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153
A fast and high quality multilevel scheme for partitioning irregular graphs
 SIAM JOURNAL ON SCIENTIFIC COMPUTING
, 1998
"... Recently, a number of researchers have investigated a class of graph partitioning algorithms that reduce the size of the graph by collapsing vertices and edges, partition the smaller graph, and then uncoarsen it to construct a partition for the original graph [Bui and Jones, Proc. ..."
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Cited by 1178 (16 self)
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Recently, a number of researchers have investigated a class of graph partitioning algorithms that reduce the size of the graph by collapsing vertices and edges, partition the smaller graph, and then uncoarsen it to construct a partition for the original graph [Bui and Jones, Proc.
Parallel Numerical Linear Algebra
, 1993
"... We survey general techniques and open problems in numerical linear algebra on parallel architectures. We first discuss basic principles of parallel processing, describing the costs of basic operations on parallel machines, including general principles for constructing efficient algorithms. We illust ..."
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Cited by 773 (26 self)
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We survey general techniques and open problems in numerical linear algebra on parallel architectures. We first discuss basic principles of parallel processing, describing the costs of basic operations on parallel machines, including general principles for constructing efficient algorithms. We illustrate these principles using current architectures and software systems, and by showing how one would implement matrix multiplication. Then, we present direct and iterative algorithms for solving linear systems of equations, linear least squares problems, the symmetric eigenvalue problem, the nonsymmetric eigenvalue problem, and the singular value decomposition. We consider dense, band and sparse matrices.
LOQO: An interior point code for quadratic programming
, 1994
"... ABSTRACT. This paper describes a software package, called LOQO, which implements a primaldual interiorpoint method for general nonlinear programming. We focus in this paper mainly on the algorithm as it applies to linear and quadratic programming with only brief mention of the extensions to convex ..."
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Cited by 191 (10 self)
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ABSTRACT. This paper describes a software package, called LOQO, which implements a primaldual interiorpoint method for general nonlinear programming. We focus in this paper mainly on the algorithm as it applies to linear and quadratic programming with only brief mention of the extensions to convex and general nonlinear programming, since a detailed paper describing these extensions were published recently elsewhere. In particular, we emphasize the importance of establishing and maintaining symmetric quasidefiniteness of the reduced KKT system. We show that the industry standard MPS format can be nicely formulated in such a way to provide quasidefiniteness. Computational results are included for a variety of linear and quadratic programming problems. 1.
Sparse matrices in Matlab: Design and implementation
, 1991
"... We have extended the matrix computation language and environment Matlab to include sparse matrix storage and operations. The only change to the outward appearance of the Matlab language is a pair of commands to create full or sparse matrices. Nearly all the operations of Matlab now apply equally to ..."
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Cited by 165 (22 self)
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We have extended the matrix computation language and environment Matlab to include sparse matrix storage and operations. The only change to the outward appearance of the Matlab language is a pair of commands to create full or sparse matrices. Nearly all the operations of Matlab now apply equally to full or sparse matrices, without any explicit action by the user. The sparse data structure represents a matrix in space proportional to the number of nonzero entries, and most of the operations compute sparse results in time proportionaltothenumber of arithmetic operations on nonzeros.
An UnsymmetricPattern Multifrontal Method for Sparse LU Factorization
 SIAM J. MATRIX ANAL. APPL
, 1994
"... Sparse matrix factorization algorithms for general problems are typically characterized by irregular memory access patterns that limit their performance on parallelvector supercomputers. For symmetric problems, methods such as the multifrontal method avoid indirect addressing in the innermost loops ..."
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Cited by 151 (27 self)
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Sparse matrix factorization algorithms for general problems are typically characterized by irregular memory access patterns that limit their performance on parallelvector supercomputers. For symmetric problems, methods such as the multifrontal method avoid indirect addressing in the innermost loops by using dense matrix kernels. However, no efficient LU factorization algorithm based primarily on dense matrix kernels exists for matrices whose pattern is very unsymmetric. We address this deficiency and present a new unsymmetricpattern multifrontal method based on dense matrix kernels. As in the classical multifrontal method, advantage is taken of repetitive structure in the matrix by factorizing more than one pivot in each frontal matrix thus enabling the use of Level 2 and Level 3 BLAS. The performance is compared with the classical multifrontal method and other unsymmetric solvers on a CRAY YMP.
A column preordering strategy for the unsymmetricpattern multifrontal method
 ACM Transactions on Mathematical Software
, 2004
"... A new method for sparse LU factorization is presented that combines a column preordering strategy with a rightlooking unsymmetricpattern multifrontal numerical factorization. The column ordering is selected to give a good a priori upper bound on fillin and then refined during numerical factoriza ..."
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Cited by 94 (5 self)
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A new method for sparse LU factorization is presented that combines a column preordering strategy with a rightlooking unsymmetricpattern multifrontal numerical factorization. The column ordering is selected to give a good a priori upper bound on fillin and then refined during numerical factorization (while preserving the bound). Pivot rows are selected to maintain numerical stability and to preserve sparsity. The method analyzes the matrix and automatically selects one of three preordering and pivoting strategies. The number of nonzeros in the LU factors computed by the method is typically less than or equal to those found by a wide range of unsymmetric sparse LU factorization methods, including leftlooking methods and prior multifrontal methods.
X.: Implementation of interior point methods for large scale linear programming
 Interior Point Methods in Mathematical Programming. Kluwer Acad Pub
, 1996
"... ..."
Stochastic Roadmap Simulation: An efficient Representation and Algorithm for Analyzing Molecular Motion
, 2002
"... Classic molecular motion simulation techniques, such as Monte Carlo (MC) simulation, generate motion pathways one at a time and spend most of their time in the local minima of the energy landscape defined over a molecular conformation space. Their high computational cost prevents them from being ..."
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Cited by 69 (16 self)
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Classic molecular motion simulation techniques, such as Monte Carlo (MC) simulation, generate motion pathways one at a time and spend most of their time in the local minima of the energy landscape defined over a molecular conformation space. Their high computational cost prevents them from being used to compute ensemble properties; properties requiring the analysis of many pathways. This paper introduces Stochastic Roadmap Simulation (SRS) as a new computational approach for exploring the kinetics of molecular motion by simultaneously examining multiple pathways. These pathways are compactly encoded in a graph, which is constructed by sampling a molecular conformation space at random. This computation, which does not trace any particular pathway explicitly, circumvents the localminima problem. Each edge in the graph represents a potential transition of the molecule and is associated with a probability indicating the likelihood of this transition. By viewing the graph as a # Department of Electrical Engineering, Stanford University, Stanford CA 94305 + Department of Biochemistry, Stanford University, Stanford CA 94305 # Department of Computer Science, Stanford University, Stanford CA 94305 Department of Computer Science, National University of Singapore, Singapore corresponding author. email : latombe@cs.stanford.edu Address: Department of Computer Science, Stanford University, Stanford CA 94305 Phone: (650) 7230350 Fax: (650) 7251449 # Department of EECS, MIT and Department of HST, Harvard Medical School, Cambridge, MA 02138 Markov chain, ensemble properties can be efficiently computed over the entire molecular energy landscape.
Fast and Effective Algorithms for Graph Partitioning and Sparse Matrix Ordering
 IBM JOURNAL OF RESEARCH AND DEVELOPMENT
, 1996
"... Graph partitioning is a fundamental problem in several scientific and engineering applications. In this paper, we describe heuristics that improve the stateoftheart practical algorithms used in graphpartitioning software in terms of both partitioning speed and quality. An important use of graph ..."
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Cited by 60 (11 self)
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Graph partitioning is a fundamental problem in several scientific and engineering applications. In this paper, we describe heuristics that improve the stateoftheart practical algorithms used in graphpartitioning software in terms of both partitioning speed and quality. An important use of graphpartitioning is in ordering sparse matrices for obtaining direct solutions to sparse systems of linear equations arising in engineering and optimization applications. The experiments reported in this paper show that the use of these heuristics results in a considerable improvement in the quality of sparsematrix orderings over conventional ordering methods, especially for sparse matrices arising in linear programming problems. In addition, our graphpartitioningbased ordering algorithm is more parallelizable than minimumdegreebased ordering algorithms, and it renders the ordered matrix more amenable to parallel factorization.
PTScotch: A tool for efficient parallel graph ordering
"... The parallel ordering of large graphs is a difficult problem, because neither minimumdegree algorithms, nor the best graph partitioning methods that are necessary to nested dissection, parallelize or scale well. This paper presents a set of algorithms, implemented in the PTScotch software package, ..."
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Cited by 57 (5 self)
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The parallel ordering of large graphs is a difficult problem, because neither minimumdegree algorithms, nor the best graph partitioning methods that are necessary to nested dissection, parallelize or scale well. This paper presents a set of algorithms, implemented in the PTScotch software package, which allows one to order large graphs in parallel, yielding orderings the quality of which is equivalent to the one of stateoftheart sequential algorithms.