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A hierarchical approach to reducing communication in parallel graph algorithms 2015

A hierarchical approach to reducing communication in paralle...

引用

20th acm sigplan symposium on principles and practice of parallel programming, PPoPP 2015

作者： Harshvardhan Amato, Nancy M. Rauchwerger, Lawrence Parasol Laboratory Department of Computer Science and Engineering Texas A and M University United States

ISBN: (纸本)9781450332057

Large-scale graph computing has become critical due to the ever-increasing size of data. However, distributed graph computations are limited in their scalability and performance due to the heavy communication inherent in such computations. this is exacerbated in scale-free networks, such as social and web graphs, which contain hub vertices that have large degrees and therefore send a large number of messages over the network. Furthermore, many graph algorithms and computations send the same data to each of the neighbors of a vertex. Our proposed approach recognizes this, and reduces communication performed by the algorithm without change to user-code, through a hierarchical machine model imposed upon the input graph. the hierarchical model takes advantage of locale information of the neighboring vertices to reduce communication, both in message volume and total number of bytes sent. It is also able to better exploit the machine hierarchy to further reduce the communication costs, by aggregating traffic between different levels of the machine hierarchy. Results of an implementation in the STAPL GL shows improved scalability and performance over the traditional level-synchronous approach, with 2.5 × - 8× improvement for a variety of graph algorithms at 12, 000+ cores.

关键词： Big data

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NUMA-aware graph-structured analytics 2015

NUMA-aware graph-structured analytics

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20th acm sigplan symposium on principles and practice of parallel programming, PPoPP 2015

作者： Zhang, Kaiyuan Chen, Rong Chen, Haibo Shanghai Key Laboratory of Scalable Computing and Systems Institute of Parallel and Distributed Systems Shanghai Jiao Tong University China

ISBN: (纸本)9781450332057

Graph-structured analytics has been widely adopted in a number of big data applications such as social computation, web-search and recommendation systems. though much prior research focuses on scaling graph-analytics on distributed environments, the strong desire on performance per core, dollar and joule has generated considerable interests of processing large-scale graphs on a single server-class machine, which may have several terabytes of RAM and 80 or more cores. However, prior graph-analytics systems are largely neutral to NUMA characteristics and thus have suboptimal performance. this paper presents a detailed study of NUMA characteristics and their impact on the efficiency of graph-analytics. Our study uncovers two insights: 1) either random or interleaved allocation of graph data will significantly hamper data locality and parallelism;2) sequential inter-node (i.e., remote) memory accesses have much higher bandwidth than both intra- and inter-node random ones. Based on them, this paper describes Polymer, a NUMA-aware graph-analytics system on multicore with two key design decisions. First, Polymer differentially allocates and places topology data, application-defined data and mutable runtime states of a graph system according to their access patterns to minimize remote accesses. Second, for some remaining random accesses, Polymer carefully converts random remote accesses into sequential remote accesses, by using lightweight replication of vertices across NUMA nodes. To improve load balance and vertex convergence, Polymer is further built with a hierarchical barrier to boost parallelism and locality, an edge-oriented balanced partitioning for skewed graphs, and adaptive data structures according to the proportion of active vertices. A detailed evaluation on an 80-core machine shows that Polymer often outperforms the state-of-the-art single-machine graph-analytics systems, including Ligra, X-Stream and Galois, for a set of popular real-world and synthetic grap

关键词： Random access storage

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PPoPP 2013 - Proceedings of the 2013 acm sigplan symposium on principles and practice of parallel programming

PPoPP 2013 - Proceedings of the 2013 ACM SIGPLAN Symposium o...

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18th acm sigplan symposium on principles and practice of parallel programming, PPoPP 2013

ISBN: (纸本)9781450319225

the proceedings contain 45 papers. the topics discussed include: a peta-scalable CPU-GPU algorithm for global atmospheric simulations;adoption protocols for fanout-optimal fault-tolerant termination detection;betweenness centrality: algorithms and implementations;complexity analysis and algorithm design for reorganizing data to minimize non-coalesced memory accesses on GPU;fast concurrent queues for x86 processors;FASTLANE: improving performance of software transactional memory for low thread counts;Ligra: a lightweight graph processing framework for shared memory;ownership passing: efficient distributed memory programming on multi-core systems;parallel suffix array and least common prefix for the GPU;Streamscan: fast scan algorithms for GPUs without global barrier synchronization;using hardware transactional memory to correct and simplify a readers-writer lock algorithm;and exploring different automata representations for efficient regular expression matching on GPUs.

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Provably good scheduling for parallel programs that use data structures through implicit batching 14

Provably good scheduling for parallel programs that use data...

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2014 19th acm sigplan symposium on principles and practice of parallel programming, PPoPP 2014

作者： Agrawal, Kunal Fineman, Jeremy T. Sheridan, Brendan Sukha, Jim Utterback, Robert Washington University in Saint Louis United States Georgetown University United States Intel Corporation United States

this poster proposes an efficient runtime scheduler that provides provable performance guarantees to parallel programs that use data structures through the use of implicit batching.

ISBN: (纸本)9781450326568

this poster proposes an efficient runtime scheduler that provides provable performance guarantees to parallel programs that use data structures through the use of implicit batching.

关键词： Data structures

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parallelizing dynamic programming through rank convergence 14

Parallelizing dynamic programming through rank convergence

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2014 19th acm sigplan symposium on principles and practice of parallel programming, PPoPP 2014

作者： Maleki, Saeed Musuvathi, Madanlal Mytkowicz, Todd Univerity of Illinois at Urbana-Champaign United States Microsoft Research United States

ISBN: (纸本)9781450326568

this paper proposes an efficient parallel algorithm for an important class of dynamic programming problems that includes Viterbi, Needleman-Wunsch, Smith-Waterman, and Longest Common Subsequence. In dynamic programming, the subproblems that do not depend on each other, and thus can be computed in parallel, form stages or wavefronts. the algorithm presented in this paper provides additional parallelism allowing multiple stages to be computed in parallel despite dependences among them. the correctness and the performance of the algorithm relies on rank convergence properties of matrix multiplication in the tropical semiring, formed with plus as the multiplicative operation and max as the additive operation. this paper demonstrates the efficiency of the parallel algorithm by showing significant speed ups on a variety of important dynamic programming problems. In particular, the parallel Viterbi decoder is up-to 24× faster (with 64 processors) than a highly optimized commercial baseline. Copyright © 2014 acm.

关键词： Dynamic programming

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Extracting logical structure and identifying stragglers in parallel execution traces 14

Extracting logical structure and identifying stragglers in p...

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2014 19th acm sigplan symposium on principles and practice of parallel programming, PPoPP 2014

作者： Isaacs, Katherine E. Gamblin, Todd Bhatele, Abhinav Bremer, Peer-Timo Schulz, Martin Hamann, Bernd Department of Computer Science University of California Davis United States Center for Applied Scientific Computing Lawrence Livermore National Laboratory United States

ISBN: (纸本)9781450326568

We introduce a new approach to automatically extract an idealized logical structure from a parallel execution trace. We use this structure to define intuitive metrics such as the lateness of a process involved in a parallel execution. By analyzing and illustrating traces in terms of logical steps, we leverage a developer's understanding of the happened-before relations in a parallel program. this technique can uncover dependency chains, elucidate communication patterns, and highlight sources and propagation of delays, all of which may be obscured in a traditional trace visualization.

关键词： Visualization

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Initial study of multi-endpoint runtime for MPI+OpenMP hybrid programming model on multi-core systems 14

Initial study of multi-endpoint runtime for MPI+OpenMP hybri...

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2014 19th acm sigplan symposium on principles and practice of parallel programming, PPoPP 2014

作者： Luo, Miao Lu, Xiaoyi Hamidouche, Khaled Kandalla, Krishna Panda, Dhabaleswar K. Dept. of Computer Science and Engineering Ohio State University United States

ISBN: (纸本)9781450326568

State-of-the-art MPI libraries rely on locks to guarantee thread-safety. this discourages application developers from using multiple threads to perform MPI operations. In this paper, we propose a high performance, lock-free multiendpoint MPI runtime, which can achieve up to 40% improvement for point-to-point operation and one representative collective operation with minimum or no modifications to the existing applications.

关键词： Locks (fasteners)

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Fine-grain parallel megabase sequence comparison with multiple heterogeneous GPUs 14

Fine-grain parallel megabase sequence comparison with multip...

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2014 19th acm sigplan symposium on principles and practice of parallel programming, PPoPP 2014

作者： De Sandes, Edans F.O. Miranda, Guillermo Melo, Alba C.M.A. Martorell, Xavier Ayguadé, Eduard University of Brasilia Brazil Universitat Politècnica de Catalunya Barcelona Supercomputing Center Spain

ISBN: (纸本)9781450326568

this paper proposes and evaluates a parallel strategy to execute the exact Smith-Waterman (SW) algorithm for megabase DNA sequences in heterogeneous multi-GPU platforms. In our strategy, the computation of a single huge SW matrix is spread over multiple GPUs, which communicate border elements to the neighbour, using a circular buffer mechanism that hides the communication overhead. We compared 4 pairs of human-chimpanzee homologous chromosomes using 2 different GPU environments, obtaining a performance of up to 140.36 GCUPS (Billion of cells processed per second) with 3 heterogeneous GPUS.

关键词： Graphics processing unit

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Triolet: A programming system that unifies algorithmic skeleton interfaces for high-performance cluster computing 14

Triolet: A programming system that unifies algorithmic skele...

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2014 19th acm sigplan symposium on principles and practice of parallel programming, PPoPP 2014

作者： Rodrigues, Christopher Jablin, thomas Dakkak, Abdul Hwu, Wen-Mei University of Illinois at Urbana-Champaign United States

ISBN: (纸本)9781450326568

Functional algorithmic skeletons promise a high-level programming interface for distributed-memory clusters that free developers from concerns of task decomposition, scheduling, and communication. Unfortunately, prior distributed functional skeleton frameworks do not deliver performance comparable to that achievable in a low-level distributed programming model such as C with MPI and OpenMP, even when used in concert with high-performance array libraries. there are several causes: they do not take advantage of shared memory on each cluster node;they impose a fixed partitioning strategy on input data;and they have limited ability to fuse loops involving skeletons that produce a variable number of outputs per input. We address these shortcomings in the Triolet programming language through a modular library design that separates concerns of parallelism, loop nesting, and data partitioning. We show how Triolet substantially improves the parallel performance of algorithms involving array traversals and nested, variable-size loops over what is achievable in Eden, a distributed variant of Haskell. We further demonstrate how Triolet can substantially simplify parallel programming relative to C with MPI and OpenMP while achieving 23.100% of its performance on a 128-core cluster. Copyright © 2014 acm.

关键词： parallel programming

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Designing and auto-tuning parallel 3-D FFT for computation-communication overlap 14

Designing and auto-tuning parallel 3-D FFT for computation-c...

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2014 19th acm sigplan symposium on principles and practice of parallel programming, PPoPP 2014

作者： Song, Sukhyun Hollingsworth, Jeffrey K. Department of Computer Science University of Maryland College Park United States

ISBN: (纸本)9781450326568

this paper presents a method to design and auto-tune a new parallel 3-D FFT code using the non-blocking MPI all-to-all operation. We achieve high performance by optimizing computation-communication overlap. Our code performs fully asynchronous communication without any support from special hardware. We also improve cache performance through loop tiling. To cope with the complex tradeoff regarding our optimization techniques, we parameterize our code and auto-tune the parameters efficiently in a large parameter space. Experimental results from two systems confirm that our code achieves a speedup of up to 1.76× over the FFTW library. Copyright © 2014 acm.

关键词： Fast Fourier transforms

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