391 research outputs found
木を用いた構造化並列プログラミング
High-level abstractions for parallel programming are still immature. Computations on complicated data structures such as pointer structures are considered as irregular algorithms. General graph structures, which irregular algorithms generally deal with, are difficult to divide and conquer. Because the divide-and-conquer paradigm is essential for load balancing in parallel algorithms and a key to parallel programming, general graphs are reasonably difficult. However, trees lead to divide-and-conquer computations by definition and are sufficiently general and powerful as a tool of programming. We therefore deal with abstractions of tree-based computations. Our study has started from Matsuzaki’s work on tree skeletons. We have improved the usability of tree skeletons by enriching their implementation aspect. Specifically, we have dealt with two issues. We first have implemented the loose coupling between skeletons and data structures and developed a flexible tree skeleton library. We secondly have implemented a parallelizer that transforms sequential recursive functions in C into parallel programs that use tree skeletons implicitly. This parallelizer hides the complicated API of tree skeletons and makes programmers to use tree skeletons with no burden. Unfortunately, the practicality of tree skeletons, however, has not been improved. On the basis of the observations from the practice of tree skeletons, we deal with two application domains: program analysis and neighborhood computation. In the domain of program analysis, compilers treat input programs as control-flow graphs (CFGs) and perform analysis on CFGs. Program analysis is therefore difficult to divide and conquer. To resolve this problem, we have developed divide-and-conquer methods for program analysis in a syntax-directed manner on the basis of Rosen’s high-level approach. Specifically, we have dealt with data-flow analysis based on Tarjan’s formalization and value-graph construction based on a functional formalization. In the domain of neighborhood computations, a primary issue is locality. A naive parallel neighborhood computation without locality enhancement causes a lot of cache misses. The divide-and-conquer paradigm is known to be useful also for locality enhancement. We therefore have applied algebraic formalizations and a tree-segmenting technique derived from tree skeletons to the locality enhancement of neighborhood computations.電気通信大学201
Parallel Selected Inversion for Space-Time Gaussian Markov Random Fields
Performing a Bayesian inference on large spatio-temporal models requires
extracting inverse elements of large sparse precision matrices for marginal
variances. Although direct matrix factorizations can be used for the inversion,
such methods fail to scale well for distributed problems when run on large
computing clusters. On the contrary, Krylov subspace methods for the selected
inversion have been gaining traction. We propose a parallel hybrid approach
based on domain decomposition, which extends the Rao-Blackwellized Monte Carlo
estimator for distributed precision matrices. Our approach exploits the
strength of Krylov subspace methods as global solvers and efficiency of direct
factorizations as base case solvers to compute the marginal variances using a
divide-and-conquer strategy. By introducing subdomain overlaps, one can achieve
a greater accuracy at an increased computational effort with little to no
additional communication. We demonstrate the speed improvements on both
simulated models and a massive US daily temperature data.Comment: 17 pages, 7 figure
Algorithm Libraries for Multi-Core Processors
By providing parallelized versions of established algorithm libraries, we ease the exploitation of the multiple cores on modern processors for the programmer. The Multi-Core STL provides basic algorithms for internal memory, while the parallelized STXXL enables multi-core acceleration for algorithms on large data sets stored on disk. Some parallelized geometric algorithms are introduced into CGAL. Further, we design and implement sorting algorithms for huge data in distributed external memory
Efficient Parallel and Distributed Algorithms for GIS Polygon Overlay Processing
Polygon clipping is one of the complex operations in computational geometry. It is used in Geographic Information Systems (GIS), Computer Graphics, and VLSI CAD. For two polygons with n and m vertices, the number of intersections can be O(nm). In this dissertation, we present the first output-sensitive CREW PRAM algorithm, which can perform polygon clipping in O(log n) time using O(n + k + k\u27) processors, where n is the number of vertices, k is the number of intersections, and k\u27 is the additional temporary vertices introduced due to the partitioning of polygons. The current best algorithm by Karinthi, Srinivas, and Almasi does not handle self-intersecting polygons, is not output-sensitive and must employ O(n^2) processors to achieve O(log n) time. The second parallel algorithm is an output-sensitive PRAM algorithm based on Greiner-Hormann algorithm with O(log n) time complexity using O(n + k) processors. This is cost-optimal when compared to the time complexity of the best-known sequential plane-sweep based algorithm for polygon clipping. For self-intersecting polygons, the time complexity is O(((n + k) log n log log n)/p) using p
In addition to these parallel algorithms, the other main contributions in this dissertation are 1) multi-core and many-core implementation for clipping a pair of polygons and 2) MPI-GIS and Hadoop Topology Suite for distributed polygon overlay using a cluster of nodes. Nvidia GPU and CUDA are used for the many-core implementation. The MPI based system achieves 44X speedup while processing about 600K polygons in two real-world GIS shapefiles 1) USA Detailed Water Bodies and 2) USA Block Group Boundaries) within 20 seconds on a 32-node (8 cores each) IBM iDataPlex cluster interconnected by InfiniBand technology
One machine, one minute, three billion tetrahedra
This paper presents a new scalable parallelization scheme to generate the 3D
Delaunay triangulation of a given set of points. Our first contribution is an
efficient serial implementation of the incremental Delaunay insertion
algorithm. A simple dedicated data structure, an efficient sorting of the
points and the optimization of the insertion algorithm have permitted to
accelerate reference implementations by a factor three. Our second contribution
is a multi-threaded version of the Delaunay kernel that is able to concurrently
insert vertices. Moore curve coordinates are used to partition the point set,
avoiding heavy synchronization overheads. Conflicts are managed by modifying
the partitions with a simple rescaling of the space-filling curve. The
performances of our implementation have been measured on three different
processors, an Intel core-i7, an Intel Xeon Phi and an AMD EPYC, on which we
have been able to compute 3 billion tetrahedra in 53 seconds. This corresponds
to a generation rate of over 55 million tetrahedra per second. We finally show
how this very efficient parallel Delaunay triangulation can be integrated in a
Delaunay refinement mesh generator which takes as input the triangulated
surface boundary of the volume to mesh
Fast -NNG construction with GPU-based quick multi-select
In this paper we describe a new brute force algorithm for building the
-Nearest Neighbor Graph (-NNG). The -NNG algorithm has many
applications in areas such as machine learning, bio-informatics, and clustering
analysis. While there are very efficient algorithms for data of low dimensions,
for high dimensional data the brute force search is the best algorithm. There
are two main parts to the algorithm: the first part is finding the distances
between the input vectors which may be formulated as a matrix multiplication
problem. The second is the selection of the -NNs for each of the query
vectors. For the second part, we describe a novel graphics processing unit
(GPU) -based multi-select algorithm based on quick sort. Our optimization makes
clever use of warp voting functions available on the latest GPUs along with
use-controlled cache. Benchmarks show significant improvement over
state-of-the-art implementations of the -NN search on GPUs
The projector algorithm: a simple parallel algorithm for computing Voronoi diagrams and Delaunay graphs
The Voronoi diagram is a certain geometric data structure which has numerous
applications in various scientific and technological fields. The theory of
algorithms for computing 2D Euclidean Voronoi diagrams of point sites is rich
and useful, with several different and important algorithms. However, this
theory has been quite steady during the last few decades in the sense that no
essentially new algorithms have entered the game. In addition, most of the
known algorithms are serial in nature and hence cast inherent difficulties on
the possibility to compute the diagram in parallel. In this paper we present
the projector algorithm: a new and simple algorithm which enables the
(combinatorial) computation of 2D Voronoi diagrams. The algorithm is
significantly different from previous ones and some of the involved concepts in
it are in the spirit of linear programming and optics. Parallel implementation
is naturally supported since each Voronoi cell can be computed independently of
the other cells. A new combinatorial structure for representing the cells (and
any convex polytope) is described along the way and the computation of the
induced Delaunay graph is obtained almost automatically.Comment: This is a major revision; re-organization and better presentation of
some parts; correction of several inaccuracies; improvement of some proofs
and figures; added references; modification of the title; the paper is long
but more than half of it is composed of proofs and references: it is
sufficient to look at pages 5, 7--11 in order to understand the algorith
On The Parallelization Of Integer Polynomial Multiplication
With the advent of hardware accelerator technologies, multi-core processors and GPUs, much effort for taking advantage of those architectures by designing parallel algorithms has been made. To achieve this goal, one needs to consider both algebraic complexity and parallelism, plus making efficient use of memory traffic, cache, and reducing overheads in the implementations.
Polynomial multiplication is at the core of many algorithms in symbolic computation such as real root isolation which will be our main application for now.
In this thesis, we first investigate the multiplication of dense univariate polynomials with integer coefficients targeting multi-core processors. Some of the proposed methods are based on well-known serial classical algorithms, whereas a novel algorithm is designed to make efficient use of the targeted hardware. Experimentation confirms our theoretical analysis.
Second, we report on the first implementation of subproduct tree techniques on many-core architectures. These techniques are basically another application of polynomial multiplication, but over a prime field. This technique is used in multi-point evaluation and interpolation of polynomials with coefficients over a prime field
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