Hierarchical Filter and Refinement System Over Large Polygonal Datasets on CPU-GPU

In this paper, we introduce our hierarchical filter and refinement technique that we have developed for parallel geometric intersection operations involving large polygons and polylines. The inputs are two layers of large polygonal datasets and the computations are spatial intersection on a pair of cross-layer polygons. These intersections are the compute-intensive spatial data analytic kernels in spatial join and map overlay computations. We have extended the classical filter and refine algorithms using PolySketch Filter to improve the performance of geospatial computations. In addition to filtering polygons by their Minimum Bounding Rectangle (MBR), our hierarchical approach explores further filtering using tiles (smaller MBRs) to increase the effectiveness of filtering and decrease the computational workload in the refinement phase. We have implemented this filter and refine system on CPU and GPU by using OpenMP and OpenACC. After using R-tree, on average, our filter technique can still discard 69% of polygon pairs which do not have segment intersection points. PolySketch filter reduces on average 99.77% of the workload of finding line segment intersections. PNP based task reduction and Striping algorithms filter out on average 95.84% of the workload of Point-in-Polygon tests. Our CPU-GPU system performs spatial join on two shapefiles, namely USA Water Bodies and USA Block Group Boundaries with 683K polygons in about 10 seconds using NVidia Titan V and Titan Xp GPU

OpenACC Based GPU Parallelization of Plane Sweep Algorithm for Geometric Intersection

Line segment intersection is one of the elementary operations in computational geometry. Complex problems in Geographic Information Systems (GIS) like finding map overlays or spatial joins using polygonal data require solving segment intersections. Plane sweep paradigm is used for finding geometric intersection in an efficient manner. However, it is difficult to parallelize due to its in-order processing of spatial events. We present a new fine-grained parallel algorithm for geometric intersection and its CPU and GPU implementation using OpenMP and OpenACC. To the best of our knowledge, this is the first work demonstrating an effective parallelization of plane sweep on GPUs. We chose compiler directive based approach for implementation because of its simplicity to parallelize sequential code. Using Nvidia Tesla P100 GPU, our implementation achieves around 40X speedup for line segment intersection problem on 40K and 80K data sets compared to sequential CGAL library

MPI-Vector-IO: Parallel I/O and Partitioning for Geospatial Vector Data

In recent times, geospatial datasets are growing in terms of size, complexity and heterogeneity. High performance systems are needed to analyze such data to produce actionable insights in an efficient manner. For polygonal a.k.a vector datasets, operations such as I/O, data partitioning, communication, and load balancing becomes challenging in a cluster environment. In this work, we present MPI-Vector-IO 1 , a parallel I/O library that we have designed using MPI-IO specifically for partitioning and reading irregular vector data formats such as Well Known Text. It makes MPI aware of spatial data, spatial primitives and provides support for spatial data types embedded within collective computation and communication using MPI message-passing library. These abstractions along with parallel I/O support are useful for parallel Geographic Information System (GIS) application development on HPC platforms

A Heterogeneous High Performance Computing Framework For Ill-Structured Spatial Join Processing

The frequently employed spatial join processing over two large layers of polygonal datasets to detect cross-layer polygon pairs (CPP) satisfying a join-predicate faces challenges common to ill-structured sparse problems, namely, that of identifying the few intersecting cross-layer edges out of the quadratic universe. The algorithmic engineering challenge is compounded by GPGPU SIMT architecture. Spatial join involves lightweight filter phase typically using overlap test over minimum bounding rectangles (MBRs) to discard majority of CPPs, followed by refinement phase to rigorously test the join predicate over the edges of the surviving CPPs. In this dissertation, we develop new techniques - algorithms, data structure, i/o, load balancing and system implementation - to accelerate the two-phase spatial-join processing. We present a new filtering technique, called Common MBR Filter (CMF), which changes the overall characteristic of the spatial join algorithms wherein the refinement phase is no longer the computational bottleneck. CMF is designed based on the insight that intersecting cross-layer edges must lie within the rectangular intersection of the MBRs of CPPs, their common MBRs (CMBR). We also address a key limitation of CMF for class of spatial datasets with either large or dense active CMBRs by extended CMF, called CMF-grid, that effectively employs both CMBR and grid techniques by embedding a uniform grid over CMBR of each CPP, but of suitably engineered sizes for different CPPs. To show efficiency of CMF-based filters, extensive mathematical and experimental analysis is provided. Then, two GPU-based spatial join systems are proposed based on two CMF versions including four components: 1) sort-based MBR filter, 2) CMF/CMF-grid, 3) point-in-polygon test, and, 4) edge-intersection test. The systems show two orders of magnitude speedup over the optimized sequential GEOS C++ library. Furthermore, we present a distributed system of heterogeneous compute nodes to exploit GPU-CPU computing in order to scale up the computation. A load balancing model based on Integer Linear Programming (ILP) is formulated for this system. We also provide three heuristic algorithms to approximate the ILP. Finally, we develop MPI-cuda-GIS system based on this heterogeneous computing model by integrating our CUDA-based GPU system into a newly designed distributed framework designed based on Message Passing Interface (MPI). Experimental results show good scalability and performance of MPI-cuda-GIS system

X-Device Query Processing by Bitwise Distribution

The diversity of hardware components within a single system calls for strategies for efficient cross-device data processing. For exam- ple, existing approaches to CPU/GPU co-processing distribute individual relational operators to the “most appropriate” device. While pleasantly simple, this strategy has a number of problems: it may leave the “inappropriate” devices idle while overloading the “appropriate” device and putting a high pressure on the PCI bus. To address these issues we distribute data among the devices by par- tially decomposing relations at the granularity of individual bits. Each of the resulting bit-partitions is stored and processed on one of the available devices. Using this strategy, we implemented a processor for spatial range queries that makes efficient use of all available devices. The performance gains achieved indicate that bitwise distribution makes a good cross-device processing strategy

Improving the performance of similarity joins using graphics processing unit

Ankara : The Department of Computer Engineering and the Graduate School of Engineering and Science of Bilkent University, 2012.Thesis (Master's) -- Bilkent University, 2012.Includes bibliographical refences.The similarity join is an important operation in data mining and it is used in many applications from varying domains. A similarity join operator takes one or two sets of data points and outputs pairs of points whose distances in the data space is within a certain threshold value, ". The baseline nested loop approach computes the distances between all pairs of objects. When considering large set of objects which yield too long query time for nested loop paradigm, accelerating such operator becomes more important. The computing capability of recent GPUs with the help of a general purpose parallel computing architecture (CUDA) has attracted many researches. With this motivation, we propose two similarity join algorithms for Graphics Processing Unit (GPU). To exploit the advantages of general purpose GPU computing, we rst propose an improved nested loop join algorithm (GPU-INLJ) for the speci c environment of GPU. Also we present a partitioning-based join algorithm (KMEANS-JOIN) that guarantees each partition can be joined independently without missing any join pair. Our experiments demonstrate massive performance gains and the suitability of our algorithms for large datasets.Korkmaz, ZeynepM.S

Hierarchical and Adaptive Filter and Refinement Algorithms for Geometric Intersection Computations on GPU

Geometric intersection algorithms are fundamental in spatial analysis in Geographic Information System (GIS). This dissertation explores high performance computing solution for geometric intersection on a huge amount of spatial data using Graphics Processing Unit (GPU). We have developed a hierarchical filter and refinement system for parallel geometric intersection operations involving large polygons and polylines by extending the classical filter and refine algorithm using efficient filters that leverage GPU computing. The inputs are two layers of large polygonal datasets and the computations are spatial intersection on pairs of cross-layer polygons. These intersections are the compute-intensive spatial data analytic kernels in spatial join and map overlay operations in spatial databases and GIS. Efficient filters, such as PolySketch, PolySketch++ and Point-in-polygon filters have been developed to reduce refinement workload on GPUs. We also showed the application of such filters in speeding-up line segment intersections and point-in-polygon tests. Programming models like CUDA and OpenACC have been used to implement the different versions of the Hierarchical Filter and Refine (HiFiRe) system. Experimental results show good performance of our filter and refinement algorithms. Compared to standard R-tree filter, on average, our filter technique can still discard 76% of polygon pairs which do not have segment intersection points. PolySketch filter reduces on average 99.77% of the workload of finding line segment intersections. Compared to existing Common Minimum Bounding Rectangle (CMBR) filter that is applied on each cross-layer candidate pair, the workload after using PolySketch-based CMBR filter is on average 98% smaller. The execution time of our HiFiRe system on two shapefiles, namely USA Water Bodies (contains 464K polygons) and USA Block Group Boundaries (contains 220K polygons), is about 3.38 seconds using NVidia Titan V GPU