ..."
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Cited by 59 (11 self)
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Recently, several external memory techniques have been developed for a wide variety of graphics and visualization problems, including surface simplification, volume rendering, isosurface generation, ray tracing, surface reconstruction, and so on. This work has had significant impact given that in recent years there has been a rapid increase in the raw size of datasets. Several technological trends are contributing to this, such as the development of highresolution 3D scanners, and the need to visualize ASCIsize (Accelerated Strategic Computing Initiative) datasets. Another important push for this kind of technology is the growing speed gap between main memory and caches, which penalizes algorithms that do not optimize for coherence of access. Because of these reasons, much research in computer graphics focuses on developing outofcore (and often cachefriendly) techniques. This paper surveys fundamental issues, current problems, and unresolved questions, and aims to provide graphics researchers and professionals with an effective knowledge of current techniques, as well as the foundation to develop novel techniques on their own. Keywords: Outofcore algorithms, scientific visualization, computer graphics, interactive rendering, volume rendering, surface simplification.
Compressing the graph structure of the web
 In IEEE Data Compression Conference (DCC
, 2001
"... A large amount of research has recently focused on the graph structure (or link structure) of the World Wide Web. This structure has proven to be extremely useful for improving the performance of search engines and other tools for navigating the web. However, since the graphs in these scenarios invo ..."
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Cited by 59 (2 self)
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A large amount of research has recently focused on the graph structure (or link structure) of the World Wide Web. This structure has proven to be extremely useful for improving the performance of search engines and other tools for navigating the web. However, since the graphs in these scenarios involve hundreds of millions of nodes and even more edges, highly spaceefficient data structures are needed to fit the data in memory. A first step in this direction was done by the DEC Connectivity Server, which stores the graph in compressed form. In this paper, we describe techniques for compressing the graph structure of the web, and give experimental results of a prototype implementation. We attempt to exploit a variety of different sources of compressibility of these graphs and of the associated set of URLs in order to obtain good compression performance on a large web graph. 1
Asymptotically Tight Bounds for Performing BMMC Permutations on Parallel Disk Systems
, 1994
"... This paper presents asymptotically equal lower and upper bounds for the number of parallel I/O operations required to perform bitmatrixmultiply/complement (BMMC) permutations on the Parallel Disk Model proposed by Vitter and Shriver. A BMMC permutation maps a source index to a target index by an a ..."
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Cited by 58 (18 self)
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This paper presents asymptotically equal lower and upper bounds for the number of parallel I/O operations required to perform bitmatrixmultiply/complement (BMMC) permutations on the Parallel Disk Model proposed by Vitter and Shriver. A BMMC permutation maps a source index to a target index by an affine transformation over GF (2), where the source and target indices are treated as bit vectors. The class of BMMC permutations includes many common permutations, such as matrix transposition (when dimensions are powers of 2), bitreversal permutations, vectorreversal permutations, hypercube permutations, matrix reblocking, Graycode permutations, and inverse Graycode permutations. The upper bound improves upon the asymptotic bound in the previous best known BMMC algorithm and upon the constant factor in the previous best known bitpermute/complement (BPC) permutation algorithm. The algorithm achieving the upper bound uses basic linearalgebra techniques to factor the characteristic matrix...
STXXL: Standard template library for XXL data sets
 In: Proc. of ESA 2005. Volume 3669 of LNCS
, 2005
"... for processing huge data sets that can fit only on hard disks. It supports parallel disks, overlapping between disk I/O and computation and it is the first I/Oefficient algorithm library that supports the pipelining technique that can save more than half of the I/Os. STXXL has been applied both in ..."
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Cited by 56 (5 self)
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for processing huge data sets that can fit only on hard disks. It supports parallel disks, overlapping between disk I/O and computation and it is the first I/Oefficient algorithm library that supports the pipelining technique that can save more than half of the I/Os. STXXL has been applied both in academic and industrial environments for a range of problems including text processing, graph algorithms, computational geometry, gaussian elimination, visualization, and analysis of microscopic images, differential cryptographic analysis, etc. The performance of STXXL and its applications is evaluated on synthetic and realworld inputs. We present the design of the library, how its performance features are supported, and demonstrate how the library integrates with STL. KEY WORDS: very large data sets; software library; C++ standard template library; algorithm engineering 1.
The Link Database: Fast Access to Graphs of the Web
"... ... graph where URLs are nodes and hyperlinks are directed edges. The Link Database provides fast access to the hyperlinks. To support a wide range of graph algorithms, we find it important to fit the Link Database into memory. In the first version of the Link Database, we achieved this fit by using ..."
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Cited by 50 (2 self)
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... graph where URLs are nodes and hyperlinks are directed edges. The Link Database provides fast access to the hyperlinks. To support a wide range of graph algorithms, we find it important to fit the Link Database into memory. In the first version of the Link Database, we achieved this fit by using machines with lots of memory (8GB), and storing each hyperlink in 32 bits. However, this approach was limited to roughly 100 million Web pages. This paper presents techniques to compress the links to accommodate larger graphs. Our techniques combine wellknown compression methods with methods that depend on the properties of the web graph. The first compression technique takes advantage of the fact that most hyperlinks on most Web pages point to other pages on the same host as the page itself. The second technique takes advantage of the fact that many pages on the same host share hyperlinks, that is, they tend to point to a common set of pages. Together, these techniques reduce space requirements to under 6 bits per link. While (de)compression adds latency to the hyperlink access time, we can still compute the strongly connected components of a 6 billionedge graph in under 20 minutes and run applications such as Kleinberg's HITS in real time. This paper describes our techniques for compressing the Link Database, and provides performance numbers for compression ratios and decompression speed.
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 46 (11 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.
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 37 (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...