Breadth First Search Traversal Research Articles

A minimalistic approach for fast computation of geodesic distances on triangular meshes

The computation of geodesic distances is an important research topic in Geometry Processing and 3D Shape Analysis as it is a basic component of many methods used in these areas. In this work, we present a minimalistic parallel algorithm based on front propagation to compute approximate geodesic distances on meshes. Our method is practical and simple to implement, and does not require any heavy pre-processing. The convergence of our algorithm depends on the number of discrete level sets around the source points from which distance information propagates. To appropriately implement our method on GPUs taking into account memory coalescence problems, we take advantage of a graph representation based on a breadth-first search traversal that works harmoniously with our parallel front propagation approach. We report experiments that show how our method scales with the size of the problem. We compare the mean error and processing time obtained by our method with such measures computed using other methods. Our method produces results in competitive times with almost the same accuracy, especially for large meshes. We also demonstrate its use for solving two classical geometry processing problems: the regular sampling problem and the Voronoi tessellation on meshes.

APINetworks Java. A Java approach to the efficient treatment of large-scale complex networks

We present a new version of the core structural package of our Application Programming Interface, APINetworks, for the treatment of complex networks in arbitrary computational environments. The new version is written in Java and presents several advantages over the previous C++ version: the portability of the Java code, the easiness of object-oriented design implementations, and the simplicity of memory management. In addition, some additional data structures are introduced for storing the sets of nodes and edges. Also, by resorting to the different garbage collectors currently available in the JVM the Java version is much more efficient than the C++ one with respect to memory management. In particular, the G1 collector is the most efficient one because of the parallel execution of G1 and the Java application. Using G1, APINetworks Java outperforms the C++ version and the well-known NetworkX and JGraphT packages in the building and BFS traversal of linear and complete networks. The better memory management of the present version allows for the modeling of much larger networks.

DI-MMAP—a scalable memory-map runtime for out-of-core data-intensive applications

We present DI-MMAP, a high-performance runtime that memory-maps large external data sets into an application's address space and shows significantly better performance than the Linux mmap system call. Our implementation is particularly effective when used with high performance locally attached Flash arrays on highly concurrent, latency-tolerant data-intensive HPC applications. We describe the kernel module and show performance results on a benchmark test suite, a new bioinformatics metagenomic classification application, and on a level-asynchronous Breadth-First Search (BFS) graph traversal algorithm. Using DI-MMAP, the metagenomics classification application performs up to 4× better than standard Linux mmap. A fully external memory configuration of BFS executes up to 7.44× faster than traditional mmap. Finally, we demonstrate that DI-MMAP shows scalable out-of-core performance for BFS traversal in main memory constrained scenarios. Such scalable memory constrained performance would allow a system with a fixed amount of memory to solve a larger problem as well as provide memory QoS guarantees for systems running multiple data-intensive applications.

I/O-efficient approximation of graph diameters by parallel cluster growing — a first experimental study

A fundamental step in the analysis of a massive graph is to compute its diameter. In the RAM model, the diameter of a connected undirected unweighted graph can be efficiently 2-approximated using a Breadth-First Search (BFS) traversal from an arbitrary node. However, if the graph is stored on disk, even an external memory BFS traversal is prohibitive, owing to the large number of I/Os it incurs. Meyer [1] proposed a parametrized algorithm to compute an approximation of graph diameter with fewer I/Os than that required for exact BFS traversal of the graph. The approach is based on growing clusters around randomly chosen vertices ‘in parallel’ until their fringes meet. We present an implementation of this algorithm and compare it with some simple heuristics and external-memory BFS in order to determine the trade-off between the approximation ratio and running-time achievable in practice. Our experiments show that with carefully chosen parameters, the new approach is indeed capable to produce surprisingly good diameter approximations in shorter time. We also confirm experimentally, that there are graph-classes where the parametrized approach runs into bad approximation ratios just as the theoretical analysis in [1] suggests.