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Low-Cost parallel Algorithms for 2:1 Octree Balance

Low-Cost Parallel Algorithms for 2:1 Octree Balance

引用

26th ieee International parallel and distributed processing symposium (IPDPS) / Workshop on High Performance Data Intensive Computing

作者： Isaac, Tobin Burstedde, Carsten Ghattas, Omar Univ Texas Austin Inst Computat Engn & Sci ICES Austin TX 78712 USA

ISBN: (纸本)9780769546759

the logical structure of a forest of octrees can be used to create scalable algorithms for parallel adaptive mesh refinement (AMR), which has recently been demonstrated for several petascale applications. Among various frequently used octree-based mesh operations, including refinement, coarsening, partitioning, and enumerating nodes, ensuring a 2:1 size balance between neighboring elements has historically been the most expensive in terms of CPU time and communication volume. the 2:1 balance operation is thus a primary target to optimize. One important component of a parallel balance algorithm is the ability to determine whether any two given octants have a consistent distance/size relation. Based on new logical concepts we propose fast algorithms for making this decision for all types of 2: 1 balance conditions in 2D and 3D. Since we are able to achieve this without constructing any parent nodes in the tree that would otherwise need to be sorted and communicated, we can significantly reduce the required memory and communication volume. In addition, we propose a lightweight collective algorithm for reversing the asymmetric communication pattern induced by non-local octant interactions. We have implemented our improvements as part of the open-source "p4est" software. Benchmarking this code with both synthetic and simulation-driven adapted meshes we are able to demonstrate much reduced runtime and excellent weak and strong scalability. On our largest benchmark problem with 5.13 x 10(11) octants the new 2:1 balance algorithm executes in less than 8 seconds on 112,128 CPU cores of the Jaguar Cray XT5 supercomputer.

关键词： Octrees Adaptive mesh refinement parallel algorithms Scientific computing High performance computing

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A graph partitioning approach to distributed RDF stores

A graph partitioning approach to distributed RDF stores

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2012 10th ieee International symposium on parallel and distributed processing with Applications, ISPA 2012

作者： Wang, Rui Chiu, Kenneth Computer Science Department State University of New York at Binghamton Binghamton NY United States

ISBN: (纸本)9780769547015

With growing of Semantic Web data, especially RDF data, managing large RDF dataset on a single machine does not scale well. Previous work has explored how to distribute RDF triples to multiple machines. However due to inefficient dataset partitioning used by these solutions, the performance of distributed store system is significantly affected. In this paper, we proposed a promising approach that utilized the graph nature of RDF datasets to minimize relations between partitions after dataset partitioning, and optimized system design based on it. As shown in our experiments, our approach can effectively reduce communication cost of query-processing messages, balance size of partitions compared with other approaches, and enhance parallelism through independent sub-querying. © 2012 ieee.

关键词： Resource Description Framework (RDF)

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Using dynamic priority time petri nets for scheduling analysis via earliest deadline first policy

Using dynamic priority time petri nets for scheduling analys...

引用

2012 10th ieee International symposium on parallel and distributed processing with Applications, ISPA 2012

作者： Karamti, Walid Mahfoudhi, Adel Kacem, Yessine Hadj CES Laboratory University of Sfax ENIS Soukra km 35 3000 Sfax Tunisia

ISBN: (纸本)9780769547015

In a previous paper [14], we investigated the expressiveness of Time Petri Nets extended with dynamic Priorities and showed that it is able to analyze the schedulability of a partitioned real-time system over a multiprocessor architecture. the scheduling analysis is proven via the Least Laxity First (LLF) policy and a set of independent tasks. In the same vein, we investigate in the present paper the applicability of the proposed approach for the Earliest Deadline First (EDF) policy to reduce the cost of preemption and we tackle the dependent tasks problem. through an experiment, we present the capacity of our approach to detect the temporal faults in scheduling. © 2012 ieee.

关键词： Real time systems

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proceedings - 9th ieee International symposium on parallel and distributed processing with Applications, ISPA 2011

Proceedings - 9th IEEE International Symposium on Parallel a...

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9th ieee International symposium on parallel and distributed processing with Applications, ISPA 2011

ISBN: (纸本)9780769544281

the proceedings contain 55 papers. the topics discussed include: an equilibrium-based approach for determining winners in combinatorial auctions;a parallel 3D delaunay triangulation method;efficient resource selection algorithm for enterprise grid systems;performance evaluation of wireless sensor networks for mobile sensor nodes considering goodput and depletion metrics;improving performance on atmospheric models through a hybrid OpenMP/MPI implementation;on using pattern matching algorithms in MapReduce applications;dynamic memory demand estimating based on the guest operating system behaviors for virtual machines;a priority-aware NoC to reduce squashes in thread level speculation for chip multiprocessors;a novel predictive and self-adaptive dynamic thread pool management;and Vega LingCloud: a resource single leasing point system to support heterogeneous application modes on shared infrastructure.

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Performance Analysis and Optimization of the Tiled Cholesky Factorization on NUMA Machines

Performance Analysis and Optimization of the Tiled Cholesky ...

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5th International symposium on parallel Architectures, Algorithms and Programming (PAAP)

作者： Jeannot, Emmanuel Inria Bordeaux Sud Ouest LaBRI Bordeaux France

We discuss some performance issues of the tiled Cholesky factorization on non-uniform memory access-time (NUMA) shared memory machines. We show how to optimize thread placement and data placement in order to achieve p... 详细信息

ISBN: (纸本)9780769548982;9781467345668

关键词： matrix decomposition parallel processing performance evaluation shared memory systems

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Reducing application-level checkpoint file sizes: Towards scalable fault tolerance solutions

Reducing application-level checkpoint file sizes: Towards sc...

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2012 10th ieee International symposium on parallel and distributed processing with Applications, ISPA 2012

作者： Cores, Iván Rodríguez, Gabriel Martín, María J. González, Patricia Computer Architecture Group University of a Coruńa Spain

ISBN: (纸本)9780769547015

Systems intended for the execution of long-running parallel applications require fault tolerant capabilities, since the probability of failure increases with the execution time and the number of nodes. Checkpointing and rollback recovery is one of the most popular techniques to provide fault tolerance support. However, in order to be useful for large scale systems, current checkpoint-recovery techniques should tackle the problem of reducing checkpointing cost. this paper addresses this issue through the reduction of the checkpoint file sizes. Different solutions to reduce the size of the checkpoints generated at application level are proposed and implemented in a checkpointing tool. Detailed experimental results on two multicore clusters show the effectiveness of the proposed methods. © 2012 ieee.

关键词： parallel programming

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Fast and Efficient Graph Traversal Algorithm for CPUs: Maximizing Single-Node Efficiency

Fast and Efficient Graph Traversal Algorithm for CPUs: Maxim...

引用

26th ieee International parallel and distributed processing symposium (IPDPS) / Workshop on High Performance Data Intensive Computing

作者： Chhugani, Jatin Satish, Nadathur Kim, Changkyu Sewall, Jason Dubey, Pradeep Intel Corp Parallel Comp Lab Santa Clara CA 95051 USA

ISBN: (纸本)9780769546759

Graph-based structures are being increasingly used to model data and relations among data in a number of fields. Graph-based databases are becoming more popular as a means to better represent such data. Graph traversal is a key component in graph algorithms such as reachability and graph matching. Since the scale of data stored and queried in these databases is increasing, it is important to obtain high performing implementations of graph traversal that can efficiently utilize the processing power of modern processors. In this work, we present a scalable Breadth-First Search Traversal algorithm for modern multi-socket, multi-core CPUs. Our algorithm uses lock- and atomic-free operations on a cache-resident structure for arbitrary sized graphs to filter out expensive main memory accesses, and completely and efficiently utilizes all available bandwidth resources. We propose a work distribution approach for multi-socket platforms that ensures load-balancing while keeping cross-socket communication low. We provide a detailed analytical model that accurately projects the performance of our single- and multi-socket traversal algorithms to within 5-10% of obtained performance. Our analytical model serves as a useful tool to analyze performance bottlenecks on modern CPUs. When measured on various synthetic and real-world graphs with a wide range of graph sizes, vertex degrees and graph diameters, our implementation on a dual-socket Intel (R) Xeon (R) X5570 (Intel microarchitecture code name Nehalem) system achieves 1.5X-13.2X performance speedup over the best reported numbers. We achieve around 1 Billion traversed edges per second on a scale-free R-MAT graph with 64M vertices and 2 Billion edges on a dual-socket Nehalem system. Our optimized algorithm is useful as a building block for efficient multi-node implementations and future exascale systems, thereby allowing them to ride the trend of increasing per-node compute and bandwidth resources.

关键词： bandwidth efficient Graph traversal multi-socket single node

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Research of soft decision modulations based on parallel combinatory spread spectrum system

Research of soft decision modulations based on parallel comb...

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2012 5th Global symposium on Millimeter-Waves, GSMM 2012

作者： Liu, Mingduo Li, Honglei Guo, Lili College of Information and Communication Engineering Harbin Engineering University Harbin 150001 China 61769 Unit of PLA Harbin 150001 China

ISBN: (纸本)9781467313032

the modulation methods are discussed in parallel combinatory spread spectrum (PCSS) system. Several modulation methods which can be demodulated without threshold judging (that is soft decision) is mainly studied. the system model is built and simulated in this paper. According to the correlation of superposition PN sequences, a new soft decision QPSK modulation in PCSS system is proposed. this simulation results show that the reliability of proposed soft decision QPSK modulation is better than that of hard decision QPSK modulation and this method is useful in engineering application. © 2012 ieee.

关键词： Spectroscopy

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High Performance Non-uniform FFT on Modern x86-based Multi-core Systems

High Performance Non-uniform FFT on Modern x86-based Multi-c...

引用

26th ieee International parallel and distributed processing symposium (IPDPS) / Workshop on High Performance Data Intensive Computing

作者： Kalamkar, Dhiraj D. Trzasko, Joshua D. Sridharan, Srinivas Smelyanskiy, Mikhail Kim, Daehyun Manduca, Armando Shu, Yunhong Bernstein, Matt A. Kaul, Bharat Dubey, Pradeep Intel Labs Parallel Comp Lab Bangalore Karnataka India Intel Labs Parallel Comp Lab Santa Clara CA 95052 USA Mayo Clin Dept Physiol & Biomed Engn Rochester MN 55905 USA Mayo Clin Dept Radiol Rochester MN 55905 USA

ISBN: (纸本)9780769546759

the Non-Uniform Fast Fourier Transform (NUFFT) is a generalization of FFT to non-equidistant samples. It has many applications which vary from medical imaging to radio astronomy to the numerical solution of partial differential equations. Despite recent advances in speeding up NUFFT on various platforms, its practical applications are still limited, due to its high computational cost, which is significantly dominated by the convolution of a signal between a non-uniform and uniform grids. the computational cost of the NUFFT is particularly detrimental in cases which require fast reconstruction times, such as iterative 3D non-Cartesian MRI reconstruction. We propose novel and highly scalable parallel algorithm for performing NUFFT on x86-based multi-core CPUs. the high performance of our algorithm relies on good SIMD utilization and high parallel efficiency. On convolution, we demonstrate on average 90% SIMD efficiency using SSE, as well up to linear scalability using a quad-socket 40-core Intel (R) Xeon (R) E7-4870 Processors based system. As a result, on dual socket Intel (R) Xeon (R) X5670 based server, our NUFFT implementation is more than 4x faster compared to the best available NUFFT3D implementation, when run on the same hardware. On Intel (R) Xeon (R) E5-2670 processor based server, our NUFFT implementation is 1.5X faster than any published NUFFT implementation today. Such speed improvement opens new usages for NUFFT. For example, iterative multichannel reconstruction of a 240x240x240 image could execute in just over 3 minutes, which is on the same order as contemporary non-iterative (and thus less-accurate) 3D NUFFT-based MRI reconstructions.

关键词： Non-uniform FFT parallelization Scalability Vectorization

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Cache performance and efficiency factors of parallel data structures

Cache performance and efficiency factors of parallel data st...

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2012 10th ieee International symposium on parallel and distributed processing with Applications, ISPA 2012

作者： Dudás, Ákos Sándor, Juhász Department of Automation and Applied Informatics Budapest University of Technology and Economics Magyar Tudósok krt. 2 QB207 1117 Budapest Hungary

ISBN: (纸本)9780769547015

Multi-core CPUs are very efficient at executing multiple threads at the same time without significant performance penalty;this capability, however, results in increasing demand for the memory and the caches, which not only have to serve multiple parallel requests but also have to endure the consequences of parallel programming. the performance of parallel applications is not only limited by the CPU and the internal level of parallelism that the algorithms and data structures allow, but is also restricted by their memory characteristics. Altering the data structure for example to work with machine word-sized pointers required by atomic operations incurs additional cache misses, while a lock protecting a critical section not only consumes memory, but could also be responsible for increased memory traffic for cache-line invalidations when acquired or released. We investigate these effects and analyze the behavior of different parallelization mechanisms, both blocking and lock-free solutions, through the example of a basic data structure: a hash table. © 2012 ieee.

关键词： parallel programming

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