Computational methods for finding long simple cycles in complex networks

© 2017 Elsevier B.V. Detection of long simple cycles in real-world complex networks finds many applications in layout algorithms, information flow modelling, as well as in bioinformatics. In this paper, we propose two computational methods for finding long cycles in real-world networks. The first method is an exact approach based on our own integer linear programming formulation of the problem and a data mining pipeline. This pipeline ensures that the problem is solved as a sequence of integer linear programs. The second method is a multi-start local search heuristic, which combines an initial construction of a long cycle using depth-first search with four different perturbation operators. Our experimental results are presented for social network samples, graphs studied in the network science field, graphs from DIMACS series, and protein-protein interaction networks. These results show that our formulation leads to a significantly more efficient exact approach to solve the problem than a previous formulation. For 14 out of 22 networks, we have found the optimal solutions. The potential of heuristics in this problem is also demonstrated, especially in the context of large-scale problem instances

Hybrid Bridge-Based Memetic Algorithms for Finding Bottlenecks in Complex Networks

We propose a memetic approach to find bottlenecks in complex networks based on searching for a graph partitioning with minimum conductance. Finding the optimum of this problem, also known in statistical mechanics as the Cheeger constant, is one of the most interesting NP-hard network optimisation problems. The existence of low conductance minima indicates bottlenecks in complex networks. However, the problem has not yet been explored in depth in the context of applied discrete optimisation and evolu- tionary approaches to solve it. In this paper, the use of a memetic frame- work is explored to solve the minimum condutance problem. The approach combines a hybrid method of initial population generation based on bridge identification and local optima sampling with a steady-state evolutionary process with two local search subroutines. These two local search subrou- tines have complementary qualities. Efficiency of three crossover operators is explored, namely one-point crossover, uniform crossover, and our own par- tition crossover. Experimental results are presented for both artificial and real-world complex networks. Results for Barab ́asi-Albert model of scale-free networks are presented, as well as results for samples of social networks and protein-protein interaction networks. These indicate that both well-informed initial population generation and the use of a crossover seem beneficial in solving the problem in large-scale

Evaluation of High Performance Fortran through Application Kernels

Since the definition of the High Performance Fortran (HPF) standard, we have been maintaining a suite of application kernel codes with the aim of using them to evaluate the available compilers. This paper presents the results and conclusions from this study, for sixteen codes, on compilers from IBM, DEC, and the Portland Group Inc. (PGI), and on three machines: a DEC Alphafarm, an IBM SP-2, and a Cray T3D. From this, we hope to show the prospective HPF user that scalable performance is possible with modest effort, yet also where the current weaknesses lay

Exploration of the InfoMall Concept Building on the Electronic InfoMall

This document describes: the InfoMall concept; how it is employed by the Northeast Parallel Architectures center (NPAC) as a technology transfer program, how it could be used by Rome Laboratory and by the United States Air Force Materiel Command (US AFMC). A description of the “Electronic InfoMall” system built on the World Wide Web as a pilot project for Rome Laboratory is also given as well as some experiences building WWW systems for academic, commerce and industry. It should be emphasized that this document is primarily a description of the potential uses of the InfoMall concept and the human interactive processes involved in InfoMall and is not primarily about the HPCC technologies that make the InfoMall process work. These technologies are well described elsewhere although we summarize their main features in this document

Exploiting High Performance Fortran for Computational Fluid Dynamics, volume 919

We discuss the High Performance Fortran data parallel programming language as an aid to software engineering and as a tool for exploiting High Performance Computing systems for computational uid dynamics applications. We discuss the use of intrinsic functions, data distribution directives and explicitly parallel constructs to optimize performance by minimizing communications requirements in a portable manner. In particular we use an implicit method such as the ADI algorithm to illustrate the major issues. We focus on regular mesh problems, since these can be efficiently represented by the existing HPF definition, but also discuss issues arising from the use of irregular meshes that are influencing a revised definition for HPF-2. Some of the codes discussed are available on the World Wide Web at http://www.npac.syr.edu/hpfa/ along with other educational and discussion material related to applications in HPF

High Performance Fortran and Possible Extensions to support Conjugate Gradient Algorithms

We evaluate the High-Performance Fortran (HPF) language for the compact expression and efficient implementation of conjugate gradient iterative matrix-solvers on High Performance Computing and Communications(HPCC) platforms. We discuss the use of intrinsic functions, data distribution directives and explicitly parallel constructs to optimize performance by minimizing communications requirements in a portable manner. We focus on implementations using the existing HPF definitions but also discuss issues arising that may influence a revised definition for HPF-2. Some of the codes discussed are available on the World Wide Web at http://www.npac.syr.edu/hpfa/ alongwith other educational and discussion material related to applications in HPF

National HPCC Software Exchange

This report describes an effort to construct a National HPCC Software Exchange (NHSE). This system shows how the evolving National Information Infrastructure (NII) can be used to facilitate sharing of software and information among members of the High Performance Computing and Communications (HPCC) community. To access the system use the URL: http://www.netlib.org/nse/

GraphCombEx: A Software Tool for Exploration of Combinatorial Optimisation Properties of Large Graphs

We present a prototype of a software tool for exploration of multiple combinatorial optimisation problems in large real-world and synthetic complex networks. Our tool, called GraphCombEx (an acronym of Graph Combinatorial Explorer), provides a unified framework for scalable computation and presentation of high-quality suboptimal solutions and bounds for a number of widely studied combinatorial optimisation problems. Efficient representation and applicability to large-scale graphs and complex networks are particularly considered in its design. The problems currently supported include maximum clique, graph colouring, maximum independent set, minimum vertex clique covering, minimum dominating set, as well as the longest simple cycle problem. Suboptimal solutions and intervals for optimal objective values are estimated using scalable heuristics. The tool is designed with extensibility in mind, with the view of further problems and both new fast and high-performance heuristics to be added in the future. GraphCombEx has already been successfully used as a support tool in a number of recent research studies using combinatorial optimisation to analyse complex networks, indicating its promise as a research software tool