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Acceleration of an Asynchronous Message Driven Programming Paradigm on IBM Blue Gene/Q

Acceleration of an Asynchronous Message Driven Programming P...

引用

ieee 27th International parallel and distributed processing symposium (IPDPS)

作者： Kumar, Sameer Sun, Yanhua Kale, Laxmikant V. IBM TJ Watson Res Ctr Yorktown Hts NY 10598 USA Univ Illinois Urbana Urbana Urbana IL USA

ISBN: (纸本)9780769549712

IBM Blue Gene/Q is the next generation Blue Gene machine that can scale to tens of Peta Flops with 16 cores and 64 hardware threads per node. However, significant efforts are required to fully exploit its capacity on various applications, spanning multiple programming models. In this paper, we focus on the asynchronous message driven parallel programming model - Charm++. Since its behavior (asynchronous) is substantially different from MPI, that presents a challenge in porting it efficiently to BG/Q. On the other hand, the significant synergy between BG/Q software and Charm++ creates opportunities for effective utilization of BG/Q resources. We describe various novel fine-grained threading techniques in Charm++ to exploit the hardware features of the BG/Q compute chip. these include the use of L2 atomics to implement lockless producer-consumer queues to accelerate communication between threads, fast memory allocators, hardware communication threads that are awakened via low overhead interrupts from the BG/Q wakeup unit. Burst of short messages is processed by using the ManytoMany interface to reduce runtime overhead. We also present techniques to optimize NAMD computation via Quad processing Unit (QPX) vector instructions and the acceleration of message rate via communication threads to optimize the Particle Mesh Ewald (PME) computation. We demonstrate the benefits of our techniques via two benchmarks, 3D Fast Fourier Transform, and the molecular dynamics application NAMD. For the 92,000-atom ApoA1 molecule, we achieved 683 mu s/step with PME every 4 steps and 782 mu s/step with PME every step.

关键词： IBM computers fast Fourier transforms molecular dynamics method multiprocessing systems parallel machines parallel programming

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Efficient parallel and distributed algorithms for GIS polygonal overlay processing

Efficient parallel and distributed algorithms for GIS polygo...

引用

2013 ieee 37th Annual Computer Software and Applications Conference, COMPSAC 2013

作者： Puri, Satish Prasad, Sushil K. Department of Computer Science Georgia State University Atlanta 30303 GA United States

ISBN: (纸本)9780769549798

Polygon overlay is one of the complex operations in Geographic Information Systems (GIS). In GIS, a typical polygon tends to be large in size often consisting of thousands of vertices. Sequential algorithms for this problem are in abundance in literature and most of the parallel algorithms concentrate on parallelizing edge intersection phase only. Our research aims to develop parallel algorithms to find overlay for two input polygons which can be extended to handle multiple polygons and implement it on General Purpose Graphics processing Units (GPGPU) which offers massive parallelism at relatively low cost. Moreover, spatial data files tend to be large in size (in GBs) and the underlying overlay computation is highly irregular and compute intensive. MapReduce paradigm is now standard in industry and academia for processing large-scale data. Motivated by MapReduce programming model, we propose to develop and implement scalable distributed algorithms to solve large-scale overlay processing in this dissertation. © 2013 ieee.

关键词： MapReduce

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Scaling Techniques for Massive Scale-Free Graphs in distributed (External) Memory

Scaling Techniques for Massive Scale-Free Graphs in Distribu...

引用

ieee 27th International parallel and distributed processing symposium (IPDPS)

作者： Pearce, Roger Gokhale, Maya Amato, Nancy M. Texas A&M Univ Parasol Lab College Stn TX 77843 USA Lawrence Livermore Natl Lab Ctr Appl Sci Comp Livermore CA USA

ISBN: (纸本)9780769549712

We present techniques to process large scale-free graphs in distributed memory. Our aim is to scale to trillions of edges, and our research is targeted at leadership class supercomputers and clusters with local non-volatile memory, e. g., NAND Flash. We apply an edge list partitioning technique, designed to accommodate high-degree vertices (hubs) that create scaling challenges when processing scale-free graphs. In addition to partitioning hubs, we use ghost vertices to represent the hubs to reduce communication hotspots. We present a scaling study with three important graph algorithms: Breadth-First Search (BFS), K-Core decomposition, and Triangle Counting. We also demonstrate scalability on BG/P Intrepid by comparing to best known Graph500 results [1]. We show results on two clusters with local NVRAM storage that are capable of traversing trillion-edge scale-free graphs. By leveraging node-local NAND Flash, our approach can process thirty-two times larger datasets with only a 39% performance degradation in Traversed Edges Per Second (TEPS).

关键词： parallel algorithms graph algorithms big data distributed computing

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Design optimization of energy-And security-critical distributed real-time embedded systems

Design optimization of energy-And security-critical distribu...

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2013 ieee 37th Annual Computer Software and Applications Conference, COMPSAC 2013

作者： Zhang, Xia Zhan, Jinyu Jiang, Wei Ma, Yue Jiang, Ke School of Information and Software Engineering University of Electronic Science and Technology China Department of Computer and Information Science Linkoping University Sweden

ISBN: (纸本)9780769549798

In this paper, we approach the design of energy-And security-critical distributed real-time embedded systems from the early mapping and scheduling phases. Modern distributed Embedded Systems (DESs) are common to be connected to external networks, which is beneficial for various purposes, but also opens up the gate for potential security attacks. However, security protections in DESs result in significant time and energy overhead. In this work, we focus on the problem of providing the best confidentiality protection of internal communication in DESs under time and energy constraints. the complexity of finding the optimal solution grows exponentially as problem size grows. therefore, we propose an efficient genetic algorithm based heuristic for solving the problem. Extensive experiments demonstrate the efficiency of the proposed technique. © 2013 ieee.

关键词： Mapping

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Further Improvement on GPU-Based parallel Implementation of WRF 5-Layer thermal Diffusion Scheme

Further Improvement on GPU-Based Parallel Implementation of ...

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19th ieee International Conference on parallel and distributed Systems (ICPADS)

作者： Huang, Melin Huang, Bormin Mielikainen, Jarno Huang, H. -L Allen Goldberg, Mitchell D. Mehta, Ajay Univ Wisconsin Madison Space Sci & Engn Ctr Madison WI 53706 USA Natl Ocean & Atmospher Adm Joint Polar Satellite Syst Off Silver Spring MD USA

ISBN: (纸本)9781479920815

the Weather Research and Forecasting (WRF) model has been widely employed for weather prediction and atmospheric simulation with dual purposes in forecasting and research. Land-surface models (LSMs) are parts of the WRF model, which is used to provide information of heat and moisture fluxes over land and sea-ice points. the 5-layer thermal diffusion simulation is an LSM based on the MM5 soil temperature model with an energy budget made up of sensible, latent, and radiative heat fluxes. Owing to the feature of no interactions among horizontal grid points, the LSMs are very favorable for massively parallel processing. the study presented in this article demonstrates the parallel computing efforts on the WRF 5-layer thermal diffusion scheme using Graphics processing Unit (GPU). Since this scheme is only one intermediate module of the entire WRF model, the involvement of the I/O transfer does not occur in the intermediate process. By employing one NVIDIA GTX 680 GPU in the case without I/O transfer, our optimization efforts on the GPU-based 5-layer thermal diffusion scheme can reach a speedup as high as 247.5x with respect to one CPU core, whereas the speedup for one CPU socket with respect to one CPU core is only 3.1x. We can even boost the speedup to 332x with respect to one CPU core when three GPUs are applied.

关键词： 5-layer thermal diffusion Compute Unified Device Architecture (CUDA) Graphics processing Unit (GPU) speedup Weather Research and Forecasting (WRF)

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parallel file download in peer-to-peer networks with random service capacities

Parallel file download in peer-to-peer networks with random ...

引用

2013 ieee 37th Annual Computer Software and Applications Conference, COMPSAC 2013

作者： Li, Keqin Department of Computer Science State University of New York New Paltz NY 12561 United States

ISBN: (纸本)9780769549798

It is well known that the method of parallel downloading can be used to reduce file download times in a peer-to-peer (P2P) network. there has been little investigation on parallel download and chunk allocation for source peers with random service capacities. the main contribution of this paper is to address the problem of efficient parallel file download in P2P networks with random service capacities. A precise analysis of the expected download time is given when the service capacity of a source peer is a random variable. A general framework is developed for analyzing the expected download time of a parallel download and chunk allocation algorithm, and is applied to the analysis of several algorithms. Two chunk allocation algorithms for parallel download are proposed. It is observed that the performance of parallel download can be significantly improved by using the method of probing high-capacity peers. One such algorithm is proposed and its expected parallel download time is analyzed. the performance of these parallel file download algorithms in P2P networks with random service capacities are compared. © 2013 ieee.

关键词： Peer to peer networks

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Sequential and parallel restart policies for constraint-based local search

Sequential and parallel restart policies for constraint-base...

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2013 ieee 37th Annual Computer Software and Applications Conference, COMPSAC 2013

作者： Caniou, Yves Codognet, Philippe JFLI CNRS University of Tokyo Tokyo Japan

ISBN: (纸本)9780769549798

We study in this paper the influence of the restart policy on the sequential and parallel performance of combinatorial search problems. Our evaluation relies on several experiments using a constraint-based local search method, named Adaptive Search, and a few combinatorial problems such as Magic Square and Costas Array Problems. © 2013 ieee.

关键词： Local search (optimization)

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Patterns and exemplars: Compelling strategies for teaching parallel and distributed computing to CS undergraduates

Patterns and exemplars: Compelling strategies for teaching p...

引用

2013 ieee 37th Annual Computer Software and Applications Conference, COMPSAC 2013

作者： Adams, Joel Brown, Richard Shoop, Elizabeth Calvin College United States St. Olaf College United States Macalester College United States

ISBN: (纸本)9780769549798

parallel programming patterns provide enduring principles that serve as a conceptual framework to orient students when they set out to solve problems. Learning patterns enables students to quickly gain the intellectual and coding skills they will need to embrace the future of parallel and distributed computing (PDC). Exemplars consisting of representative and compelling applied problems, together with implementations in different parallel technologies, constitute a valuable resource for learning and teaching. parallel programming patterns and exemplar applications naturally complement each other, and together provide a unified and practical strategy for PDC education at multiple course levels. We present two strategies we have used for incorporating patterns into undergraduate CS courses, examine the potential of exemplars, and indicate how patterns and exemplars reinforce each other. © 2013 ieee.

关键词： parallel programming

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Performance analysis of diffusion LMS in multitask networks

Performance analysis of diffusion LMS in multitask networks

引用

5th ieee International Workshop on Computational Advances in Multi-Sensor Adaptive processing (CAMSAP)

作者： Chen, Jie Richard, Cedric Univ Nice Sophia Antipolis Lab Lagrange Nice France

ISBN: (纸本)9781467331463;9781467331449

Diffusion LMS algorithm has been extensively studied during the last few years. this efficient approach allows to address distributed optimization problems over sensor networks in the case where the nodes have to collaboratively estimate a single parameter vector. Nevertheless, real-life problems are often multitask-oriented in the sense that the optimum parameter vector may not be the same for every node. In this paper, we conduct a theoretical analysis on the stochastic behavior of diffusion LMS when, either intentionally or unintentionally, applied to multitask problems, that is, in a situation where the founding hypothesis of this algorithm is violated. Simulation results validate our theoretical model. theoretical analysis and simulation show that collaboration can be still beneficial, and depends on antagonistic effects of the estimation bias-variance trade-off. this work provides a theoretical justification for the need to derive new cooperative algorithms specifically dedicated to multitask problems.

关键词： parallel processing (COMPUTERS) Levamisole learning management system random behavior theoretical analysis diffusion

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distributed loop scheduling schemes for cloud systems

Distributed loop scheduling schemes for cloud systems

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2013 ieee 37th Annual Computer Software and Applications Conference, COMPSAC 2013

作者： Han, Yiming Chronopoulos, Anthony T. Department of Computer Science University of Texas at San Antonio San Antonio TX United States

ISBN: (纸本)9780769549798

Cloud computing infrastructure offers the computing resources as a homogeneous collection of virtual machine instances by different hardware on figurations, which is transparent to end users. In fact, the computational powers of these virtual machine instances are different and behaves as a heterogeneous environment. thus, scheduling and load balancing for high performance computations become challenging on such systems. In this paper, we propose a hierarchical distributed scheduling scheme suitable for parallel loops with independent iterations on a cloud computing system. We also evaluate various performance aspects associated with our distributed scheduling scheme. © 2013 ieee.

关键词： Virtual machine

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