Sparse Matrix Ordering Research Articles

Neural Acceleration of Graph Based Utility Functions for Sparse Matrices

Many graph-based algorithms in high performance computing (HPC) use approximate solutions due to having algorithms that are computationally expensive or serial in nature. Neural acceleration, i.e., the process of speeding up approximation computation elements via artificial neural networks, is relatively new and has not focused on HPC graph-based algorithms. In this paper, we propose a starting point for applying models for neural acceleration to graph-based HPC algorithms utilizing an understanding of the connectivity computational pattern, recursive neural networks, and graph neural networks. We demonstrate these techniques on the problem related to the utility functions of sparse matrix ordering and fill-in (i.e., zero elements becoming nonzero during factorization) calculations. The problem of sparse matrix ordering is commonly used for issues related to load balancing, improving memory reuse, or reducing computational and memory costs in direct sparse linear solver methods. These utility functions are ideal for demonstration as they comprise a number of different graph-based subproblems, and thus demonstrate the usefulness of our method over a wide range. We show that we can accurately approximate the best ordering and the nonzero count of the sparse factorization matrix while speeding up the calculation by as much as 30.3× over the traditional serial method.

PMORSy: parallel sparse matrix ordering software for fill-in minimization

In this paper we present PMORSy—a new parallel software package for symmetric sparse matrix ordering on shared memory systems. The NP-complete fill-in minimization problem is solved by means of multilevel nested dissection algorithm with modifications for vertex separators. Parallel processing is done in a task-based fashion with the granularity tuning. We employ threading techniques on shared memory using OpenMP 3.0 technology as opposed to the Message Passing Interface-based approach widely used for parallel sparse matrix ordering. Experimental results on symmetric matrices from the University of Florida Sparse Matrix Collection and matrices from finite-element analysis of three-dimensional strength problems show that our implementation is competitive to the ParMETIS and PT-Scotch libraries both in ordering quality and performance. The PMORSy library is publicly available from the Lobachevsky State University Supercomputing Center web-site.

On sparse matrix orderings in interior point methods

The major computational task of most interior point implementations is solving systems of equations with symmetric coefficient matrix by direct factorization methods, therefore, the performance of Cholesky-like factorizations is a critical issue. In the case of sparse and large problems the efficiency of the factorizations is closely related to the exploitation of the nonzero structure of the problem. A number of techniques were developed for fill-reducing sparse matrix orderings which make Cholesky factorizations more efficient by reducing the necessary floating point computations. We present a variant of the nested dissection algorithm incorporating special techniques that are beneficial for graph partitioning problems arising in the ordering step of interior point implementations. We illustrate the behavior of our algorithm and provide numerical results and comparisons with other sparse matrix ordering algorithms.

Fast recommendation on bibliographic networks with sparse-matrix ordering and partitioning

Graphs and matrices are widely used in algorithms for social network analyses. Since the number of interactions is much less than the possible number of interactions, the graphs and matrices used in the analyses are usually sparse. In this paper, we propose an efficient implementation of a sparse-matrix computation which arises in our publicly available citation recommendation service theadvisor as well as in many other recommendation systems. The recommendation algorithm uses a sparse matrix generated from the citation graph. We observed that the nonzero pattern of this matrix is highly irregular and the computation suffers from high number of cache misses. We propose techniques for storing the matrix in memory efficiently and we reduced the number of cache misses with ordering and partitioning. Experimental results show that our techniques are highly efficient in reducing the query processing time which is highly crucial for a web service.

Seriation in the Presence of Errors: NP-Hardness of l ∞ -Fitting Robinson Structures to Dissimilarity Matrices

In this paper, we establish that the following fitting problem is NP-hard: given a finite set X and a dissimilarity measure d on X (d is a symmetric function from X2 to the nonnegative real numbers and vanishing on the diagonal), we wish to find a Robinsonian dissimilarity dR on X minimizing the l∞-error ||d − d R||∞ = maxx,y∈X{|d(x, y) − dR(x, y)|} between d and dR. Recall that a dissimilarity dR on X is called monotone (or Robinsonian) if there exists a total order ≺ on X such that x ≺ z ≺ y implies that d(x, y) ≥ max{d(x, z), d(z, y)}. The Robinsonian dissimilarities appear in seriation and clustering problems, in sparse matrix ordering and DNA sequencing.

Towards a Tighter Coupling of Bottom-Up and Top-Down Sparse Matrix Ordering Methods

Most state-of-the-art ordering schemes for sparse matrices are a hybrid of a bottom-up method such as minimum degree and a top-down scheme such as George's nested dissection. In this paper we present an ordering algorithm that achieves a tighter coupling of bottom-up and top-down methods. In our methodology vertex separators are interpreted as the boundaries of the remaining elements in an unfinished bottom-up ordering. As a consequence, we are using bottom-up techniques such as quotient graphs and special node selection strategies for the construction of vertex separators. Once all separators have been found, we are using them as a skeleton for the computation of several bottom-up orderings. Experimental results show that the orderings obtained by our scheme are in general better than those obtained by other ordering codes.

Hybridizing nested dissection and halo approximate minimum degree for efficient sparse matrix ordering

Minimum degree and nested dissection are the two most popular reordering schemes used to reduce fill-in and operation count when factoring and solving sparse matrices. Most of the state-of-the-art ordering packages hybridize these methods by performing incomplete nested dissection and ordering by minimum degree the subgraphs associated with the leaves of the separation tree, but most often only loose couplings have been achieved, resulting in poorer performance than could have been expected. This paper presents a tight coupling of the nested dissection and halo approximate minimum degree algorithms, which allows the minimum degree algorithm to use exact degrees on the boundaries of the subgraphs passed to it and to yield back not only the ordering of the nodes of the subgraph, but also the amalgamated assembly subtrees, for efficient block computations. Experimental results show the performance improvement of this hybridization, both in terms of fill-in reduction and increase of concurrency on a parallel sparse block symmetric solver. Copyright © 2000 John Wiley & Sons, Ltd.

A Parallel Algorithm for Multilevel Graph Partitioning and Sparse Matrix Ordering

In this paper we present a parallel formulation of the multilevel graph partitioning and sparse matrix ordering algorithm. A key feature of our parallel formulation (that distinguishes it from other proposed parallel formulations of multilevel algorithms) is that it partitions the vertices of the graph intopparts while distributing the overall adjacency matrix of the graph among allpprocessors. This mapping results in substantially smaller communication than one-dimensional distribution for graphs with relatively high degree, especially if the graph is randomly distributed among the processors. We also present a parallel algorithm for computing a minimal cover of a bipartite graph which is a key operation for obtaining a small vertex separator that is useful for computing the fill reducing ordering of sparse matrices. Our parallel algorithm achieves a speedup of up to 56 on 128 processors for moderate size problems, further reducing the already moderate serial run time of multilevel schemes. Furthermore, the quality of the produced partitions and orderings are comparable to those produced by the serial multilevel algorithm that has been shown to outperform both spectral partitioning and multiple minimum degree.