AN INTERACTIVE ENVIRONMENT TO MANIPULATE LARGE GRAPHS (2009)
Interactive environments such as MATLAB and STAR-P have made numerical computing tremendously accessible to engineers and scientists. They allow people are not well–versed in the art of numerical...
OBTAINING BOUNDS ON THE TWO NORM OF A MATRIX FROM THE SPLITTING LEMMA (2008)
Doron Chen, John R. Gilbert, Sivan Toledo
Abstract. The splitting lemma is one of the two main tools of support theory, a framework for bounding the condition number of definite and semidefinite preconditioned linear systems. The splitting...
Timothy A. Davis, John R. Gilbert, Stefan I. Larimore, Esmond G. Ng
Sparse Gaussian elimination with partial pivoting computes the factorization PAQ = LU of a sparse matrix A, where the row ordering P is selected during factorization using standard partial pivoting...
AN INTERACTIVE ENVIRONMENT TO MANIPULATE LARGE GRAPHS (2008)
Interactive environments such as MATLAB and STAR-P have made numerical computing tremendously accessible to engineers and scientists. They allow people who are not well– versed in the art of...
Fast Sorting on a Distributed-Memory Architecture (2008)
David R. Cheng, Viral Shah, John R. Gilbert, Alan Edelman
Abstract — We consider the often-studied problem of sorting, for a parallel computer. Given an input array distributed evenly over p processors, the task is to compute the sorted output array, also...
Yi-ju Li, Sofia A. Oliveira, Puting Xu, Eden R. Martin, Judith E. Stenger, Clemens R. Scherzer, ...
† These authors contributed equally to the manuscript.
High–performance graph algorithms from parallel sparse (2008)
John R. Gilbert, Steven Reinhardt, Viral Shah
matrices
Timothy A. Davis, John R. Gilbert, Stefan I. Larimore, Esmond G. Ng
Two codes are discussed, COLAMD and SYMAMD, that compute approximate minimum degree orderings for sparse matrices in two contexts: (1) sparse partial pivoting, which requires a sparsity preserving...
Fast Sorting on a Distributed-Memory Architecture (2008)
David R. Cheng, Viral Shah, John R. Gilbert, Alan Edelman
Abstract — The abstract goes here.
OBTAINING BOUNDS ON THE TWO NORM OF A MATRIX FROM THE SPLITTING LEMMA ∗ (2008)
Doron Chen, John R. Gilbert, Sivan Toledo
Abstract. The splitting lemma is one of the two main tools of support theory, a framework for bounding the condition number of definite and semidefinite preconditioned linear systems. The splitting...
On the Representation and Multiplication of Hypersparse Matrices (2008)
Multicore processors are marking the beginning of a new era of computing where massive parallelism is available and necessary. Slightly slower but easy to parallelize kernels are becoming more...
Siddhartha Chatterjee, John R. Gilbert, Leonid Oliker, Robert Schreiber, Thomas J. Sheffler, Prof Siddhartha Chatterjee
'95 conferences. y
Toward an Efficient Column Minimum Degree Code for Symmetric Multiprocessors (2007)
Tzu-yi Chen, John R. Gilbert, Sivan Toledo
Ordering the columns of a nonsymmetric sparse matrix can reduce the fill created in its factorization. Minimum-degree is a popular heuristic for ordering symmetric matrices; a variant that can be...
James W. Demmel, Stanley C. Eisenstat, John R. Gilbert, Xiaoye S. Li
Abstract. We investigate several ways to improve the performance of sparse LU factorization with partial pivoting, as used to solve unsymmetric linear systems. We introduce the notion of unsymmetric...
Eric J. Schwabe, Guy E. Blelloch, Anja Feldmann, Omar Ghattas, John R. Gilbert, David R. O'hallaron, ...
This paper is a report on ongoing work in developing automated systems for the partitioning, placement, and routing of data that is necessary for the efficient parallel solution of large problems in...
Hans L. Bodlaender, John R. Gilbert
Various parameters of graphs connected to sparse matrix factorization and other applications can be approximated using an algorithm of Leighton et al. that finds vertex separators of graphs. The...
Modeling programmer workflows with Timed Markov Models (2007)
Andrew Funk, John R. Gilbert, David Mizell, Viral Shah
Software development is a complex process. Many factors influence programmer productivity – experience, choice of programming language, etc. – but comparisons of their effects are primarily...
A Novel Parallel Sorting Algorithm for Contemporary Architectures (2007)
David R. Cheng, Viral B. Shah, John R. Gilbert, Alan Edelman
Traditionally, the field of scientific computing has been dominated by numerical methods. However, modern scientific codes often combine numerical methods with combinatorial methods. Sorting, a...
A comparative analysis of the information content in long and short SAGE libraries (2006)
Li, Yi-Ju, Xu, Puting, Qin, Xuejun, Schmechel, Donald E, Hulette, Christine M, Haines, Jonathan L, ...
Abstract Background Serial Analysis of Gene Expression (SAGE) is a powerful tool to determine gene expression profiles. Two types of SAGE libraries, ShortSAGE and LongSAGE, are classified based on...
Sage Libraries, Yi-ju Li, Puting Xu, Xuejun Qin, Donald E Schmechel, Christine M Hulette, ...
© 2006 Li et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License
Fast Sorting on a Distributed-Memory Architecture (2004)
Cheng, David R., Shah, Viral, Gilbert, John R., Edelman, Alan
We consider the often-studied problem of sorting, for a parallel computer. Given an input array distributed evenly over p processors, the task is to compute the sorted output array, also distributed...
Fast Sorting on a Distributed-Memory Architecture (2004)
Cheng, David R., Shah, Viral, Gilbert, John R., Edelman, Alan
We consider the often-studied problem of sorting, for a parallel computer. Given an input array distributed evenly over p processors, the task is to compute the sorted output array, also distributed...
Schmidt, Silke, Scott, William K, Postel, Eric A, Agarwal, Anita, Hauser, Elizabeth R, De La Paz, Monica A, ...
Abstract Background Age-related macular degeneration (AMD) is a complex disorder that is responsible for the majority of central vision loss in older adults living in developed countries. Phenotypic...
Star-P: High productivity parallel computing (2004)
Ron Choy, Alan Edelman, John R. Gilbert, Viral Shah, David Cheng
Star-P ‡ is an interactive parallel scientific computing environment. It aims to make parallel programming more accessible. Star-P borrows ideas from Matlab*P [3], but is a new development....
Sparse matrices in Matlab*P: Design and implementation (2004)
Abstract. Matlab*P is a flexible interactive system that enables computational scientists and engineers to use a high-level language to program cluster computers. The Matlab*P user writes code in the...
Li, Yi-Ju, Oliveira, Sofia A., Xu, Puting, Martin, Eden R., Stenger, Judith E., Hulette, Christine, ...
Li, Yi-Ju, Oliveira, Sofia A., Xu, Puting, Martin, Eden R., Stenger, Judith E., Scherzer, Clemens R., ...
We previously reported genetic linkage of loci controlling age-at-onset in Alzheimer disease (AD) and Parkinson disease (PD) to a 15 cM region on chromosome 10q. Given the large number of genes in...
Li, Yi-Ju, Oliveira, Sofia A., Xu, Puting, Martin, Eden R., Stenger, Judith E., Scherzer, Clemens R., ...
We previously reported genetic linkage of loci controlling age-at-onset in Alzheimer disease (AD) and Parkinson's disease (PD) to a 15 cM region on chromosome 10q. Given the large number of...
Li, Yi-Ju, Oliveira, Sofia A., Xu, Puting, Martin, Eden R., Stenger, Judith E., Scherzer, Clemens R., ...
We previously reported genetic linkage of loci controlling age-at-onset in Alzheimer disease (AD) and Parkinson disease (PD) to a 15 cM region on chromosome 10q. Given the large number of genes in...
Variations of a Pebble Game on Graphs. (2002)
Gilbert,John R., Tarjan,Robert E.
Two variations are examined of a one-person pebble game played on directed graphs, which has been studied as a model of register allocation. The black-white pebble game of Cook and Sethi is shown to...
A Note on the Column Elimination Tree (2001)
Gilbert, John R., Grigori, Laura
This short communication considers the LU factorization with partial pivoting and shows that an all-at-once result is possible for the structure prediction of the column dependencies in L and U....
A Note on the Column Elimination Tree (2001)
Gilbert, John R., Grigori, Laura
This short communication considers the LU factorization with partial pivoting and shows that an all-at-once result is possible for the structure prediction of the column dependencies in L and U....
A Note on the Column Elimination Tree (2001)
Gilbert, John R., Grigori, Laura
This short communication considers the LU factorization with partial pivoting and shows that an all-at-once result is possible for the structure prediction of the column dependencies in L and U....
Computing row and column counts for sparse QR and LU factorization (2001)
John R. Gilbert, Xiaoye S. Li, Esmond G. Ng, Barry W. Peyton
We present algorithms to determine the number of nonzeros in each row and column of the factors of a sparse matrix, for both the QR factorization and the LU factorization with partial pivoting. The...
Support-graph preconditioners (2001)
Marshall Bern, John R. Gilbert, Bruce Hendrickson, Nhat Nguyen
Abstract. We present a little-known preconditioning technique, called support-graph preconditioning, and use it to analyze two classes of preconditioners. The technique was first described in a talk...
Support-graph preconditioners (2001)
Marshall Bern, John R. Gilbert, Bruce Hendrickson, Nhat Nguyen
Abstract. We present a preconditioning technique, called support-graph preconditioning, and use it to analyze two classes of preconditioners. The technique was first described in a talk by Pravin...
Myotilin is mutated in limb girdle muscular dystrophy 1A (2000)
Hauser, Michael A., Horrigan, Stephen K., Salmikangas, Paula, Torian, Udana M., Viles, Kristi D., Dancel, Ria, ...
We have identified a mutation in the myotilin gene in a large North American family of German descent expressing an autosomal dominant form of limb girdle muscular dystrophy (LGMD1A). We have...
An asynchronous parallel supernodal algorithm for sparse Gaussian elimination (1999)
James W. Demmel, John R. Gilbert, Xiaoyes. Li
Abstract. Although Gaussian elimination with partial pivoting is a robust algorithm to solve unsymmetric sparse linear systems of equations, it is difficult to implement efficiently on parallel...
A supernodal approach to sparse partial pivoting (1999)
James W. Demmel, Stanley C. Eisenstat, John R. Gilbert, Xiaoye S. Li
We investigate several ways to improve the performance of sparse LU factorization with partial pivoting, as used to solve unsymmetric linear systems. To perform most of the numerical computation in...
A supernodal approach to sparse partial pivoting (1999)
James W. Demmel, Stanley C. Eisenstat, John R. Gilbert, Xiaoye S. Li
We investigate several ways to improve the performance of sparse LU factorization with partial pivoting, as used to solve unsymmetric linear systems. To perform most of the numerical computation in...
Toward an efficient column minimum degree code for symmetric multiprocessors (1999)
Tzu-yi Chen, John R. Gilbert, Sivan Toledo
Ordering the columns of a nonsymmetric sparse matrix can reduce the fill created in its factorization. Minimum-degree is a popular heuristic for ordering symmetric matrices; a variant that can be...
James W. Demmel, John R. Gilbert, Xiaoye S. Li
This document describes a collection of three related ANSI C subroutine libraries for solving sparse linear systems of equations AX = B. Here A is a square, nonsingular, n \Theta n sparse matrix, and...
High-Performance Out-of-Core Sparse LU Factorization (1999)
We present an out-of-core sparse nonsymmetric LU-factorization algorithm with partial pivoting. We have implemented the algorithm and our experiments show that it can easily factor matrices whose...
A supernodal approach to sparse partial pivoting (1999)
James W. Demmel, Stanley C. Eisenstat, John R. Gilbert, Xiaoyes. Li
Abstract. We investigate several ways to improve the performance of sparse LU factorization with partial pivoting, as used to solve unsymmetric linear systems. We introduce the notion of unsymmetric...
Flume Computer-Aided Design (CAD): Integrated CAD for Microflume Components and Systems (1998)
Gilbert, John R., Deshpande, Manish
This effort was aimed at developing a computer-aided design (CAD) system to allow start-to-finish design of a broad class of micromechanical fluid systems. The NetFlow program, previously completed...
Star-P: High Productivity Parallel Computing (1998)
Choy, Ron, Edleman, Alan, Gilbert, John R., Shah, Viral, Cheng, David
Star-P is an interactive parallel scientific computing environment. It aims to make parallel programming more accessible. Star-P borrows ideas from Matlab-P, but is a new development. Currently only...
Aspect-oriented programming of sparse matrix code (1997)
John Irwin, John Irwin, Jean-marc Loingtier, Jean-marc Loingtier, John R. Gilbert, John R. Gilbert, ...
the material is concerned, specifically the rights of translation, reprinting, re-use of illustrations, recitation, broadcasting, reproduction on microfilms or in any other way, and storage in data...
An Asynchronous Parallel Supernodal Algorithm for Sparse Gaussian Elimination (1997)
James W. Demmel, John R. Gilbert, Xiaoye S. Li
Although Gaussian elimination with partial pivoting is a robust algorithm to solve unsymmetric sparse linear systems of equations, it is difficult to implement efficiently on parallel machines,...
An assessment of incomplete-LU preconditioners for nonsymmetric linear systems (1997)
We report on an extensive experiment to compare an iterative solver preconditioned by several versions of incomplete LU factorization with a sparse direct solver using LU factorization with partial...
James W. Demmel, John R. Gilbert, Xiaoye S. Li, I Sequential Superlu
Contents I Sequential SuperLU 3 1 Introduction 4 1.1 About SuperLU : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : 4 1.2 Availability : : : : : : : : : : : : : : : : : :...
An Asynchronous Parallel Supernodal Algorithm for Sparse Gaussian Elimination (1997)
James Demmel John, John R. Gilbert, Xiaoye S. Li
Although Gaussian elimination with partial pivoting is a robust algorithm to solve unsymmetric sparse linear systems of equations, it is difficult to implement efficiently on parallel machines,...
An Assessment of Incomplete-LU Preconditioners for Nonsymmetric Linear Systems (1997)
John Gilbert Sivan, John R. Gilbert, Sivan Toledo
. We report on an extensive experiment to compare an iterative solver preconditioned by several versions of incomplete LU factorization with a sparse direct solver using LU factorization with partial...
An Asynchronous Parallel Supernodal Algorithm for Sparse Gaussian Elimination (1997)
James Demmel John, John R. Gilbert, Xiaoye S. Li
Although Gaussian elimination with partial pivoting is a robust algorithm to solve unsymmetric sparse linear systems of equations, it is difficult to implement efficiently on parallel machines,...
An Asynchronous Parallel Supernodal Algorithm for Sparse Gaussian Elimination (1997)
James Demmel, John R. Gilbert, Xiaoye S. Li
Although Gaussian elimination with partial pivoting is a robust algorithm to solve unsymmetric sparse linear systems of equations, it is difficult to implement efficiently on parallel machines,...
James W. Demmel, John R. Gilbert, Xiaoye S. Li
This document describes a collection of three related ANSI C subroutine libraries for solving sparse linear systems of equations AX = B. Here A is a square, nonsingular, n n sparse matrix, and X and...
Direct all correspondence to: (1996)
Siddhartha Chatterjee, John R. Gilbert, Leonid Oliker, Robert Schreiber, Thomas J. Sheffler, Siddhartha Chatterjee, ...
*This work was performed while Chatterjee and Sheffier were postdoctoral scientists at RIACS, and Schreiber was a senior scientist at R1ACS. This work was supported by the NAS Systems Division via...
Sparse Gaussian Elimination on High Performance Computers (1996)
Committee In Charge, Katherine A. Yelick, John R. Gilbert, Phillip Colella, Xiaoye S. Li, Xiaoye S. Li, ...
by
An approximate minimum degree ordering algorithm (1996)
Timothy A. Davis, John R. Gilbert, Stefan I. Larimore, Esmond G. Ng
algorithm
Automated Parallel Solution of Unstructured PDE Problems (1996)
Anja Feldmann, Omar Ghattas, John R. Gilbert, Gary L. Miller, David R. O'hallaron, Eric J. Schwabe, ...
This article describes Archimedes, an automated system for solving partial differential equations on geometrically complex domains using distributed memory supercomputers. The tasks of such a system...
Partitioning Meshes with Lines and Planes (1996)
Feng Cao John, John R. Gilbert, Shang-hua Teng
We investigate several geometric methods for dividing an irregular mesh into pieces of roughly equal size with few interconnecting edges. All these methods are based on cutting a mesh with a line (in...
Automated Parallel Solution of Unstructured PDE Problems (1996)
Anja Feldmann, Omar Ghattas, John R. Gilbert, Gary L. Miller, David R. O'Hallaron, Eric J. Schwabe, ...
This article describes Archimedes, an automated system for solving partial differential equations on geometrically complex domains using distributed memory supercomputers. The tasks of such a system...
Sparse Gaussian Elimination on High Performance Computers (1996)
Katherine A. Yelick, John R. Gilbert, Phillip Colella, Xiaoye S. Li, Xiaoye S. Li, Xiaoye S. Li
Sparse Gaussian Elimination on High Performance Computers by Xiaoye S. Li Doctor of Philosophy in Computer Science University of California at Berkeley James W. Demmel, Chair This dissertation...
Partitioning Meshes with Lines and Planes (1996)
Feng Cao, John R. Gilbert, Shang-Hua Teng
We investigate several geometric methods for dividing an irregular mesh into pieces of roughly equal size with few interconnecting edges. All these methods are based on cutting a mesh with a line (in...
Algorithms for Automatic Alignment of Arrays (1996)
Siddhartha Chatterjee, John R. Gilbert, Leonid Oliker, Robert Schreiber, Thomas J. Sheffler, Prof Siddhartha Chatterjee
Aggregate data objects (such as arrays) are distributed across the processor memories when compiling a data-parallel language for a distributed-memory machine. The mapping determines the amount of...
Aligning parallel arrays to reduce communication (1995)
Thomas J. Sheffler, Robert Schreiber, John R. Gilbert, Siddhartha Chatterjee, Thomas J. Sheffler, Robert Schreiber, ...
Axis and stride alignment is an important optimization in compiling data-parallel programs for distributed-memory machines. We previously developed an optimal algorithm for aligning array...
minimum elimination tree height (1995)
Hans L. Bodlaender, Hans L. Bodlaender, John R. Gilbert, John R. Gilbert, Hjlmtr Hafsteinsson, Hjlmtr Hafsteinsson, ...
We show how the value of various parameters of graphs connected to sparse matrix factorization and other applications can be approximated using an algorithm of Leighton et al. that finds vertex...
Geometric mesh partitioning: Implementation and experiments (1995)
John R. Gilbert, Gary L. Miller, Shang-hua Teng
We investigate a method of dividing an irregular mesh into equal-sized pieces with few interconnecting edges. The method's novel feature is that it exploits the geometric coordinates of the mesh...
A Supernodal Approach to Sparse Partial Pivoting (1995)
James Demmel Stanley, Stanley C. Eisenstat, John R. Gilbert, Xiaoye S. Li
We investigate several ways to improve the performance of sparse LU factorization with partial pivoting, as used to solve unsymmetric linear systems. To perform most of the numerical computation in...
A Supernodal Approach to Sparse Partial Pivoting (1995)
James W. Demmel, Stanley C. Eisenstat, John R. Gilbert, Xiaoye S. Li
We investigate several ways to improve the performance of sparse LU factorization with partial pivoting, as used to solve unsymmetric linear systems. To perform most of the numerical computation in...
Efficient Distribution Analysis via Graph Contraction (1995)
Thomas J. Sheffler, Robert Schreiber, William Pugh, John R. Gilbert, Siddhartha Chatterjee
Alignment and distribution of data by an optimizing compiler is a dream of both manufacturers and users of parallel computers. The distribution problem has been formulated as an NP-complete graph...
Geometric Spectral Partitioning (1995)
Tony F. Chan, John R. Gilbert, Shang-Hua Teng
We investigate a new method for partitioning a graph into two equal-sized pieces with few connecting edges. We combine ideas from two recently suggested partitioning algorithms, spectral bisection...
Generating Local Addresses and Communication Sets for Data-Parallel Programs (1995)
Siddhartha Chatterjee, John R. Gilbert, Robert Schreiber, Shang-Hua Teng, ...
Generating local addresses and communication sets is an important issue in distributedmemory implementations of data-parallel languages such as High Performance Fortran. We demonstrate a storage...
Aligning Parallel Arrays to Reduce Communication (1995)
Thomas J. Sheffler, Robert Schreiber, John R. Gilbert, Siddhartha Chatterjee
Axis and stride alignment is an important optimization in compiling data-parallel programs for distributed-memory machines. We previously developed an optimal algorithm for aligning array...
Array distribution in data-parallel programs (1994)
Siddhartha Chatterjee, John R. Gilbert, Robert Schreiber, Thomas J. Shefl:ler, Siddhartha Chatterjee, John R. Gilbert, ...
We consider dism_oution at compile time of the array data in a distributed-memory implementation of a data-parallel program written in a language like Fortran 90. We allow dynamic redistribution of...
Array distribution in data-parallel programs (1994)
Siddhartha Chatterjee, John R. Gilbert, Robert Schreiber, Thomas J. Sheffler, Siddhartha Chatterjee, John R. Gilbert, ...
We consider distribution at compile time of the array data in a distributed-memory implementation of a data-parallel program written m a language like Fortran 90. We allow dynamic redistribution of...
An Efficient Algorithm to Compute Row and Column Counts for Sparse Cholesky Factorization (1994)
John R. Gilbert, Esmond G. Ng, Barry W. Peyton
Let an undirected graph G be given, along with a specified depthfirst spanning tree T . We give almost-linear-time algorithms to solve the following two problems: First, for every vertex v, compute...
Predicting Structure In Sparse Matrix Computations (1994)
. Many sparse matrix algorithms---for example, solving a sparse system of linear equations---begin by predicting the nonzero structure of the output of a matrix computation from the nonzero structure...
Geometric Spectral Partitioning (1994)
Tony Chan, John R. Gilbert, Shang-hua Teng
We investigate a new method for partitioning a graph into two equal-sized pieces with few connecting edges. We combine ideas from two recently suggested partitioning algorithms, spectral bisection...
Separators in Graphs with Negative and Multiple Vertex Weights (1994)
Hristo N. Djidjev, John R. Gilbert
A separator theorem for a class of graphs asserts that every graph in the class can be divided approximately in half by removing a set of vertices of specified size. Nontrivial separator theorems...
Modeling Data-Parallel Programs with the Alignment-Distribution Graph (1994)
Siddhartha Chatterjee, John R. Gilbert, Robert Schreiber, Thomas J. Sheffler
We present an intermediate representation of a program called the Alignment-Distribution Graph that exposes the communication requirements of the program. The representation exploits ideas developed...
Array Distribution in Data-Parallel Programs (1994)
Siddhartha Chatterjee, John R. Gilbert, Robert Schreiber, Thomas J. Sheffler
We consider distribution at compile time of the array data in a distributed-memory implementation of a dataparallel program written in a language like Fortran 90. We allow dynamic redistribution of...
Elimination Structures For Unsymmetric Sparse LU Factors (1993)
. The elimination tree is central to the study of Cholesky factorization of sparse symmetric positive definite matrices. In this paper, we generalize the elimination tree to a structure appropriate...
Separators and Structure Prediction in Sparse Orthogonal Factorization (1993)
John R. Gilbert, Esmond G. Ng, Barry W. Peyton
In the factorization A = QR of a matrix A, the orthogonal matrix Q can be represented either explicitly (as a matrix) or implicitly (as a matrix H of Householder vectors). We derive both upper and...
Mobile and Replicated Alignment of Arrays in Data-Parallel Programs (1993)
Siddhartha Chatterjee, John R. Gilbert, Robert Schreiber
When a data-parallel language like Fortran 90 is compiled for a distributed-memory machine, aggregate data objects (such as arrays) are distributed across the processor memories. The mapping...
Automatic Array Alignment in Data-Parallel Programs (1993)
Siddhartha Chatterjee John, John R. Gilbert
Data-parallel languages likeFortran 90 express parallelism in the form of operations on data aggregates such as arrays. Misalignment of the operands of an array operation can reduce program...
The Alignment-Distribution Graph (1993)
Siddhartha Chatterjee, John R. Gilbert, Robert Schreiber
Implementing a data-parallel language such as Fortran 90 on a distributed-memory parallel computer requires distributing aggregate data objects (such as arrays) among the memory modules attached to...
The alignment-distribution graph (1993)
Alignment-distribution Graph, Uncl As, Siddhartha Chatterjee, Siddhartha Chatterjee, Siddhartha Chatterjee, John R. Gilbert, ...
Implementing a data-parallel language such as Formm 90 on a distn_outed-memory parallel computer requires distn"outing aggregate data objects (such as arrays) among the memory modules...
Highly parallel sparse Cholesky factorization (1992)
John R. Gilbert, Robert Schreiber
Abstract. We develop and compare several fine-grained parallel algorithms to compute the Cholesky factorization of a sparse matrix. Our experimental implementations are on the Connection Machine, a...
Sparse matrices in MATLAB: Design and implementation (1992)
John R. Gilbert, Cleve Moler, Robert Schreiber
Abstract. 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...
Optimal Evaluation of Array Expressions on Massively Parallel Machines (1992)
Siddhartha Chatterjee Research, Siddhartha Chatterjee, John R. Gilbert, Robert Schreiber, Shang-hua Teng
this article was presented at the Second Workshop on Languages, Compilers, and Runtime Environments for Distributed Memory Multiprocessors, Boulder, Colorado, September 30#October 2, 1992.
Separators in Graphs with Negative and Multiple Vertex Weights (1992)
Hristo Djidjev John, John R. Gilbert
A separator theorem for a class of graphs asserts that every graph in the class can be divided approximately in half by removing a set of vertices of specified size. Nontrivial separator theorems...
Predicting Structure In Nonsymmetric Sparse Matrix Factorizations (1992)
John R. Gilbert, Esmond G. Ng, G. Ng
. Many computations on sparse matrices have a phase that predicts the nonzero structure of the output, followed by a phase that actually performs the numerical computation. We study structure...
Highly parallel sparse Cholesky factorization (1992)
John R. Gilbert, John R. Gilbert, Robert Schreiber, Robert Schreiber
We develop and compare several fine-grained parallel algorithms to compute the Cholesky factorisation of a sparse matrix. Our experi-mental implementations are on the Connection Machine, a...
Sparse Matrices in MATLAB: Design and Implementation (1991)
John R. Gilbert, Cleve Moler, Robert Schreiber
: 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...
Optimal expression evaluation for data parallel architectures (1991)
John R. Gilbert, John R. Gilbert, Robert Schreiber, Robert Schreiber
N92-I1696
Parallel Cholesky Factorization of Sparse Matrices (1987)
Gilbert, John R., Hafsteinsson, Hjalmtyr
We describe a parallel algorithm for finding the Cholesky factorization of a sparse symmetric positive definite matrix A. The algorithm runs in $O(h \log n)$ time with $m\*$ processors, where $h$ is...
Parallel Cholesky Factorization of Sparse Matrices (1987)
Gilbert, John R., Hafsteinsson, Hjalmtyr
We describe a parallel algorithm for finding the Cholesky factorization of a sparse symmetric positive definite matrix A. The algorithm runs in $O(h \log n)$ time with $m\*$ processors, where $h$ is...
A Parallel Graph Partitioning Algorithm for a Message-Passing Multiprocessor (1987)
Gilbert, John R., Zmijewski, Earl
We develop a parallel algorithm for partitioning the vertices of a graph into $p \geq 2$ sets in such a way that few edges connect vertices in different sets. The algorithm is intended for a...
A Parallel Graph Partitioning Algorithm for a Message-Passing Multiprocessor (1987)
Gilbert, John R., Zmijewski, Earl
We develop a parallel algorithm for partitioning the vertices of a graph into $p \geq 2$ sets in such a way that few edges connect vertices in different sets. The algorithm is intended for a...
A Parallel Algorithm for Finding Fill in a Sparse Symmetric Matrix (1986)
Gilbert, John R., Hafsteinsson, Hjalmtyr
We describe a parallel algorithm for finding the fill that occurs when a sparse symmetric positive definite matrix A is factored into its Cholesky factor L. The algorithm is in two steps: First we...
A Parallel Algorithm for Finding Fill in a Sparse Symmetric Matrix (1986)
Gilbert, John R., Hafsteinsson, Hjalmtyr
We describe a parallel algorithm for finding the fill that occurs when a sparse symmetric positive definite matrix A is factored into its Cholesky factor L. The algorithm is in two steps: First we...
Sparse Partial Pivoting in Time Proportional to Arithmetic Operations (1986)
Gilbert, John R., Peierls, Timothy
Existing sparse partial pivoting algorithms can spend asymptomatically more time manipulating data structures than doing arithmetic, although they are tuned to be efficient on many large problems. We...
Sparse Partial Pivoting in Time Proportional to Arithmetic Operations (1986)
Gilbert, John R., Peierls, Timothy
Existing sparse partial pivoting algorithms can spend asymptomatically more time manipulating data structures than doing arithmetic, although they are tuned to be efficient on many large problems. We...
Some Nested Dissection Order is Nearly Optimal (1986)
The minimum fill problem is to reorder the rows and columns of a given sparse symmetric matrix so that its triangular factor is as sparse as possible. Equivalently, it is to find the smallest set of...
Some Nested Dissection Order is Nearly Optimal (1986)
The minimum fill problem is to reorder the rows and columns of a given sparse symmetric matrix so that its triangular factor is as sparse as possible. Equivalently, it is to find the smallest set of...
Predicting Structure in Sparse Matrix Computations (1986)
We describe the results of an experiment in which the Nuprl proof development system was used in conjunction with a collection of simple proof-assisting programs to constructively prove a substantial...
Predicting Structure in Sparse Matrix Computations (1986)
We describe the results of an experiment in which the Nuprl proof development system was used in conjunction with a collection of simple proof-assisting programs to constructively prove a substantial...
A Parallel Algorithm for Large Sparse Cholesky Factorization on a Multiprocessor (1986)
Zmijewski, Earl, Gilbert, John R.
We develop an algorithm for computing the symbolic and numeric Cholesky factorization of a large sparse symmetric positive definite matrix. The algorithm is intended for a message-passing...
A Parallel Algorithm for Large Sparse Cholesky Factorization on a Multiprocessor (1986)
Zmijewski, Earl, Gilbert, John R.
We develop an algorithm for computing the symbolic and numeric Cholesky factorization of a large sparse symmetric positive definite matrix. The algorithm is intended for a message-passing...
Computing a Sparse Basis for the Null Space (1986)
Gilbert, John R., Heath, Michael T.
We present algorithms for computing a sparse basis for the null space of a sparse underdetermined matrix. We describe several possible computational strategies, both combinatorial and...
Computing a Sparse Basis for the Null Space (1986)
Gilbert, John R., Heath, Michael T.
We present algorithms for computing a sparse basis for the null space of a sparse underdetermined matrix. We describe several possible computational strategies, both combinatorial and...
Wide Quotient Trees for Finite Element Problems (1985)
Zmijewski, Earl, Gilbert, John R.
In solving the system of linear equations $Ax = b$ where $A$ is an $n \times n$ large sparse symmetric positive definite matrix, one important objective is to minimize fill. One approach is to...
Wide Quotient Trees for Finite Element Problems (1985)
Zmijewski, Earl, Gilbert, John R.
In solving the system of linear equations $Ax = b$ where $A$ is an $n \times n$ large sparse symmetric positive definite matrix, one important objective is to minimize fill. One approach is to...
Predicting Fill for Sparse Orthogonal Factorization (1983)
Coleman, Thomas F., Edenbrandt, Anders, Gilbert, John R.
In solving large sparse linear least squares problems $Ax \cong b$, several different numeric methods involve computing the same upper triangular factor $R$ of $A$. It is of interest to be able to...
Predicting Fill for Sparse Orthogonal Factorization (1983)
Coleman, Thomas F., Edenbrandt, Anders, Gilbert, John R.
In solving large sparse linear least squares problems $Ax \cong b$, several different numeric methods involve computing the same upper triangular factor $R$ of $A$. It is of interest to be able to...
Graph Coloring Using Eigenvalue Decomposition (1983)
Aspvall, Bengt, Gilbert, John R.
Determining whether the vertices of a graph can be colored using $k$ different colors so that no two adjacent vertices receive the same color is a well-known NP-complete problem. Graph coloring is...
Graph Coloring Using Eigenvalue Decomposition (1983)
Aspvall, Bengt, Gilbert, John R.
Determining whether the vertices of a graph can be colored using $k$ different colors so that no two adjacent vertices receive the same color is a well-known NP-complete problem. Graph coloring is...
A Separator Theorem for Chordal Graphs (1982)
Gilbert, John R., Rose, Donald J.
Chordal graphs are undirected graphs in which every cycle of length at least four has a chord. They are sometimes called rigid circuit graphs or perfect elimination graphs; the last name reflects...
A Separator Theorem for Chordal Graphs (1982)
Gilbert, John R., Rose, Donald J.
Chordal graphs are undirected graphs in which every cycle of length at least four has a chord. They are sometimes called rigid circuit graphs or perfect elimination graphs; the last name reflects...
A Separator Theorem for Graphs of Bounded Genus (1982)
Gilbert, John R., Hutchinson, Joan P., Tarjan, Robert Endre
Many divide-and-conquer algorithms on graphs are based on finding a small set of vertices or edges whose removal divides the graph roughly in half. Most graphs do not have the necessary small...
A Separator Theorem for Graphs of Bounded Genus (1982)
Gilbert, John R., Hutchinson, Joan P., Tarjan, Robert Endre
Many divide-and-conquer algorithms on graphs are based on finding a small set of vertices or edges whose removal divides the graph roughly in half. Most graphs do not have the necessary small...
Schmidt, Silke, Scott, William K, Postel, Eric A, Agarwal, Anita, Hauser, Elizabeth R, De La Paz, Monica A, ...
Martin, Eden R., Lai, Eric H., Gilbert, John R., Rogala, Allison R., Afshari, A. J., Riley, John, ...
There has been great interest in the prospects of using single-nucleotide polymorphisms (SNPs) in the search for complex disease genes, and several initiatives devoted to the identification and...
Investigation of autism and GABA receptor subunit genes in multiple ethnic groups
Collins, Ann L., Ma, Deqiong, Whitehead, Patrice L., Martin, Eden R., Wright, Harry H., Abramson, Ruth K., ...
Autism is a neurodevelopmental disorder of complex genetics, characterized by impairment in social interaction and communication, as well as repetitive behavior. Multiple lines of evidence, including...
Boyles, Abee L., Billups, Ashley V., Deak, Kristen L., Siegel, Deborah G., Mehltretter, Lorraine, Slifer, Susan H., ...
A comparative analysis of the information content in long and short SAGE libraries
Li, Yi-Ju, Xu, Puting, Qin, Xuejun, Schmechel, Donald E, Hulette, Christine M, Haines, Jonathan L, ...
Phenotypic Homogeneity Provides Increased Support for Linkage on Chromosome 2 in Autistic Disorder
Shao, Yujun, Raiford, Kimberly L., Wolpert, Chantelle M., Cope, Heidi A., Ravan, Sarah A., Ashley-Koch, Allison A., ...
Autistic disorder (AutD) is a neurodevelopmental disorder characterized by significant disturbances in social, communicative, and behavioral functioning. A two-stage genomic screen analysis of 99...
Age at Onset in Two Common Neurodegenerative Diseases Is Genetically Controlled
Li, Yi-Ju, Scott, William K., Hedges, Dale J., Zhang, Fengyu, Gaskell, P. Craig, Nance, Martha A., ...
To identify genes influencing age at onset (AAO) in two common neurodegenerative diseases, a genomic screen was performed for AAO in families with Alzheimer disease (AD; n=449) and Parkinson disease...
Schmidt, Silke, Scott, William K, Postel, Eric A, Agarwal, Anita, Hauser, Elizabeth R, De La Paz, Monica A, ...
Ordered-Subsets Linkage Analysis Detects Novel Alzheimer Disease Loci on Chromosomes 2q34 and 15q22
Scott, William K., Hauser, Elizabeth R., Schmechel, Donald E., Welsh-Bohmer, Kathleen A., Small, Gary W., Roses, Allen D., ...
Alzheimer disease (AD) is a complex disorder characterized by a wide range, within and between families, of ages at onset of symptoms. Consideration of age at onset as a covariate in genetic-linkage...
Martin, Eden R., Lai, Eric H., Gilbert, John R., Rogala, Allison R., Afshari, A. J., Riley, John, ...
There has been great interest in the prospects of using single-nucleotide polymorphisms (SNPs) in the search for complex disease genes, and several initiatives devoted to the identification and...
Investigation of autism and GABA receptor subunit genes in multiple ethnic groups
Collins, Ann L., Ma, Deqiong, Whitehead, Patrice L., Martin, Eden R., Wright, Harry H., Abramson, Ruth K., ...
Autism is a neurodevelopmental disorder of complex genetics, characterized by impairment in social interaction and communication, as well as repetitive behavior. Multiple lines of evidence, including...
Boyles, Abee L., Billups, Ashley V., Deak, Kristen L., Siegel, Deborah G., Mehltretter, Lorraine, Slifer, Susan H., ...
A comparative analysis of the information content in long and short SAGE libraries
Li, Yi-Ju, Xu, Puting, Qin, Xuejun, Schmechel, Donald E, Hulette, Christine M, Haines, Jonathan L, ...
Genetic linkage mapping of chromosome 17 markers and neurofibromatosis type 1
Vance, Jeffery M., Pericak-Vance, Margaret A., Yamaoka, Larry H., Speer, Marcy C., Rosenwasser, George O. D., Small, Kent, ...
The von Recklinghausen neurofibromatosis (NF1) gene has been localized to the pericentromeric region of chromosome 17. We have screened six multigenerational families with multiple, tightly linked...
Specific Regional Transcription of Apolipoprotein E in Human Brain Neurons
Xu, Pu-Ting, Gilbert, John R., Qiu, Hui-Ling, Ervin, John, Rothrock-Christian, Tracie R., Hulette, Christine, ...
In central nervous system injury and disease, apolipoprotein E (APOE, gene; apoE, protein) might be involved in neuronal injury and death indirectly through extracellular effects and/or more directly...
Licastro, Federico, Campbell, Iain L., Kincaid, Carrie, Veinbergs, Isaac, Van Uden, Emily, Rockenstein, Edward, ...
This study was designed to explore the possible functional relationships between apolipoprotein E (apoE) and the protease inhibitor α-1-antichymotrypsin in the aging mouse brain and in Alzheimer’s...
Genome-wide Association Study Implicates a Chromosome 12 Risk Locus for Late-Onset Alzheimer Disease
Beecham, Gary W., Martin, Eden R., Li, Yi-Ju, Slifer, Michael A., Gilbert, John R., Haines, Jonathan L., ...
Only Apolipoprotein E polymorphisms have been consistently associated with the risk of late-onset Alzheimer disease (LOAD), but they represent only a minority of the underlying genetic effect. To...