The in-memory graph layout or organization has a considerable impact on the time and energy efficiency of distributed memory graph computations. It affects memory locality, inter-task load balance, communication time, and overall memory utilization. Graph layout could refer to partitioning or replication of vertex and edge arrays, selective replication of data structures that hold meta-data, and reordering vertex and edge identifiers. In this work, we present DGL, a fast, parallel, and memory-efficient distributed graph layout strategy that is specifically designed for small-world networks (low-diameter graphs with skewed vertex degree distributions). Label propagation-based partitioning and a scalable BFS-based ordering are the main steps in the layout strategy. We show that the DGL layout can significantly improve end-to-end performance of five challenging graph analytics workloads: PageRank, a parallel subgraph enumeration program, tuned implementations of breadth-first search and single-source shortest paths, and RDF3X-MPI, a distributed SPARQL query processing engine. Using these benchmarks, we additionally offer a comprehensive analysis on how graph layout affects the performance of graph analytics with variable computation and communication characteristics.
We selected METIS and RCM for comparison to the partitioning and ordering aspects of , as they represent the most popular and current state-of-the-art approaches for these problems in terms of both speed of computation and quality produced. There are various other partitioning algorithms and methods, including multi-level partitioners similar to METIS @cite_61 @cite_20 @cite_56 , coordinate and geometry-based partitioners @cite_36 , and hypergraph partitioners @cite_30 . Hypergraph partitioners can often calculate higher quality partitions than graph partitioners for regular matrices, but at a considerably higher cost to compute. Other graph partitioners have utilized label propagation in single or multilevel approaches @cite_63 @cite_43 @cite_57 @cite_29 , demonstrating improved algorithm execution times with these partitions versus methods.
@cite_61 @cite_30 @cite_36 @cite_29 @cite_56 @cite_57 @cite_43 @cite_63 @cite_20
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In this work, we show the deficiencies of the graph model for decomposing sparse matrices for parallel matrix-vector multiplication. Then, we propose two hypergraph models which avoid all deficiencies of the graph model. The proposed models reduce the decomposition problem to the well-known hypergraph partitioning problem widely encountered in circuit partitioning in VLSI. We have implemented fast Kernighan-Lin based graph and hypergraph partitioning heuristics and used the successful multilevel graph partitioning tool (Metis) for the experimental evaluation of the validity of the proposed hypergraph models. We have also developed a multilevel hypergraph partitioning heuristic for experimenting the performance of the multilevel approach on hypergraph partitioning. Experimental results on sparse matrices, selected from Harwell-Boeing collection and NETLIB suite, confirm both the validity of our proposed hypergraph models and appropriateness of the multilevel approach to hypergraph partitioning. The balanced graph partitioning consists in dividing the vertices of an undirected graph into a given number of subsets of approximately equal size, such that the number of edges crossing the subsets is minimized. In this work, we present a multilevel memetic algorithm for this NP-hard problem that relies on a powerful grouping recombination operator and a dedicated local search procedure. The proposed operator tends to preserve the backbone with respect to a set of parent individuals, i.e. the grouping of vertices which is same throughout each parent individual. Although our approach requires significantly longer computing time compared to some current state-of-art graph partitioning algorithms such as SCOTCH, METIS, CHACO, JOSTLE, etc., it competes very favorably with these approaches in terms of solution quality. Moreover, it easily reaches or improves on the best partitions ever reported in the literature. In this work, we show that the standard graph-partitioning-based decomposition of sparse matrices does not reflect the actual communication volume requirement for parallel matrix-vector multiplication. We propose two computational hypergraph models which avoid this crucial deficiency of the graph model. The proposed models reduce the decomposition problem to the well-known hypergraph partitioning problem. The recently proposed successful multilevel framework is exploited to develop a multilevel hypergraph partitioning tool PaToH for the experimental verification of our proposed hypergraph models. Experimental results on a wide range of realistic sparse test matrices confirm the validity of the proposed hypergraph models. In the decomposition of the test matrices, the hypergraph models using PaToH and hMeTiS result in up to 63 percent less communication volume (30 to 38 percent less on the average) than the graph model using MeTiS, while PaToH is only 1.3-2.3 times slower than MeTiS on the average. 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.