Science.gov

Sample records for distributed parallel algorithm

  1. Parallel and Distributed Computing Combinatorial Algorithms

    DTIC Science & Technology

    1993-10-01

    FUPNDKC %2,•, PARALLEL AND DISTRIBUTED COMPUTING COMBINATORIAL ALGORITHMS 6. AUTHOR(S) 2304/DS F49620-92-J-0125 DR. LEIGHTON 7 PERFORMING ORGANIZATION NAME...on several problems involving parallel and distributed computing and combinatorial optimization. This research is reported in the numerous papers that...network decom- position. In Proceedings of the Eleventh Annual ACM Symposium on Principles of Distributed Computing , August 1992. [15] B. Awerbuch, B

  2. Parallel matrix transpose algorithms on distributed memory concurrent computers

    SciTech Connect

    Choi, J.; Walker, D.W.; Dongarra, J.J. |

    1993-10-01

    This paper describes parallel matrix transpose algorithms on distributed memory concurrent processors. It is assumed that the matrix is distributed over a P x Q processor template with a block scattered data distribution. P, Q, and the block size can be arbitrary, so the algorithms have wide applicability. The communication schemes of the algorithms are determined by the greatest common divisor (GCD) of P and Q. If P and Q are relatively prime, the matrix transpose algorithm involves complete exchange communication. If P and Q are not relatively prime, processors are divided into GCD groups and the communication operations are overlapped for different groups of processors. Processors transpose GCD wrapped diagonal blocks simultaneously, and the matrix can be transposed with LCM/GCD steps, where LCM is the least common multiple of P and Q. The algorithms make use of non-blocking, point-to-point communication between processors. The use of nonblocking communication allows a processor to overlap the messages that it sends to different processors, thereby avoiding unnecessary synchronization. Combined with the matrix multiplication routine, C = A{center_dot}B, the algorithms are used to compute parallel multiplications of transposed matrices, C = A{sup T}{center_dot}B{sup T}, in the PUMMA package. Details of the parallel implementation of the algorithms are given, and results are presented for runs on the Intel Touchstone Delta computer.

  3. A Parallel Ghosting Algorithm for The Flexible Distributed Mesh Database

    DOE PAGES

    Mubarak, Misbah; Seol, Seegyoung; Lu, Qiukai; ...

    2013-01-01

    Critical to the scalability of parallel adaptive simulations are parallel control functions including load balancing, reduced inter-process communication and optimal data decomposition. In distributed meshes, many mesh-based applications frequently access neighborhood information for computational purposes which must be transmitted efficiently to avoid parallel performance degradation when the neighbors are on different processors. This article presents a parallel algorithm of creating and deleting data copies, referred to as ghost copies, which localize neighborhood data for computation purposes while minimizing inter-process communication. The key characteristics of the algorithm are: (1) It can create ghost copies of any permissible topological order inmore » a 1D, 2D or 3D mesh based on selected adjacencies. (2) It exploits neighborhood communication patterns during the ghost creation process thus eliminating all-to-all communication. (3) For applications that need neighbors of neighbors, the algorithm can create n number of ghost layers up to a point where the whole partitioned mesh can be ghosted. Strong and weak scaling results are presented for the IBM BG/P and Cray XE6 architectures up to a core count of 32,768 processors. The algorithm also leads to scalable results when used in a parallel super-convergent patch recovery error estimator, an application that frequently accesses neighborhood data to carry out computation.« less

  4. Distributed-memory Parallel Algorithms for Matching and Coloring

    SciTech Connect

    Catalyurek, Umit; Dobrian, Florin; Gebremedhin, Assefaw H.; Halappanavar, Mahantesh; Pothen, Alex

    2011-05-31

    Graph matching and coloring constitute two fundamental classes of combinatorial problems having numerous established as well as emerging applications in computational science and engineering, high-performance computing, and informatics. We provide a snapshot of an on-going work on the design and implementation of new highly-scalable distributed-memory parallel algorithms for two prototypical problems from these classes, edge-weighted matching and distance-1 vertex coloring. Graph algorithms in general have low concurrency and poor data locality, making it challenging to achieve scalability on massively parallel machines. We overcome this challenge by employing a variety of techniques, including approximation, speculation and iteration, optimized communication, and randomization, in concert. We present preliminary results on weak and strong scalability studies conducted on an IBM Blue Gene/P machine employing up to tens of thousands of processors. The results show that the algorithms hold strong potential for computing at petascale.

  5. Parallel paving: An algorithm for generating distributed, adaptive, all-quadrilateral meshes on parallel computers

    SciTech Connect

    Lober, R.R.; Tautges, T.J.; Vaughan, C.T.

    1997-03-01

    Paving is an automated mesh generation algorithm which produces all-quadrilateral elements. It can additionally generate these elements in varying sizes such that the resulting mesh adapts to a function distribution, such as an error function. While powerful, conventional paving is a very serial algorithm in its operation. Parallel paving is the extension of serial paving into parallel environments to perform the same meshing functions as conventional paving only on distributed, discretized models. This extension allows large, adaptive, parallel finite element simulations to take advantage of paving`s meshing capabilities for h-remap remeshing. A significantly modified version of the CUBIT mesh generation code has been developed to host the parallel paving algorithm and demonstrate its capabilities on both two dimensional and three dimensional surface geometries and compare the resulting parallel produced meshes to conventionally paved meshes for mesh quality and algorithm performance. Sandia`s {open_quotes}tiling{close_quotes} dynamic load balancing code has also been extended to work with the paving algorithm to retain parallel efficiency as subdomains undergo iterative mesh refinement.

  6. High performance computational chemistry: Towards fully distributed parallel algorithms

    SciTech Connect

    Guest, M.F.; Apra, E.; Bernholdt, D.E.

    1994-07-01

    An account is given of work in progress within the High Performance Computational Chemistry Group (HPCC) at the Pacific Northwest Laboratory (PNL) to develop molecular modeling software applications for massively parallel processors (MPPs). A discussion of the issues in developing scalable parallel algorithms is presented, with a particular focus on the distribution, as opposed to the replication, of key data structures. Replication of large data structures limits the maximum calculation size by imposing a low ratio of processors to memory. Only applications that distribute both data and computation across processors are truly scalable. The use of shared data structures, which may be independently accessed by each process even in a distributed-memory environment, greatly simplifies development and provides a significant performance enhancement. In describing tools to support this programming paradigm, an outline is given of the implementation and performance of a highly efficient and scalable algorithm to perform quadratically convergent, self-consistent field calculations on molecular systems. A brief account is given of the development of corresponding MPP capabilities in the areas of periodic Hartree Fock, Moeller-Plesset perturbation theory (MP2), density functional theory, and molecular dynamics. Performance figures are presented using both the Intel Touchstone Delta and Kendall Square Research KSR-2 supercomputers.

  7. Parallel grid generation algorithm for distributed memory computers

    NASA Technical Reports Server (NTRS)

    Moitra, Stuti; Moitra, Anutosh

    1994-01-01

    A parallel grid-generation algorithm and its implementation on the Intel iPSC/860 computer are described. The grid-generation scheme is based on an algebraic formulation of homotopic relations. Methods for utilizing the inherent parallelism of the grid-generation scheme are described, and implementation of multiple levELs of parallelism on multiple instruction multiple data machines are indicated. The algorithm is capable of providing near orthogonality and spacing control at solid boundaries while requiring minimal interprocessor communications. Results obtained on the Intel hypercube for a blended wing-body configuration are used to demonstrate the effectiveness of the algorithm. Fortran implementations bAsed on the native programming model of the iPSC/860 computer and the Express system of software tools are reported. Computational gains in execution time speed-up ratios are given.

  8. Parallel and Distributed Computing.

    DTIC Science & Technology

    1986-12-12

    program was devoted to parallel and distributed computing . Support for this part of the program was obtained from the present Army contract and a...Umesh Vazirani. A workshop on parallel and distributed computing was held from May 19 to May 23, 1986 and drew 141 participants. Keywords: Mathematical programming; Protocols; Randomized algorithms. (Author)

  9. Design of multiple sequence alignment algorithms on parallel, distributed memory supercomputers.

    PubMed

    Church, Philip C; Goscinski, Andrzej; Holt, Kathryn; Inouye, Michael; Ghoting, Amol; Makarychev, Konstantin; Reumann, Matthias

    2011-01-01

    The challenge of comparing two or more genomes that have undergone recombination and substantial amounts of segmental loss and gain has recently been addressed for small numbers of genomes. However, datasets of hundreds of genomes are now common and their sizes will only increase in the future. Multiple sequence alignment of hundreds of genomes remains an intractable problem due to quadratic increases in compute time and memory footprint. To date, most alignment algorithms are designed for commodity clusters without parallelism. Hence, we propose the design of a multiple sequence alignment algorithm on massively parallel, distributed memory supercomputers to enable research into comparative genomics on large data sets. Following the methodology of the sequential progressiveMauve algorithm, we design data structures including sequences and sorted k-mer lists on the IBM Blue Gene/P supercomputer (BG/P). Preliminary results show that we can reduce the memory footprint so that we can potentially align over 250 bacterial genomes on a single BG/P compute node. We verify our results on a dataset of E.coli, Shigella and S.pneumoniae genomes. Our implementation returns results matching those of the original algorithm but in 1/2 the time and with 1/4 the memory footprint for scaffold building. In this study, we have laid the basis for multiple sequence alignment of large-scale datasets on a massively parallel, distributed memory supercomputer, thus enabling comparison of hundreds instead of a few genome sequences within reasonable time.

  10. A data distributed parallel algorithm for ray-traced volume rendering

    NASA Technical Reports Server (NTRS)

    Ma, Kwan-Liu; Painter, James S.; Hansen, Charles D.; Krogh, Michael F.

    1993-01-01

    This paper presents a divide-and-conquer ray-traced volume rendering algorithm and a parallel image compositing method, along with their implementation and performance on the Connection Machine CM-5, and networked workstations. This algorithm distributes both the data and the computations to individual processing units to achieve fast, high-quality rendering of high-resolution data. The volume data, once distributed, is left intact. The processing nodes perform local ray tracing of their subvolume concurrently. No communication between processing units is needed during this locally ray-tracing process. A subimage is generated by each processing unit and the final image is obtained by compositing subimages in the proper order, which can be determined a priori. Test results on both the CM-5 and a group of networked workstations demonstrate the practicality of our rendering algorithm and compositing method.

  11. A Screen Space GPGPU Surface LIC Algorithm for Distributed Memory Data Parallel Sort Last Rendering Infrastructures

    NASA Astrophysics Data System (ADS)

    Loring, B.; Karimabadi, H.; Rortershteyn, V.

    2015-10-01

    The surface line integral convolution(LIC) visualization technique produces dense visualization of vector fields on arbitrary surfaces. We present a screen space surface LIC algorithm for use in distributed memory data parallel sort last rendering infrastructures. The motivations for our work are to support analysis of datasets that are too large to fit in the main memory of a single computer and compatibility with prevalent parallel scientific visualization tools such as ParaView and VisIt. By working in screen space using OpenGL we can leverage the computational power of GPUs when they are available and run without them when they are not. We address efficiency and performance issues that arise from the transformation of data from physical to screen space by selecting an alternate screen space domain decomposition. We analyze the algorithm's scaling behavior with and without GPUs on two high performance computing systems using data from turbulent plasma simulations.

  12. A Screen Space GPGPU Surface LIC Algorithm for Distributed Memory Data Parallel Sort Last Rendering Infrastructures

    SciTech Connect

    Loring, Burlen; Karimabadi, Homa; Rortershteyn, Vadim

    2014-07-01

    The surface line integral convolution(LIC) visualization technique produces dense visualization of vector fields on arbitrary surfaces. We present a screen space surface LIC algorithm for use in distributed memory data parallel sort last rendering infrastructures. The motivations for our work are to support analysis of datasets that are too large to fit in the main memory of a single computer and compatibility with prevalent parallel scientific visualization tools such as ParaView and VisIt. By working in screen space using OpenGL we can leverage the computational power of GPUs when they are available and run without them when they are not. We address efficiency and performance issues that arise from the transformation of data from physical to screen space by selecting an alternate screen space domain decomposition. We analyze the algorithm's scaling behavior with and without GPUs on two high performance computing systems using data from turbulent plasma simulations.

  13. Parallel multi-join query optimization algorithm for distributed sensor network in the internet of things

    NASA Astrophysics Data System (ADS)

    Zheng, Yan

    2015-03-01

    Internet of things (IoT), focusing on providing users with information exchange and intelligent control, attracts a lot of attention of researchers from all over the world since the beginning of this century. IoT is consisted of large scale of sensor nodes and data processing units, and the most important features of IoT can be illustrated as energy confinement, efficient communication and high redundancy. With the sensor nodes increment, the communication efficiency and the available communication band width become bottle necks. Many research work is based on the instance which the number of joins is less. However, it is not proper to the increasing multi-join query in whole internet of things. To improve the communication efficiency between parallel units in the distributed sensor network, this paper proposed parallel query optimization algorithm based on distribution attributes cost graph. The storage information relations and the network communication cost are considered in this algorithm, and an optimized information changing rule is established. The experimental result shows that the algorithm has good performance, and it would effectively use the resource of each node in the distributed sensor network. Therefore, executive efficiency of multi-join query between different nodes could be improved.

  14. PUMMA: Parallel Universal Matrix Multiplication Algorithms on distributed memory concurrent computers

    SciTech Connect

    Choi, Jaeyoung; Walker, D.W.; Dongarra, J.J. |

    1993-08-01

    This paper describes the Parallel Universal Matrix Multiplication Algorithms (PUMMA) on distributed memory concurrent computers. The PUMMA package includes not only the non-transposed matrix multiplication routine C = A{center_dot}B, but also transposed multiplication routines C = A{sup T}{center_dot}B, C = A{center_dot}B{sup T}, and C = A{sup T}{center_dot}B{sup T}, for a block scattered data distribution. The routines perform efficiently for a wide range of processor configurations and block sizes. The PUMMA together provide the same functionality as the Level 3 BLAS routine xGEMM. Details of the parallel implementation of the routines are given, and results are presented for runs on the Intel Touchstone Delta computer.

  15. A data distributed, parallel algorithm for ray-traced volume rendering

    SciTech Connect

    Ma, Kwan-Liu; Painter, J.S.; Hansen, C.D.; Krogh, M.F.

    1993-03-30

    This paper presents a divide-and-conquer ray-traced volume rendering algorithm and its implementation on networked workstations and a massively parallel computer, the Connection Machine CM-5. This algorithm distributes the data and the computational load to individual processing units to achieve fast, high-quality rendering of high-resolution data, even when only a modest amount of memory is available on each machine. The volume data, once distributed, is left intact. The processing nodes perform local ray-tracing of their subvolume concurrently. No communication between processing units is needed during this locally ray-tracing process. A subimage is generated by each processing unit and the final image is obtained by compositing subimages in the proper order, which can be determined a priori. Implementations and tests on a group of networked workstations and on the Thinking Machines CM-5 demonstrate the practicality of our algorithm and expose different performance tuning issues for each platform. We use data sets from medical imaging and computational fluid dynamics simulations in the study of this algorithm.

  16. A distributed parallel genetic algorithm of placement strategy for virtual machines deployment on cloud platform.

    PubMed

    Dong, Yu-Shuang; Xu, Gao-Chao; Fu, Xiao-Dong

    2014-01-01

    The cloud platform provides various services to users. More and more cloud centers provide infrastructure as the main way of operating. To improve the utilization rate of the cloud center and to decrease the operating cost, the cloud center provides services according to requirements of users by sharding the resources with virtualization. Considering both QoS for users and cost saving for cloud computing providers, we try to maximize performance and minimize energy cost as well. In this paper, we propose a distributed parallel genetic algorithm (DPGA) of placement strategy for virtual machines deployment on cloud platform. It executes the genetic algorithm parallelly and distributedly on several selected physical hosts in the first stage. Then it continues to execute the genetic algorithm of the second stage with solutions obtained from the first stage as the initial population. The solution calculated by the genetic algorithm of the second stage is the optimal one of the proposed approach. The experimental results show that the proposed placement strategy of VM deployment can ensure QoS for users and it is more effective and more energy efficient than other placement strategies on the cloud platform.

  17. A Distributed Parallel Genetic Algorithm of Placement Strategy for Virtual Machines Deployment on Cloud Platform

    PubMed Central

    Dong, Yu-Shuang; Xu, Gao-Chao; Fu, Xiao-Dong

    2014-01-01

    The cloud platform provides various services to users. More and more cloud centers provide infrastructure as the main way of operating. To improve the utilization rate of the cloud center and to decrease the operating cost, the cloud center provides services according to requirements of users by sharding the resources with virtualization. Considering both QoS for users and cost saving for cloud computing providers, we try to maximize performance and minimize energy cost as well. In this paper, we propose a distributed parallel genetic algorithm (DPGA) of placement strategy for virtual machines deployment on cloud platform. It executes the genetic algorithm parallelly and distributedly on several selected physical hosts in the first stage. Then it continues to execute the genetic algorithm of the second stage with solutions obtained from the first stage as the initial population. The solution calculated by the genetic algorithm of the second stage is the optimal one of the proposed approach. The experimental results show that the proposed placement strategy of VM deployment can ensure QoS for users and it is more effective and more energy efficient than other placement strategies on the cloud platform. PMID:25097872

  18. Totally parallel multilevel algorithms

    NASA Technical Reports Server (NTRS)

    Frederickson, Paul O.

    1988-01-01

    Four totally parallel algorithms for the solution of a sparse linear system have common characteristics which become quite apparent when they are implemented on a highly parallel hypercube such as the CM2. These four algorithms are Parallel Superconvergent Multigrid (PSMG) of Frederickson and McBryan, Robust Multigrid (RMG) of Hackbusch, the FFT based Spectral Algorithm, and Parallel Cyclic Reduction. In fact, all four can be formulated as particular cases of the same totally parallel multilevel algorithm, which are referred to as TPMA. In certain cases the spectral radius of TPMA is zero, and it is recognized to be a direct algorithm. In many other cases the spectral radius, although not zero, is small enough that a single iteration per timestep keeps the local error within the required tolerance.

  19. Parallel Wolff Cluster Algorithms

    NASA Astrophysics Data System (ADS)

    Bae, S.; Ko, S. H.; Coddington, P. D.

    The Wolff single-cluster algorithm is the most efficient method known for Monte Carlo simulation of many spin models. Due to the irregular size, shape and position of the Wolff clusters, this method does not easily lend itself to efficient parallel implementation, so that simulations using this method have thus far been confined to workstations and vector machines. Here we present two parallel implementations of this algorithm, and show that one gives fairly good performance on a MIMD parallel computer.

  20. A brief summary on formalizing parallel tensor distributions redistributions and algorithm derivations.

    SciTech Connect

    Schatz, Martin D.; Kolda, Tamara G.; van de Geijn, Robert

    2015-09-01

    Large-scale datasets in computational chemistry typically require distributed-memory parallel methods to perform a special operation known as tensor contraction. Tensors are multidimensional arrays, and a tensor contraction is akin to matrix multiplication with special types of permutations. Creating an efficient algorithm and optimized im- plementation in this domain is complex, tedious, and error-prone. To address this, we develop a notation to express data distributions so that we can apply use automated methods to find optimized implementations for tensor contractions. We consider the spin-adapted coupled cluster singles and doubles method from computational chemistry and use our methodology to produce an efficient implementation. Experiments per- formed on the IBM Blue Gene/Q and Cray XC30 demonstrate impact both improved performance and reduced memory consumption.

  1. Parallel Algorithms and Patterns

    SciTech Connect

    Robey, Robert W.

    2016-06-16

    This is a powerpoint presentation on parallel algorithms and patterns. A parallel algorithm is a well-defined, step-by-step computational procedure that emphasizes concurrency to solve a problem. Examples of problems include: Sorting, searching, optimization, matrix operations. A parallel pattern is a computational step in a sequence of independent, potentially concurrent operations that occurs in diverse scenarios with some frequency. Examples are: Reductions, prefix scans, ghost cell updates. We only touch on parallel patterns in this presentation. It really deserves its own detailed discussion which Gabe Rockefeller would like to develop.

  2. Parallel algorithm development

    SciTech Connect

    Adams, T.F.

    1996-06-01

    Rapid changes in parallel computing technology are causing significant changes in the strategies being used for parallel algorithm development. One approach is simply to write computer code in a standard language like FORTRAN 77 or with the expectation that the compiler will produce executable code that will run in parallel. The alternatives are: (1) to build explicit message passing directly into the source code; or (2) to write source code without explicit reference to message passing or parallelism, but use a general communications library to provide efficient parallel execution. Application of these strategies is illustrated with examples of codes currently under development.

  3. Implementation of Parallel Algorithms

    DTIC Science & Technology

    1993-06-30

    their socia ’ relations or to achieve some goals. For example, we define a pair-wise force law of i epulsion and attraction for a group of identical...quantization based compression schemes. Photo-refractive crystals, which provide high density recording in real time, are used as our holographic media . The...of Parallel Algorithms (J. Reif, ed.). Kluwer Academic Pu’ ishers, 1993. (4) "A Dynamic Separator Algorithm", D. Armon and J. Reif. To appear in

  4. Molecular simulation workflows as parallel algorithms: the execution engine of Copernicus, a distributed high-performance computing platform.

    PubMed

    Pronk, Sander; Pouya, Iman; Lundborg, Magnus; Rotskoff, Grant; Wesén, Björn; Kasson, Peter M; Lindahl, Erik

    2015-06-09

    Computational chemistry and other simulation fields are critically dependent on computing resources, but few problems scale efficiently to the hundreds of thousands of processors available in current supercomputers-particularly for molecular dynamics. This has turned into a bottleneck as new hardware generations primarily provide more processing units rather than making individual units much faster, which simulation applications are addressing by increasingly focusing on sampling with algorithms such as free-energy perturbation, Markov state modeling, metadynamics, or milestoning. All these rely on combining results from multiple simulations into a single observation. They are potentially powerful approaches that aim to predict experimental observables directly, but this comes at the expense of added complexity in selecting sampling strategies and keeping track of dozens to thousands of simulations and their dependencies. Here, we describe how the distributed execution framework Copernicus allows the expression of such algorithms in generic workflows: dataflow programs. Because dataflow algorithms explicitly state dependencies of each constituent part, algorithms only need to be described on conceptual level, after which the execution is maximally parallel. The fully automated execution facilitates the optimization of these algorithms with adaptive sampling, where undersampled regions are automatically detected and targeted without user intervention. We show how several such algorithms can be formulated for computational chemistry problems, and how they are executed efficiently with many loosely coupled simulations using either distributed or parallel resources with Copernicus.

  5. The Structure of Parallel Algorithms.

    DTIC Science & Technology

    1979-08-01

    parallel architectures and parallel algorithms see [Anderson and Jensen 75, Stone 75, Kung 76, Enslow 77, Kuck 77, Ramamoorthy and Li 77, Sameh 77, Heller...the Routing Time on a Parallel Computer with a Fixed Interconnection Network, In Kuck., D. J., Lawrie, D.H. and Sameh , A.H., editor, High Speed...Letters 5(4):107-112, October 1976. [ Sameh 77] Sameh , A.H. Numerical Parallel Algorithms -- A Survey. In Hifh Speed Computer and AlgorLthm Organization

  6. Predicting Protein Structure Using Parallel Genetic Algorithms.

    DTIC Science & Technology

    1994-12-01

    34 IEEE Transactions on Systems, Man and Cybernetics, 10(9) (September 1980). 16. De Jong, Kenneth A. "On Using Genetic Algoriths to Search Program...By " Predicting rotein Structure D istribticfiar.. ................ Using Parallel Genetic Algorithms ,Avaiu " ’ •"... Dist THESIS I IGeorge H...iiLite-d Approved for public release; distribution unlimited AFIT/ GCS /ENG/94D-03 Predicting Protein Structure Using Parallel Genetic Algorithms

  7. A Parallel Rendering Algorithm for MIMD Architectures

    NASA Technical Reports Server (NTRS)

    Crockett, Thomas W.; Orloff, Tobias

    1991-01-01

    Applications such as animation and scientific visualization demand high performance rendering of complex three dimensional scenes. To deliver the necessary rendering rates, highly parallel hardware architectures are required. The challenge is then to design algorithms and software which effectively use the hardware parallelism. A rendering algorithm targeted to distributed memory MIMD architectures is described. For maximum performance, the algorithm exploits both object-level and pixel-level parallelism. The behavior of the algorithm is examined both analytically and experimentally. Its performance for large numbers of processors is found to be limited primarily by communication overheads. An experimental implementation for the Intel iPSC/860 shows increasing performance from 1 to 128 processors across a wide range of scene complexities. It is shown that minimal modifications to the algorithm will adapt it for use on shared memory architectures as well.

  8. Parallel Algorithms for Image Analysis.

    DTIC Science & Technology

    1982-06-01

    8217 _ _ _ _ _ _ _ 4. TITLE (aid Subtitle) S. TYPE OF REPORT & PERIOD COVERED PARALLEL ALGORITHMS FOR IMAGE ANALYSIS TECHNICAL 6. PERFORMING O4G. REPORT NUMBER TR-1180...Continue on reverse side it neceesary aid Identlfy by block number) Image processing; image analysis ; parallel processing; cellular computers. 20... IMAGE ANALYSIS TECHNICAL 6. PERFORMING ONG. REPORT NUMBER TR-1180 - 7. AUTHOR(&) S. CONTRACT OR GRANT NUMBER(s) Azriel Rosenfeld AFOSR-77-3271 9

  9. An efficient parallel termination detection algorithm

    SciTech Connect

    Baker, A. H.; Crivelli, S.; Jessup, E. R.

    2004-05-27

    Information local to any one processor is insufficient to monitor the overall progress of most distributed computations. Typically, a second distributed computation for detecting termination of the main computation is necessary. In order to be a useful computational tool, the termination detection routine must operate concurrently with the main computation, adding minimal overhead, and it must promptly and correctly detect termination when it occurs. In this paper, we present a new algorithm for detecting the termination of a parallel computation on distributed-memory MIMD computers that satisfies all of those criteria. A variety of termination detection algorithms have been devised. Of these, the algorithm presented by Sinha, Kale, and Ramkumar (henceforth, the SKR algorithm) is unique in its ability to adapt to the load conditions of the system on which it runs, thereby minimizing the impact of termination detection on performance. Because their algorithm also detects termination quickly, we consider it to be the most efficient practical algorithm presently available. The termination detection algorithm presented here was developed for use in the PMESC programming library for distributed-memory MIMD computers. Like the SKR algorithm, our algorithm adapts to system loads and imposes little overhead. Also like the SKR algorithm, ours is tree-based, and it does not depend on any assumptions about the physical interconnection topology of the processors or the specifics of the distributed computation. In addition, our algorithm is easier to implement and requires only half as many tree traverses as does the SKR algorithm. This paper is organized as follows. In section 2, we define our computational model. In section 3, we review the SKR algorithm. We introduce our new algorithm in section 4, and prove its correctness in section 5. We discuss its efficiency and present experimental results in section 6.

  10. The Complexity of Parallel Algorithms,

    DTIC Science & Technology

    1985-11-01

    Much of this work was done in collaboration with my advisor, Ernst Mayr . He was also supported in part by ONR contract N00014-85-C-0731. F ’. Table...Helinbold and Mayr in their algorithn to compute an optimal two processor schedule [HM2]. One of the promising developments in parallel algorithms is that...lei can be solved by it fast parallel algorithmmmi if the nmlmmmibers are smiall. llehmibold and Mayr JIlM I] have slhowm that. if Ole job timies are

  11. Parallel job-scheduling algorithms

    SciTech Connect

    Rodger, S.H.

    1989-01-01

    In this thesis, we consider solving job scheduling problems on the CREW PRAM model. We show how to adapt Cole's pipeline merge technique to yield several efficient parallel algorithms for a number of job scheduling problems and one optimal parallel algorithm for the following job scheduling problem: Given a set of n jobs defined by release times, deadlines and processing times, find a schedule that minimizes the maximum lateness of the jobs and allows preemption when the jobs are scheduled to run on one machine. In addition, we present the first NC algorithm for the following job scheduling problem: Given a set of n jobs defined by release times, deadlines and unit processing times, determine if there is a schedule of jobs on one machine, and calculate the schedule if it exists. We identify the notion of a canonical schedule, which is the type of schedule our algorithm computes if there is a schedule. Our algorithm runs in O((log n){sup 2}) time and uses O(n{sup 2}k{sup 2}) processors, where k is the minimum number of distinct offsets of release times or deadlines.

  12. Parallel Implicit Algorithms for CFD

    NASA Technical Reports Server (NTRS)

    Keyes, David E.

    1998-01-01

    The main goal of this project was efficient distributed parallel and workstation cluster implementations of Newton-Krylov-Schwarz (NKS) solvers for implicit Computational Fluid Dynamics (CFD.) "Newton" refers to a quadratically convergent nonlinear iteration using gradient information based on the true residual, "Krylov" to an inner linear iteration that accesses the Jacobian matrix only through highly parallelizable sparse matrix-vector products, and "Schwarz" to a domain decomposition form of preconditioning the inner Krylov iterations with primarily neighbor-only exchange of data between the processors. Prior experience has established that Newton-Krylov methods are competitive solvers in the CFD context and that Krylov-Schwarz methods port well to distributed memory computers. The combination of the techniques into Newton-Krylov-Schwarz was implemented on 2D and 3D unstructured Euler codes on the parallel testbeds that used to be at LaRC and on several other parallel computers operated by other agencies or made available by the vendors. Early implementations were made directly in Massively Parallel Integration (MPI) with parallel solvers we adapted from legacy NASA codes and enhanced for full NKS functionality. Later implementations were made in the framework of the PETSC library from Argonne National Laboratory, which now includes pseudo-transient continuation Newton-Krylov-Schwarz solver capability (as a result of demands we made upon PETSC during our early porting experiences). A secondary project pursued with funding from this contract was parallel implicit solvers in acoustics, specifically in the Helmholtz formulation. A 2D acoustic inverse problem has been solved in parallel within the PETSC framework.

  13. Parallel implementation and evaluation of motion estimation system algorithms on a distributed memory multiprocessor using knowledge based mappings

    NASA Technical Reports Server (NTRS)

    Choudhary, Alok Nidhi; Leung, Mun K.; Huang, Thomas S.; Patel, Janak H.

    1989-01-01

    Several techniques to perform static and dynamic load balancing techniques for vision systems are presented. These techniques are novel in the sense that they capture the computational requirements of a task by examining the data when it is produced. Furthermore, they can be applied to many vision systems because many algorithms in different systems are either the same, or have similar computational characteristics. These techniques are evaluated by applying them on a parallel implementation of the algorithms in a motion estimation system on a hypercube multiprocessor system. The motion estimation system consists of the following steps: (1) extraction of features; (2) stereo match of images in one time instant; (3) time match of images from different time instants; (4) stereo match to compute final unambiguous points; and (5) computation of motion parameters. It is shown that the performance gains when these data decomposition and load balancing techniques are used are significant and the overhead of using these techniques is minimal.

  14. A parallel algorithm for random searches

    NASA Astrophysics Data System (ADS)

    Wosniack, M. E.; Raposo, E. P.; Viswanathan, G. M.; da Luz, M. G. E.

    2015-11-01

    We discuss a parallelization procedure for a two-dimensional random search of a single individual, a typical sequential process. To assure the same features of the sequential random search in the parallel version, we analyze the former spatial patterns of the encountered targets for different search strategies and densities of homogeneously distributed targets. We identify a lognormal tendency for the distribution of distances between consecutively detected targets. Then, by assigning the distinct mean and standard deviation of this distribution for each corresponding configuration in the parallel simulations (constituted by parallel random walkers), we are able to recover important statistical properties, e.g., the target detection efficiency, of the original problem. The proposed parallel approach presents a speedup of nearly one order of magnitude compared with the sequential implementation. This algorithm can be easily adapted to different instances, as searches in three dimensions. Its possible range of applicability covers problems in areas as diverse as automated computer searchers in high-capacity databases and animal foraging.

  15. PIPS-SBB: A Parallel Distributed-Memory Branch-and-Bound Algorithm for Stochastic Mixed-Integer Programs

    DOE PAGES

    Munguia, Lluis-Miquel; Oxberry, Geoffrey; Rajan, Deepak

    2016-05-01

    Stochastic mixed-integer programs (SMIPs) deal with optimization under uncertainty at many levels of the decision-making process. When solved as extensive formulation mixed- integer programs, problem instances can exceed available memory on a single workstation. In order to overcome this limitation, we present PIPS-SBB: a distributed-memory parallel stochastic MIP solver that takes advantage of parallelism at multiple levels of the optimization process. We also show promising results on the SIPLIB benchmark by combining methods known for accelerating Branch and Bound (B&B) methods with new ideas that leverage the structure of SMIPs. Finally, we expect the performance of PIPS-SBB to improve furthermore » as more functionality is added in the future.« less

  16. PIPS-SBB: A Parallel Distributed-Memory Branch-and-Bound Algorithm for Stochastic Mixed-Integer Programs

    SciTech Connect

    Munguia, Lluis-Miquel; Oxberry, Geoffrey; Rajan, Deepak

    2016-05-01

    Stochastic mixed-integer programs (SMIPs) deal with optimization under uncertainty at many levels of the decision-making process. When solved as extensive formulation mixed- integer programs, problem instances can exceed available memory on a single workstation. In order to overcome this limitation, we present PIPS-SBB: a distributed-memory parallel stochastic MIP solver that takes advantage of parallelism at multiple levels of the optimization process. We also show promising results on the SIPLIB benchmark by combining methods known for accelerating Branch and Bound (B&B) methods with new ideas that leverage the structure of SMIPs. Finally, we expect the performance of PIPS-SBB to improve further as more functionality is added in the future.

  17. PIPS-SBB: A Parallel Distributed-Memory Branch-and-Bound Algorithm for Stochastic Mixed-Integer Programs

    SciTech Connect

    Munguia, Lluis-Miquel; Oxberry, Geoffrey; Rajan, Deepak

    2016-05-01

    Stochastic mixed-integer programs (SMIPs) deal with optimization under uncertainty at many levels of the decision-making process. When solved as extensive formulation mixed- integer programs, problem instances can exceed available memory on a single workstation. In order to overcome this limitation, we present PIPS-SBB: a distributed-memory parallel stochastic MIP solver that takes advantage of parallelism at multiple levels of the optimization process. We also show promising results on the SIPLIB benchmark by combining methods known for accelerating Branch and Bound (B&B) methods with new ideas that leverage the structure of SMIPs. Finally, we expect the performance of PIPS-SBB to improve further as more functionality is added in the future.

  18. Mapping robust parallel multigrid algorithms to scalable memory architectures

    NASA Technical Reports Server (NTRS)

    Overman, Andrea; Vanrosendale, John

    1993-01-01

    The convergence rate of standard multigrid algorithms degenerates on problems with stretched grids or anisotropic operators. The usual cure for this is the use of line or plane relaxation. However, multigrid algorithms based on line and plane relaxation have limited and awkward parallelism and are quite difficult to map effectively to highly parallel architectures. Newer multigrid algorithms that overcome anisotropy through the use of multiple coarse grids rather than line relaxation are better suited to massively parallel architectures because they require only simple point-relaxation smoothers. The parallel implementation of a V-cycle multiple semi-coarsened grid (MSG) algorithm or distributed-memory architectures such as the Intel iPSC/860 and Paragon computers is addressed. The MSG algorithms provide two levels of parallelism: parallelism within the relaxation or interpolation on each grid and across the grids on each multigrid level. Both levels of parallelism must be exploited to map these algorithms effectively to parallel architectures. A mapping of an MSG algorithm to distributed-memory architectures that demonstrate how both levels of parallelism can be exploited is described. The results is a robust and effective multigrid algorithm for distributed-memory machines.

  19. Parallel algorithms for unconstrained optimizations by multisplitting

    SciTech Connect

    He, Qing

    1994-12-31

    In this paper a new parallel iterative algorithm for unconstrained optimization using the idea of multisplitting is proposed. This algorithm uses the existing sequential algorithms without any parallelization. Some convergence and numerical results for this algorithm are presented. The experiments are performed on an Intel iPSC/860 Hyper Cube with 64 nodes. It is interesting that the sequential implementation on one node shows that if the problem is split properly, the algorithm converges much faster than one without splitting.

  20. A parallel algorithm for global routing

    NASA Technical Reports Server (NTRS)

    Brouwer, Randall J.; Banerjee, Prithviraj

    1990-01-01

    A Parallel Hierarchical algorithm for Global Routing (PHIGURE) is presented. The router is based on the work of Burstein and Pelavin, but has many extensions for general global routing and parallel execution. Main features of the algorithm include structured hierarchical decomposition into separate independent tasks which are suitable for parallel execution and adaptive simplex solution for adding feedthroughs and adjusting channel heights for row-based layout. Alternative decomposition methods and the various levels of parallelism available in the algorithm are examined closely. The algorithm is described and results are presented for a shared-memory multiprocessor implementation.

  1. Genetic algorithms using SISAL parallel programming language

    SciTech Connect

    Tejada, S.

    1994-05-06

    Genetic algorithms are a mathematical optimization technique developed by John Holland at the University of Michigan [1]. The SISAL programming language possesses many of the characteristics desired to implement genetic algorithms. SISAL is a deterministic, functional programming language which is inherently parallel. Because SISAL is functional and based on mathematical concepts, genetic algorithms can be efficiently translated into the language. Several of the steps involved in genetic algorithms, such as mutation, crossover, and fitness evaluation, can be parallelized using SISAL. In this paper I will l discuss the implementation and performance of parallel genetic algorithms in SISAL.

  2. Linear Bregman algorithm implemented in parallel GPU

    NASA Astrophysics Data System (ADS)

    Li, Pengyan; Ke, Jue; Sui, Dong; Wei, Ping

    2015-08-01

    At present, most compressed sensing (CS) algorithms have poor converging speed, thus are difficult to run on PC. To deal with this issue, we use a parallel GPU, to implement a broadly used compressed sensing algorithm, the Linear Bregman algorithm. Linear iterative Bregman algorithm is a reconstruction algorithm proposed by Osher and Cai. Compared with other CS reconstruction algorithms, the linear Bregman algorithm only involves the vector and matrix multiplication and thresholding operation, and is simpler and more efficient for programming. We use C as a development language and adopt CUDA (Compute Unified Device Architecture) as parallel computing architectures. In this paper, we compared the parallel Bregman algorithm with traditional CPU realized Bregaman algorithm. In addition, we also compared the parallel Bregman algorithm with other CS reconstruction algorithms, such as OMP and TwIST algorithms. Compared with these two algorithms, the result of this paper shows that, the parallel Bregman algorithm needs shorter time, and thus is more convenient for real-time object reconstruction, which is important to people's fast growing demand to information technology.

  3. Array distribution in data-parallel programs

    NASA Technical Reports Server (NTRS)

    Chatterjee, Siddhartha; Gilbert, John R.; Schreiber, Robert; Sheffler, Thomas J.

    1994-01-01

    We consider distribution at compile time of the array data in a distributed-memory implementation of a data-parallel program written in a language like Fortran 90. We allow dynamic redistribution of data and define a heuristic algorithmic framework that chooses distribution parameters to minimize an estimate of program completion time. We represent the program as an alignment-distribution graph. We propose a divide-and-conquer algorithm for distribution that initially assigns a common distribution to each node of the graph and successively refines this assignment, taking computation, realignment, and redistribution costs into account. We explain how to estimate the effect of distribution on computation cost and how to choose a candidate set of distributions. We present the results of an implementation of our algorithms on several test problems.

  4. A parallel Jacobson-Oksman optimization algorithm. [parallel processing (computers)

    NASA Technical Reports Server (NTRS)

    Straeter, T. A.; Markos, A. T.

    1975-01-01

    A gradient-dependent optimization technique which exploits the vector-streaming or parallel-computing capabilities of some modern computers is presented. The algorithm, derived by assuming that the function to be minimized is homogeneous, is a modification of the Jacobson-Oksman serial minimization method. In addition to describing the algorithm, conditions insuring the convergence of the iterates of the algorithm and the results of numerical experiments on a group of sample test functions are presented. The results of these experiments indicate that this algorithm will solve optimization problems in less computing time than conventional serial methods on machines having vector-streaming or parallel-computing capabilities.

  5. Data-parallel algorithms for image computing

    NASA Astrophysics Data System (ADS)

    Carlotto, Mark J.

    1990-11-01

    Data-parallel algorithms for image computing on the Connection Machine are described. After a brief review of some basic programming concepts in *Lip, a parallel extension of Common Lisp, data-parallel programming paradigms based on a local (diffusion-like) model of computation, the scan model of computation, a general interprocessor communications model, and a region-based model are introduced. Algorithms for connected component labeling, distance transformation, Voronoi diagrams, finding minimum cost paths, local means, shape-from-shading, hidden surface calculations, affine transformation, oblique parallel projection, and spatial operations over regions are presented. An new algorithm for interpolating irregularly spaced data via Voronoi diagrams is also described.

  6. Efficient Parallel Algorithm For Direct Numerical Simulation of Turbulent Flows

    NASA Technical Reports Server (NTRS)

    Moitra, Stuti; Gatski, Thomas B.

    1997-01-01

    A distributed algorithm for a high-order-accurate finite-difference approach to the direct numerical simulation (DNS) of transition and turbulence in compressible flows is described. This work has two major objectives. The first objective is to demonstrate that parallel and distributed-memory machines can be successfully and efficiently used to solve computationally intensive and input/output intensive algorithms of the DNS class. The second objective is to show that the computational complexity involved in solving the tridiagonal systems inherent in the DNS algorithm can be reduced by algorithm innovations that obviate the need to use a parallelized tridiagonal solver.

  7. Runtime support for parallelizing data mining algorithms

    NASA Astrophysics Data System (ADS)

    Jin, Ruoming; Agrawal, Gagan

    2002-03-01

    With recent technological advances, shared memory parallel machines have become more scalable, and offer large main memories and high bus bandwidths. They are emerging as good platforms for data warehousing and data mining. In this paper, we focus on shared memory parallelization of data mining algorithms. We have developed a series of techniques for parallelization of data mining algorithms, including full replication, full locking, fixed locking, optimized full locking, and cache-sensitive locking. Unlike previous work on shared memory parallelization of specific data mining algorithms, all of our techniques apply to a large number of common data mining algorithms. In addition, we propose a reduction-object based interface for specifying a data mining algorithm. We show how our runtime system can apply any of the technique we have developed starting from a common specification of the algorithm.

  8. Parallel simulated annealing algorithms for cell placement on hypercube multiprocessors

    NASA Technical Reports Server (NTRS)

    Banerjee, Prithviraj; Jones, Mark Howard; Sargent, Jeff S.

    1990-01-01

    Two parallel algorithms for standard cell placement using simulated annealing are developed to run on distributed-memory message-passing hypercube multiprocessors. The cells can be mapped in a two-dimensional area of a chip onto processors in an n-dimensional hypercube in two ways, such that both small and large cell exchange and displacement moves can be applied. The computation of the cost function in parallel among all the processors in the hypercube is described, along with a distributed data structure that needs to be stored in the hypercube to support the parallel cost evaluation. A novel tree broadcasting strategy is used extensively for updating cell locations in the parallel environment. A dynamic parallel annealing schedule estimates the errors due to interacting parallel moves and adapts the rate of synchronization automatically. Two novel approaches in controlling error in parallel algorithms are described: heuristic cell coloring and adaptive sequence control.

  9. Parallel simulated annealing algorithms for cell placement on hypercube multiprocessors

    NASA Technical Reports Server (NTRS)

    Banerjee, Prithviraj; Jones, Mark Howard; Sargent, Jeff S.

    1990-01-01

    Two parallel algorithms for standard cell placement using simulated annealing are developed to run on distributed-memory message-passing hypercube multiprocessors. The cells can be mapped in a two-dimensional area of a chip onto processors in an n-dimensional hypercube in two ways, such that both small and large cell exchange and displacement moves can be applied. The computation of the cost function in parallel among all the processors in the hypercube is described, along with a distributed data structure that needs to be stored in the hypercube to support the parallel cost evaluation. A novel tree broadcasting strategy is used extensively for updating cell locations in the parallel environment. A dynamic parallel annealing schedule estimates the errors due to interacting parallel moves and adapts the rate of synchronization automatically. Two novel approaches in controlling error in parallel algorithms are described: heuristic cell coloring and adaptive sequence control.

  10. A parallel variable metric optimization algorithm

    NASA Technical Reports Server (NTRS)

    Straeter, T. A.

    1973-01-01

    An algorithm, designed to exploit the parallel computing or vector streaming (pipeline) capabilities of computers is presented. When p is the degree of parallelism, then one cycle of the parallel variable metric algorithm is defined as follows: first, the function and its gradient are computed in parallel at p different values of the independent variable; then the metric is modified by p rank-one corrections; and finally, a single univariant minimization is carried out in the Newton-like direction. Several properties of this algorithm are established. The convergence of the iterates to the solution is proved for a quadratic functional on a real separable Hilbert space. For a finite-dimensional space the convergence is in one cycle when p equals the dimension of the space. Results of numerical experiments indicate that the new algorithm will exploit parallel or pipeline computing capabilities to effect faster convergence than serial techniques.

  11. A parallel algorithm for channel routing on a hypercube

    NASA Technical Reports Server (NTRS)

    Brouwer, Randall; Banerjee, Prithviraj

    1987-01-01

    A new parallel simulated annealing algorithm for channel routing on a P processor hypercube is presented. The basic idea used is to partition a set of tracks equally among processors in the hypercube. In parallel, P/2 pairs of processors perform displacements and exchanges of nets between tracks, compute the changes in cost functions, and accept moves using a parallel annealing criteria. Through the use of a unique distributed data structure, it is possible to minimize message traffic and add versatility and efficiency in a parallel routing tool. The algorithm has been implemented and is being tested on some of the popular channel problems from the literature.

  12. Parallel Algorithms for the Exascale Era

    SciTech Connect

    Robey, Robert W.

    2016-10-19

    New parallel algorithms are needed to reach the Exascale level of parallelism with millions of cores. We look at some of the research developed by students in projects at LANL. The research blends ideas from the early days of computing while weaving in the fresh approach brought by students new to the field of high performance computing. We look at reproducibility of global sums and why it is important to parallel computing. Next we look at how the concept of hashing has led to the development of more scalable algorithms suitable for next-generation parallel computers. Nearly all of this work has been done by undergraduates and published in leading scientific journals.

  13. A parallelization of the row-searching algorithm

    NASA Astrophysics Data System (ADS)

    Yaici, Malika; Khaled, Hayet; Khaled, Zakia; Bentahar, Athmane

    2012-11-01

    The problem dealt in this paper concerns the parallelization of the row-searching algorithm which allows the search for linearly dependant rows on a given matrix and its implementation on MPI (Message Passing Interface) environment. This algorithm is largely used in control theory and more specifically in solving the famous diophantine equation. An introduction to the diophantine equation is presented, then two parallelization approaches of the algorithm are detailed. The first distributes a set of rows on processes (processors) and the second makes a distribution per blocks. The sequential algorithm and its two parallel forms are implemented using MPI routines, then modelled using UML (Unified Modelling Language) and finally evaluated using algorithmic complexity.

  14. Parallel algorithms for contour extraction and coding

    NASA Astrophysics Data System (ADS)

    Dinstein, Its'hak; Landau, Gad M.

    1990-07-01

    A parallel approach to contour extraction and coding on an Exclusive Read Exclusive Write (EREW) Parallel Random Access Machine (PRAM) is presented and analyzed. The algorithm is intended for binary images. The labeled contours can be represented by lists of coordinates, and/or chain codes, and/or any other user designed codes. Using O(n2/log n) processors, the algorithm runs in O(logn) time, where n by n is the size of the processed binary image.

  15. MULTIOBJECTIVE PARALLEL GENETIC ALGORITHM FOR WASTE MINIMIZATION

    EPA Science Inventory

    In this research we have developed an efficient multiobjective parallel genetic algorithm (MOPGA) for waste minimization problems. This MOPGA integrates PGAPack (Levine, 1996) and NSGA-II (Deb, 2000) with novel modifications. PGAPack is a master-slave parallel implementation of a...

  16. MULTIOBJECTIVE PARALLEL GENETIC ALGORITHM FOR WASTE MINIMIZATION

    EPA Science Inventory

    In this research we have developed an efficient multiobjective parallel genetic algorithm (MOPGA) for waste minimization problems. This MOPGA integrates PGAPack (Levine, 1996) and NSGA-II (Deb, 2000) with novel modifications. PGAPack is a master-slave parallel implementation of a...

  17. Parallel Architectures and Algorithms for Image Understanding

    DTIC Science & Technology

    1990-05-17

    A 11. TITLE (Include Security Classification) -. Parallel Architectures.’and Algorithms for Image Understanding Final Thchnical Report 12. PERSONAL...AUTHOR(S) R. Nevatia and V.K. Prasanna-Kumar 13a. TYPE OF REPORT 113b. TIME COVERED 14. DATE OF REPORT (Year, Month, Day) 15. PAGE COUNT Final Technical...identified. A generic parallel model.. of computation employing electro optical d vices is developed. Parallel techniques for image computations are

  18. Parallel Algorithms for PDE Solvers

    DTIC Science & Technology

    1988-07-15

    This report lists all of the 39 scientific publications , these, technical reports and conference presentations supported by the grant AFOSR 84-0385. The principal focus of the results are in 1) The Collocation Method: New versions developed for parallel machines, new results on the convergence and new

  19. Parallel algorithms for semi-lagrangian advection

    NASA Astrophysics Data System (ADS)

    Malevsky, A. V.; Thomas, S. J.

    1997-08-01

    Numerical time step limitations associated with the explicit treatment of advection-dominated problems in computational fluid dynamics are often relaxed by employing Eulerian-Lagrangian methods. These are also known as semi-Lagrangian methods in the atmospheric sciences. Such methods involve backward time integration of a characteristic equation to find the departure point of a fluid particle arriving at a Eulerian grid point. The value of the advected field at the departure point is obtained by interpolation. Both the trajectory integration and repeated interpolation influence accuracy. We compare the accuracy and performance of interpolation schemes based on piecewise cubic polynomials and cubic B-splines in the context of a distributed memory, parallel computing environment. The computational cost and interprocessor communication requirements for both methods are reported. Spline interpolation has better conservation properties but requires the solution of a global linear system, initially appearing to hinder a distributed memory implementation. The proposed parallel algorithm for multidimensional spline interpolation has almost the same communication overhead as local piecewise polynomial interpolation. We also compare various techniques for tracking trajectories given different values for the Courant number. Large Courant numbers require a high-order ODE solver involving multiple interpolations of the velocity field.

  20. Parallel algorithms for dynamically partitioning unstructured grids

    SciTech Connect

    Diniz, P.; Plimpton, S.; Hendrickson, B.; Leland, R.

    1994-10-01

    Grid partitioning is the method of choice for decomposing a wide variety of computational problems into naturally parallel pieces. In problems where computational load on the grid or the grid itself changes as the simulation progresses, the ability to repartition dynamically and in parallel is attractive for achieving higher performance. We describe three algorithms suitable for parallel dynamic load-balancing which attempt to partition unstructured grids so that computational load is balanced and communication is minimized. The execution time of algorithms and the quality of the partitions they generate are compared to results from serial partitioners for two large grids. The integration of the algorithms into a parallel particle simulation is also briefly discussed.

  1. Parallel Computing Strategies for Irregular Algorithms

    NASA Technical Reports Server (NTRS)

    Biswas, Rupak; Oliker, Leonid; Shan, Hongzhang; Biegel, Bryan (Technical Monitor)

    2002-01-01

    Parallel computing promises several orders of magnitude increase in our ability to solve realistic computationally-intensive problems, but relies on their efficient mapping and execution on large-scale multiprocessor architectures. Unfortunately, many important applications are irregular and dynamic in nature, making their effective parallel implementation a daunting task. Moreover, with the proliferation of parallel architectures and programming paradigms, the typical scientist is faced with a plethora of questions that must be answered in order to obtain an acceptable parallel implementation of the solution algorithm. In this paper, we consider three representative irregular applications: unstructured remeshing, sparse matrix computations, and N-body problems, and parallelize them using various popular programming paradigms on a wide spectrum of computer platforms ranging from state-of-the-art supercomputers to PC clusters. We present the underlying problems, the solution algorithms, and the parallel implementation strategies. Smart load-balancing, partitioning, and ordering techniques are used to enhance parallel performance. Overall results demonstrate the complexity of efficiently parallelizing irregular algorithms.

  2. Parallel Genetic Algorithm for Alpha Spectra Fitting

    NASA Astrophysics Data System (ADS)

    García-Orellana, Carlos J.; Rubio-Montero, Pilar; González-Velasco, Horacio

    2005-01-01

    We present a performance study of alpha-particle spectra fitting using parallel Genetic Algorithm (GA). The method uses a two-step approach. In the first step we run parallel GA to find an initial solution for the second step, in which we use Levenberg-Marquardt (LM) method for a precise final fit. GA is a high resources-demanding method, so we use a Beowulf cluster for parallel simulation. The relationship between simulation time (and parallel efficiency) and processors number is studied using several alpha spectra, with the aim of obtaining a method to estimate the optimal processors number that must be used in a simulation.

  3. Numerical Algorithms and Parallel Tasking.

    DTIC Science & Technology

    1984-07-01

    34 Principal Investigator, Virginia Klema, Research Staff, George Cybenko and Elizabeth Ducot . During the period, May 15, 1983 through May 14, 1984...Virginia Klema and Elizabeth Ducot have been supported for four months, and George Cybenko has been supported for one month. During this time system...algorithms or applications is the responsibility of the user. Virginia Klema and Elizabeth Ducot presented a description of the concurrent computing

  4. Experiences with the PGAPack Parallel Genetic Algorithm library

    SciTech Connect

    Levine, D.; Hallstrom, P.; Noelle, D.; Walenz, B.

    1997-07-01

    PGAPack is the first widely distributed parallel genetic algorithm library. Since its release, several thousand copies have been distributed worldwide to interested users. In this paper we discuss the key components of the PGAPack design philosophy and present a number of application examples that use PGAPack.

  5. Parallel, Distributed Scripting with Python

    SciTech Connect

    Miller, P J

    2002-05-24

    Parallel computers used to be, for the most part, one-of-a-kind systems which were extremely difficult to program portably. With SMP architectures, the advent of the POSIX thread API and OpenMP gave developers ways to portably exploit on-the-box shared memory parallelism. Since these architectures didn't scale cost-effectively, distributed memory clusters were developed. The associated MPI message passing libraries gave these systems a portable paradigm too. Having programmers effectively use this paradigm is a somewhat different question. Distributed data has to be explicitly transported via the messaging system in order for it to be useful. In high level languages, the MPI library gives access to data distribution routines in C, C++, and FORTRAN. But we need more than that. Many reasonable and common tasks are best done in (or as extensions to) scripting languages. Consider sysadm tools such as password crackers, file purgers, etc ... These are simple to write in a scripting language such as Python (an open source, portable, and freely available interpreter). But these tasks beg to be done in parallel. Consider the a password checker that checks an encrypted password against a 25,000 word dictionary. This can take around 10 seconds in Python (6 seconds in C). It is trivial to parallelize if you can distribute the information and co-ordinate the work.

  6. Empirical study of parallel LRU simulation algorithms

    NASA Technical Reports Server (NTRS)

    Carr, Eric; Nicol, David M.

    1994-01-01

    This paper reports on the performance of five parallel algorithms for simulating a fully associative cache operating under the LRU (Least-Recently-Used) replacement policy. Three of the algorithms are SIMD, and are implemented on the MasPar MP-2 architecture. Two other algorithms are parallelizations of an efficient serial algorithm on the Intel Paragon. One SIMD algorithm is quite simple, but its cost is linear in the cache size. The two other SIMD algorithm are more complex, but have costs that are independent on the cache size. Both the second and third SIMD algorithms compute all stack distances; the second SIMD algorithm is completely general, whereas the third SIMD algorithm presumes and takes advantage of bounds on the range of reference tags. Both MIMD algorithm implemented on the Paragon are general and compute all stack distances; they differ in one step that may affect their respective scalability. We assess the strengths and weaknesses of these algorithms as a function of problem size and characteristics, and compare their performance on traces derived from execution of three SPEC benchmark programs.

  7. Adapting Eclat algorithm to parallel environments with Charm++ library

    NASA Astrophysics Data System (ADS)

    Puścian, Marek; Grabski, Waldemar

    2016-09-01

    In this paper we describe Eclat algorithm that is adapted to deal with growing data repositories. The presented solution utilizes Master-Slave scheme to distribute data mining tasks among available computation nodes. Several improvements have been proposed and successfully implemented using Charm++ library. This paper introduces optimization techniques to reduce communication cost and synchronization overhead. It also discusses results of the performance of parallel Eclat algorithm against different databases and compares it with parallel Apriori algorithm. The proposed approach has been illustrated with many experiments and measurements performed using multiprocessor and multithreaded computer platform.

  8. Parallel algorithms for mapping pipelined and parallel computations

    NASA Technical Reports Server (NTRS)

    Nicol, David M.

    1988-01-01

    Many computational problems in image processing, signal processing, and scientific computing are naturally structured for either pipelined or parallel computation. When mapping such problems onto a parallel architecture it is often necessary to aggregate an obvious problem decomposition. Even in this context the general mapping problem is known to be computationally intractable, but recent advances have been made in identifying classes of problems and architectures for which optimal solutions can be found in polynomial time. Among these, the mapping of pipelined or parallel computations onto linear array, shared memory, and host-satellite systems figures prominently. This paper extends that work first by showing how to improve existing serial mapping algorithms. These improvements have significantly lower time and space complexities: in one case a published O(nm sup 3) time algorithm for mapping m modules onto n processors is reduced to an O(nm log m) time complexity, and its space requirements reduced from O(nm sup 2) to O(m). Run time complexity is further reduced with parallel mapping algorithms based on these improvements, which run on the architecture for which they create the mappings.

  9. Fast parallel algorithms for short-range molecular dynamics

    SciTech Connect

    Plimpton, S.

    1993-05-01

    Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a subset of atoms; the second assigns each a subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently -- those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 10,000,000 atoms on three parallel supercomputers, the nCUBE 2, Intel iPSC/860, and Intel Delta. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and the Intel Delta performs about 30 times faster than a single Y-MP processor and 12 times faster than a single C90 processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

  10. Parallel distributed computing using Python

    NASA Astrophysics Data System (ADS)

    Dalcin, Lisandro D.; Paz, Rodrigo R.; Kler, Pablo A.; Cosimo, Alejandro

    2011-09-01

    This work presents two software components aimed to relieve the costs of accessing high-performance parallel computing resources within a Python programming environment: MPI for Python and PETSc for Python. MPI for Python is a general-purpose Python package that provides bindings for the Message Passing Interface (MPI) standard using any back-end MPI implementation. Its facilities allow parallel Python programs to easily exploit multiple processors using the message passing paradigm. PETSc for Python provides access to the Portable, Extensible Toolkit for Scientific Computation (PETSc) libraries. Its facilities allow sequential and parallel Python applications to exploit state of the art algorithms and data structures readily available in PETSc for the solution of large-scale problems in science and engineering. MPI for Python and PETSc for Python are fully integrated to PETSc-FEM, an MPI and PETSc based parallel, multiphysics, finite elements code developed at CIMEC laboratory. This software infrastructure supports research activities related to simulation of fluid flows with applications ranging from the design of microfluidic devices for biochemical analysis to modeling of large-scale stream/aquifer interactions.

  11. Parallel Algorithms for Computer Vision.

    DTIC Science & Technology

    1989-01-01

    1989 EPLEC89 08 4D EApproved for public release; distribution is unlimited. Prepared for: Defense Advanced Research Projects Agency 1400 Wilson...SOURCE OF FUNDING NUMBERS 1400 Wilson Boulevard PROGRAM PROJECT TASK [WORK UNIT Arl ington, VA 22209-230 ELEMENT NO. No. NO. 1ACCESSION NO. l 1...34 sponsored by the Defense Advanced Research Projects Agency (DARPA), and administered by the U.S. Army Engineer Topographic Laboratories (ETL). !The time

  12. Scheduling parallel programs in distributed systems

    SciTech Connect

    Rommel, C.G.

    1988-01-01

    Scheduling parallel programs under the processor-sharing discipline for uniprocessors, multiprocessors, and distributed systems was studied. Two classes of parallel programs are considered: those without any IPC (called Fork-Join jobs) and those with asynchronous and uniform IPC (called clusters). The study is divided into two parts: (1) develops analytical solutions for Fork-Join Jobs on uniprocessors and multiprocessors; and (2) develops and evaluates via simulation Fork-Join jobs and clusters on distributed systems. The types of site scheduling studied are TS-PS where tasks of a job are scheduled independently at processor-sharing servers, JS-PS in which tasks of a job are scheduled as a single entity at processor-sharing servers, and FCFS where tasks of a job are scheduled independently by order of arrival. For Poisson job arrivals and exponentially distributed task service times, analytical solutions and computationally efficient bounds were found for Fork-Join TS-PS and JS-PS job response times. An algorithm was developed to schedule parallel programs in distributed systems. Over a wide range of parameters the algorithms was found to be superior to both no-load balancing, NLB, and shortest-queue first scheduling, SQF.

  13. Parallel algorithms for the spectral transform method

    SciTech Connect

    Foster, I.T.; Worley, P.H.

    1994-04-01

    The spectral transform method is a standard numerical technique for solving partial differential equations on a sphere and is widely used in atmospheric circulation models. Recent research has identified several promising algorithms for implementing this method on massively parallel computers; however, no detailed comparison of the different algorithms has previously been attempted. In this paper, we describe these different parallel algorithms and report on computational experiments that we have conducted to evaluate their efficiency on parallel computers. The experiments used a testbed code that solves the nonlinear shallow water equations or a sphere; considerable care was taken to ensure that the experiments provide a fair comparison of the different algorithms and that the results are relevant to global models. We focus on hypercube- and mesh-connected multicomputers with cut-through routing, such as the Intel iPSC/860, DELTA, and Paragon, and the nCUBE/2, but also indicate how the results extend to other parallel computer architectures. The results of this study are relevant not only to the spectral transform method but also to multidimensional FFTs and other parallel transforms.

  14. Parallel algorithms for the spectral transform method

    SciTech Connect

    Foster, I.T.; Worley, P.H.

    1997-05-01

    The spectral transform method is a standard numerical technique for solving partial differential equations on a sphere and is widely used in atmospheric circulation models. Recent research has identified several promising algorithms for implementing this method on massively parallel computers; however, no detailed comparison of the different algorithms has previously been attempted. In this paper, the authors describe these different parallel algorithms and report on computational experiments that they have conducted to evaluate their efficiency on parallel computers. The experiments used a testbed code that solves the nonlinear shallow water equations on a sphere; considerable care was taken to ensure that the experiments provide a fair comparison of the different algorithms and that the results are relevant to global models. The authors focus on hypercube- and mesh-connected multicomputers with cut-through routing, such as the Intel iPSC/860, DELTA, and Paragon, and the nCUBE/2, but they also indicate how the results extend to other parallel computer architectures. The results of this study are relevant not only to the spectral transform method but also to multidimensional fast Fourier transforms (FFTs) and other parallel transforms.

  15. A parallel adaptive mesh refinement algorithm

    NASA Technical Reports Server (NTRS)

    Quirk, James J.; Hanebutte, Ulf R.

    1993-01-01

    Over recent years, Adaptive Mesh Refinement (AMR) algorithms which dynamically match the local resolution of the computational grid to the numerical solution being sought have emerged as powerful tools for solving problems that contain disparate length and time scales. In particular, several workers have demonstrated the effectiveness of employing an adaptive, block-structured hierarchical grid system for simulations of complex shock wave phenomena. Unfortunately, from the parallel algorithm developer's viewpoint, this class of scheme is quite involved; these schemes cannot be distilled down to a small kernel upon which various parallelizing strategies may be tested. However, because of their block-structured nature such schemes are inherently parallel, so all is not lost. In this paper we describe the method by which Quirk's AMR algorithm has been parallelized. This method is built upon just a few simple message passing routines and so it may be implemented across a broad class of MIMD machines. Moreover, the method of parallelization is such that the original serial code is left virtually intact, and so we are left with just a single product to support. The importance of this fact should not be underestimated given the size and complexity of the original algorithm.

  16. Analysis of a parallel multigrid algorithm

    NASA Technical Reports Server (NTRS)

    Chan, Tony F.; Tuminaro, Ray S.

    1989-01-01

    The parallel multigrid algorithm of Frederickson and McBryan (1987) is considered. This algorithm uses multiple coarse-grid problems (instead of one problem) in the hope of accelerating convergence and is found to have a close relationship to traditional multigrid methods. Specifically, the parallel coarse-grid correction operator is identical to a traditional multigrid coarse-grid correction operator, except that the mixing of high and low frequencies caused by aliasing error is removed. Appropriate relaxation operators can be chosen to take advantage of this property. Comparisons between the standard multigrid and the new method are made.

  17. Internal combustion engine control for series hybrid electric vehicles by parallel and distributed genetic programming/multiobjective genetic algorithms

    NASA Astrophysics Data System (ADS)

    Gladwin, D.; Stewart, P.; Stewart, J.

    2011-02-01

    This article addresses the problem of maintaining a stable rectified DC output from the three-phase AC generator in a series-hybrid vehicle powertrain. The series-hybrid prime power source generally comprises an internal combustion (IC) engine driving a three-phase permanent magnet generator whose output is rectified to DC. A recent development has been to control the engine/generator combination by an electronically actuated throttle. This system can be represented as a nonlinear system with significant time delay. Previously, voltage control of the generator output has been achieved by model predictive methods such as the Smith Predictor. These methods rely on the incorporation of an accurate system model and time delay into the control algorithm, with a consequent increase in computational complexity in the real-time controller, and as a necessity relies to some extent on the accuracy of the models. Two complementary performance objectives exist for the control system. Firstly, to maintain the IC engine at its optimal operating point, and secondly, to supply a stable DC supply to the traction drive inverters. Achievement of these goals minimises the transient energy storage requirements at the DC link, with a consequent reduction in both weight and cost. These objectives imply constant velocity operation of the IC engine under external load disturbances and changes in both operating conditions and vehicle speed set-points. In order to achieve these objectives, and reduce the complexity of implementation, in this article a controller is designed by the use of Genetic Programming methods in the Simulink modelling environment, with the aim of obtaining a relatively simple controller for the time-delay system which does not rely on the implementation of real time system models or time delay approximations in the controller. A methodology is presented to utilise the miriad of existing control blocks in the Simulink libraries to automatically evolve optimal control

  18. Parallel Clustering Algorithms for Structured AMR

    SciTech Connect

    Gunney, B T; Wissink, A M; Hysom, D A

    2005-10-26

    We compare several different parallel implementation approaches for the clustering operations performed during adaptive gridding operations in patch-based structured adaptive mesh refinement (SAMR) applications. Specifically, we target the clustering algorithm of Berger and Rigoutsos (BR91), which is commonly used in many SAMR applications. The baseline for comparison is a simplistic parallel extension of the original algorithm that works well for up to O(10{sup 2}) processors. Our goal is a clustering algorithm for machines of up to O(10{sup 5}) processors, such as the 64K-processor IBM BlueGene/Light system. We first present an algorithm that avoids the unneeded communications of the simplistic approach to improve the clustering speed by up to an order of magnitude. We then present a new task-parallel implementation to further reduce communication wait time, adding another order of magnitude of improvement. The new algorithms also exhibit more favorable scaling behavior for our test problems. Performance is evaluated on a number of large scale parallel computer systems, including a 16K-processor BlueGene/Light system.

  19. The PRISM project: Infrastructure and algorithms for parallel eigensolvers

    SciTech Connect

    Bischof, C.; Sun, X.; Huss-Lederman, S.; Tsao, A.

    1993-12-31

    The goal of the PRISM project is the development of infrastructure and algorithms for the parallel solution of eigenvalue problems. We are currently investigating a complete eigensolver based on the Invariant Subspace Decomposition Algorithm for dense symmetric matrices (SYISDA). After briefly reviewing the SYISDA approach, we discuss the algorithmic highlights of a distributed-memory implementation of an eigensolver based on this approach. These include a fast matrix-matrix multiplication algorithm, a new approach to parallel band reduction and tridiagonalization, and a harness for coordinating the divide-and-conquer parallelism in the problem. We also present performance results of these kernels as well as the overall SYISDA implementation on the Intel Touchstone Delta prototype and the IBM SP/1.

  20. Parallelization of a blind deconvolution algorithm

    NASA Astrophysics Data System (ADS)

    Matson, Charles L.; Borelli, Kathy J.

    2006-09-01

    Often it is of interest to deblur imagery in order to obtain higher-resolution images. Deblurring requires knowledge of the blurring function - information that is often not available separately from the blurred imagery. Blind deconvolution algorithms overcome this problem by jointly estimating both the high-resolution image and the blurring function from the blurred imagery. Because blind deconvolution algorithms are iterative in nature, they can take minutes to days to deblur an image depending how many frames of data are used for the deblurring and the platforms on which the algorithms are executed. Here we present our progress in parallelizing a blind deconvolution algorithm to increase its execution speed. This progress includes sub-frame parallelization and a code structure that is not specialized to a specific computer hardware architecture.

  1. Parallel Formulations of Tree-Projection Based Sequence Mining Algorithms

    DTIC Science & Technology

    2003-01-20

    Keywords: frequent sequential patterns, database projection algorithms, data mining , parallel processing ∗This work was supported by NSF CCR-9972519... data mining research. These frequently occurring patterns can be used to find association rules and/or to extract prevalent patterns that exist in the...Distributed Computing (Special Issue on High Performance Data Mining ), 2000. [2] R. Agrawal and J.C. Shafer. Parallel mining of association rules. IEEE

  2. Parallelization of Edge Detection Algorithm using MPI on Beowulf Cluster

    NASA Astrophysics Data System (ADS)

    Haron, Nazleeni; Amir, Ruzaini; Aziz, Izzatdin A.; Jung, Low Tan; Shukri, Siti Rohkmah

    In this paper, we present the design of parallel Sobel edge detection algorithm using Foster's methodology. The parallel algorithm is implemented using MPI message passing library and master/slave algorithm. Every processor performs the same sequential algorithm but on different part of the image. Experimental results conducted on Beowulf cluster are presented to demonstrate the performance of the parallel algorithm.

  3. A near-optimum parallel planarization algorithm.

    PubMed

    Takefuji, Y; Lee, K C

    1989-09-15

    A near-optimum parallel planarization algorithm is presented. The planarization algorithm, which is designed to embed a graph on a plane, uses a large number of simple processing elements called neurons. The proposed system, composed of an N x N neural network array (where N is the number of vertices), not only generates a near-maximal planar subgraph from a nonplanar graph or a planar graph but also embeds the subgraph on a single plane within 0(1) time. The algorithm can be used in multiple-layer problems such as designing printed circuit boards and routing very-large-scale integration circuits.

  4. Research in Parallel Algorithms and Software for Computational Aerosciences

    NASA Technical Reports Server (NTRS)

    Domel, Neal D.

    1996-01-01

    Phase 1 is complete for the development of a computational fluid dynamics CFD) parallel code with automatic grid generation and adaptation for the Euler analysis of flow over complex geometries. SPLITFLOW, an unstructured Cartesian grid code developed at Lockheed Martin Tactical Aircraft Systems, has been modified for a distributed memory/massively parallel computing environment. The parallel code is operational on an SGI network, Cray J90 and C90 vector machines, SGI Power Challenge, and Cray T3D and IBM SP2 massively parallel machines. Parallel Virtual Machine (PVM) is the message passing protocol for portability to various architectures. A domain decomposition technique was developed which enforces dynamic load balancing to improve solution speed and memory requirements. A host/node algorithm distributes the tasks. The solver parallelizes very well, and scales with the number of processors. Partially parallelized and non-parallelized tasks consume most of the wall clock time in a very fine grain environment. Timing comparisons on a Cray C90 demonstrate that Parallel SPLITFLOW runs 2.4 times faster on 8 processors than its non-parallel counterpart autotasked over 8 processors.

  5. Research in Parallel Algorithms and Software for Computational Aerosciences

    NASA Technical Reports Server (NTRS)

    Domel, Neal D.

    1996-01-01

    Phase I is complete for the development of a Computational Fluid Dynamics parallel code with automatic grid generation and adaptation for the Euler analysis of flow over complex geometries. SPLITFLOW, an unstructured Cartesian grid code developed at Lockheed Martin Tactical Aircraft Systems, has been modified for a distributed memory/massively parallel computing environment. The parallel code is operational on an SGI network, Cray J90 and C90 vector machines, SGI Power Challenge, and Cray T3D and IBM SP2 massively parallel machines. Parallel Virtual Machine (PVM) is the message passing protocol for portability to various architectures. A domain decomposition technique was developed which enforces dynamic load balancing to improve solution speed and memory requirements. A host/node algorithm distributes the tasks. The solver parallelizes very well, and scales with the number of processors. Partially parallelized and non-parallelized tasks consume most of the wall clock time in a very fine grain environment. Timing comparisons on a Cray C90 demonstrate that Parallel SPLITFLOW runs 2.4 times faster on 8 processors than its non-parallel counterpart autotasked over 8 processors.

  6. Research on parallel algorithm for sequential pattern mining

    NASA Astrophysics Data System (ADS)

    Zhou, Lijuan; Qin, Bai; Wang, Yu; Hao, Zhongxiao

    2008-03-01

    Sequential pattern mining is the mining of frequent sequences related to time or other orders from the sequence database. Its initial motivation is to discover the laws of customer purchasing in a time section by finding the frequent sequences. In recent years, sequential pattern mining has become an important direction of data mining, and its application field has not been confined to the business database and has extended to new data sources such as Web and advanced science fields such as DNA analysis. The data of sequential pattern mining has characteristics as follows: mass data amount and distributed storage. Most existing sequential pattern mining algorithms haven't considered the above-mentioned characteristics synthetically. According to the traits mentioned above and combining the parallel theory, this paper puts forward a new distributed parallel algorithm SPP(Sequential Pattern Parallel). The algorithm abides by the principal of pattern reduction and utilizes the divide-and-conquer strategy for parallelization. The first parallel task is to construct frequent item sets applying frequent concept and search space partition theory and the second task is to structure frequent sequences using the depth-first search method at each processor. The algorithm only needs to access the database twice and doesn't generate the candidated sequences, which abates the access time and improves the mining efficiency. Based on the random data generation procedure and different information structure designed, this paper simulated the SPP algorithm in a concrete parallel environment and implemented the AprioriAll algorithm. The experiments demonstrate that compared with AprioriAll, the SPP algorithm had excellent speedup factor and efficiency.

  7. Parallelized quantum Monte Carlo algorithm with nonlocal worm updates.

    PubMed

    Masaki-Kato, Akiko; Suzuki, Takafumi; Harada, Kenji; Todo, Synge; Kawashima, Naoki

    2014-04-11

    Based on the worm algorithm in the path-integral representation, we propose a general quantum Monte Carlo algorithm suitable for parallelizing on a distributed-memory computer by domain decomposition. Of particular importance is its application to large lattice systems of bosons and spins. A large number of worms are introduced and its population is controlled by a fictitious transverse field. For a benchmark, we study the size dependence of the Bose-condensation order parameter of the hard-core Bose-Hubbard model with L×L×βt=10240×10240×16, using 3200 computing cores, which shows good parallelization efficiency.

  8. Parallelization of the Pipelined Thomas Algorithm

    NASA Technical Reports Server (NTRS)

    Povitsky, A.

    1998-01-01

    In this study the following questions are addressed. Is it possible to improve the parallelization efficiency of the Thomas algorithm? How should the Thomas algorithm be formulated in order to get solved lines that are used as data for other computational tasks while processors are idle? To answer these questions, two-step pipelined algorithms (PAs) are introduced formally. It is shown that the idle processor time is invariant with respect to the order of backward and forward steps in PAs starting from one outermost processor. The advantage of PAs starting from two outermost processors is small. Versions of the pipelined Thomas algorithms considered here fall into the category of PAs. These results show that the parallelization efficiency of the Thomas algorithm cannot be improved directly. However, the processor idle time can be used if some data has been computed by the time processors become idle. To achieve this goal the Immediate Backward pipelined Thomas Algorithm (IB-PTA) is developed in this article. The backward step is computed immediately after the forward step has been completed for the first portion of lines. This enables the completion of the Thomas algorithm for some of these lines before processors become idle. An algorithm for generating a static processor schedule recursively is developed. This schedule is used to switch between forward and backward computations and to control communications between processors. The advantage of the IB-PTA over the basic PTA is the presence of solved lines, which are available for other computations, by the time processors become idle.

  9. An algorithm on distributed mining association rules

    NASA Astrophysics Data System (ADS)

    Xu, Fan

    2005-12-01

    With the rapid development of the Internet/Intranet, distributed databases have become a broadly used environment in various areas. It is a critical task to mine association rules in distributed databases. The algorithms of distributed mining association rules can be divided into two classes. One is a DD algorithm, and another is a CD algorithm. A DD algorithm focuses on data partition optimization so as to enhance the efficiency. A CD algorithm, on the other hand, considers a setting where the data is arbitrarily partitioned horizontally among the parties to begin with, and focuses on parallelizing the communication. A DD algorithm is not always applicable, however, at the time the data is generated, it is often already partitioned. In many cases, it cannot be gathered and repartitioned for reasons of security and secrecy, cost transmission, or sheer efficiency. A CD algorithm may be a more appealing solution for systems which are naturally distributed over large expenses, such as stock exchange and credit card systems. An FDM algorithm provides enhancement to CD algorithm. However, CD and FDM algorithms are both based on net-structure and executing in non-shareable resources. In practical applications, however, distributed databases often are star-structured. This paper proposes an algorithm based on star-structure networks, which are more practical in application, have lower maintenance costs and which are more practical in the construction of the networks. In addition, the algorithm provides high efficiency in communication and good extension in parallel computation.

  10. Iterative algorithms for large sparse linear systems on parallel computers

    NASA Technical Reports Server (NTRS)

    Adams, L. M.

    1982-01-01

    Algorithms for assembling in parallel the sparse system of linear equations that result from finite difference or finite element discretizations of elliptic partial differential equations, such as those that arise in structural engineering are developed. Parallel linear stationary iterative algorithms and parallel preconditioned conjugate gradient algorithms are developed for solving these systems. In addition, a model for comparing parallel algorithms on array architectures is developed and results of this model for the algorithms are given.

  11. Parallel algorithms for boundary value problems

    NASA Technical Reports Server (NTRS)

    Lin, Avi

    1990-01-01

    A general approach to solve boundary value problems numerically in a parallel environment is discussed. The basic algorithm consists of two steps: the local step where all the P available processors work in parallel, and the global step where one processor solves a tridiagonal linear system of the order P. The main advantages of this approach are two fold. First, this suggested approach is very flexible, especially in the local step and thus the algorithm can be used with any number of processors and with any of the SIMD or MIMD machines. Secondly, the communication complexity is very small and thus can be used as easily with shared memory machines. Several examples for using this strategy are discussed.

  12. Parallel algorithms for boundary value problems

    NASA Technical Reports Server (NTRS)

    Lin, Avi

    1991-01-01

    A general approach to solve boundary value problems numerically in a parallel environment is discussed. The basic algorithm consists of two steps: the local step where all the P available processors work in parallel, and the global step where one processor solves a tridiagonal linear system of the order P. The main advantages of this approach are twofold. First, this suggested approach is very flexible, especially in the local step and thus the algorithm can be used with any number of processors and with any of the SIMD or MIMD machines. Secondly, the communication complexity is very small and thus can be used as easily with shared memory machines. Several examples for using this strategy are discussed.

  13. Parallel algorithms for boundary value problems

    NASA Technical Reports Server (NTRS)

    Lin, Avi

    1991-01-01

    A general approach to solve boundary value problems numerically in a parallel environment is discussed. The basic algorithm consists of two steps: the local step where all the P available processors work in parallel, and the global step where one processor solves a tridiagonal linear system of the order P. The main advantages of this approach are twofold. First, this suggested approach is very flexible, especially in the local step and thus the algorithm can be used with any number of processors and with any of the SIMD or MIMD machines. Secondly, the communication complexity is very small and thus can be used as easily with shared memory machines. Several examples for using this strategy are discussed.

  14. Coupled cluster algorithms for networks of shared memory parallel processors

    NASA Astrophysics Data System (ADS)

    Bentz, Jonathan L.; Olson, Ryan M.; Gordon, Mark S.; Schmidt, Michael W.; Kendall, Ricky A.

    2007-05-01

    As the popularity of using SMP systems as the building blocks for high performance supercomputers increases, so too increases the need for applications that can utilize the multiple levels of parallelism available in clusters of SMPs. This paper presents a dual-layer distributed algorithm, using both shared-memory and distributed-memory techniques to parallelize a very important algorithm (often called the "gold standard") used in computational chemistry, the single and double excitation coupled cluster method with perturbative triples, i.e. CCSD(T). The algorithm is presented within the framework of the GAMESS [M.W. Schmidt, K.K. Baldridge, J.A. Boatz, S.T. Elbert, M.S. Gordon, J.J. Jensen, S. Koseki, N. Matsunaga, K.A. Nguyen, S. Su, T.L. Windus, M. Dupuis, J.A. Montgomery, General atomic and molecular electronic structure system, J. Comput. Chem. 14 (1993) 1347-1363]. (General Atomic and Molecular Electronic Structure System) program suite and the Distributed Data Interface [M.W. Schmidt, G.D. Fletcher, B.M. Bode, M.S. Gordon, The distributed data interface in GAMESS, Comput. Phys. Comm. 128 (2000) 190]. (DDI), however, the essential features of the algorithm (data distribution, load-balancing and communication overhead) can be applied to more general computational problems. Timing and performance data for our dual-level algorithm is presented on several large-scale clusters of SMPs.

  15. Parallelized FVM algorithm for three-dimensional viscoelastic flows

    NASA Astrophysics Data System (ADS)

    Dou, H.-S.; Phan-Thien, N.

    A parallel implementation for the finite volume method (FVM) for three-dimensional (3D) viscoelastic flows is developed on a distributed computing environment through Parallel Virtual Machine (PVM). The numerical procedure is based on the SIMPLEST algorithm using a staggered FVM discretization in Cartesian coordinates. The final discretized algebraic equations are solved with the TDMA method. The parallelisation of the program is implemented by a domain decomposition strategy, with a master/slave style programming paradigm, and a message passing through PVM. A load balancing strategy is proposed to reduce the communications between processors. The three-dimensional viscoelastic flow in a rectangular duct is computed with this program. The modified Phan-Thien-Tanner (MPTT) constitutive model is employed for the equation system closure. Computing results are validated on the secondary flow problem due to non-zero second normal stress difference N2. Three sets of meshes are used, and the effect of domain decomposition strategies on the performance is discussed. It is found that parallel efficiency is strongly dependent on the grid size and the number of processors for a given block number. The convergence rate as well as the total efficiency of domain decomposition depends upon the flow problem and the boundary conditions. The parallel efficiency increases with increasing problem size for given block number. Comparing to two-dimensional flow problems, 3D parallelized algorithm has a lower efficiency owing to largely overlapped block interfaces, but the parallel algorithm is indeed a powerful means for large scale flow simulations.

  16. Optical flow optimization using parallel genetic algorithm

    NASA Astrophysics Data System (ADS)

    Zavala-Romero, Olmo; Botella, Guillermo; Meyer-Bäse, Anke; Meyer Base, Uwe

    2011-06-01

    A new approach to optimize the parameters of a gradient-based optical flow model using a parallel genetic algorithm (GA) is proposed. The main characteristics of the optical flow algorithm are its bio-inspiration and robustness against contrast, static patterns and noise, besides working consistently with several optical illusions where other algorithms fail. This model depends on many parameters which conform the number of channels, the orientations required, the length and shape of the kernel functions used in the convolution stage, among many more. The GA is used to find a set of parameters which improve the accuracy of the optical flow on inputs where the ground-truth data is available. This set of parameters helps to understand which of them are better suited for each type of inputs and can be used to estimate the parameters of the optical flow algorithm when used with videos that share similar characteristics. The proposed implementation takes into account the embarrassingly parallel nature of the GA and uses the OpenMP Application Programming Interface (API) to speedup the process of estimating an optimal set of parameters. The information obtained in this work can be used to dynamically reconfigure systems, with potential applications in robotics, medical imaging and tracking.

  17. Parallelism of the SANDstorm hash algorithm.

    SciTech Connect

    Torgerson, Mark Dolan; Draelos, Timothy John; Schroeppel, Richard Crabtree

    2009-09-01

    Mainstream cryptographic hashing algorithms are not parallelizable. This limits their speed and they are not able to take advantage of the current trend of being run on multi-core platforms. Being limited in speed limits their usefulness as an authentication mechanism in secure communications. Sandia researchers have created a new cryptographic hashing algorithm, SANDstorm, which was specifically designed to take advantage of multi-core processing and be parallelizable on a wide range of platforms. This report describes a late-start LDRD effort to verify the parallelizability claims of the SANDstorm designers. We have shown, with operating code and bench testing, that the SANDstorm algorithm may be trivially parallelized on a wide range of hardware platforms. Implementations using OpenMP demonstrates a linear speedup with multiple cores. We have also shown significant performance gains with optimized C code and the use of assembly instructions to exploit particular platform capabilities.

  18. Embodied and Distributed Parallel DJing.

    PubMed

    Cappelen, Birgitta; Andersson, Anders-Petter

    2016-01-01

    Everyone has a right to take part in cultural events and activities, such as music performances and music making. Enforcing that right, within Universal Design, is often limited to a focus on physical access to public areas, hearing aids etc., or groups of persons with special needs performing in traditional ways. The latter might be people with disabilities, being musicians playing traditional instruments, or actors playing theatre. In this paper we focus on the innovative potential of including people with special needs, when creating new cultural activities. In our project RHYME our goal was to create health promoting activities for children with severe disabilities, by developing new musical and multimedia technologies. Because of the users' extreme demands and rich contribution, we ended up creating both a new genre of musical instruments and a new art form. We call this new art form Embodied and Distributed Parallel DJing, and the new genre of instruments for Empowering Multi-Sensorial Things.

  19. Predicting mining activity with parallel genetic algorithms

    USGS Publications Warehouse

    Talaie, S.; Leigh, R.; Louis, S.J.; Raines, G.L.; Beyer, H.G.; O'Reilly, U.M.; Banzhaf, Arnold D.; Blum, W.; Bonabeau, C.; Cantu-Paz, E.W.; ,; ,

    2005-01-01

    We explore several different techniques in our quest to improve the overall model performance of a genetic algorithm calibrated probabilistic cellular automata. We use the Kappa statistic to measure correlation between ground truth data and data predicted by the model. Within the genetic algorithm, we introduce a new evaluation function sensitive to spatial correctness and we explore the idea of evolving different rule parameters for different subregions of the land. We reduce the time required to run a simulation from 6 hours to 10 minutes by parallelizing the code and employing a 10-node cluster. Our empirical results suggest that using the spatially sensitive evaluation function does indeed improve the performance of the model and our preliminary results also show that evolving different rule parameters for different regions tends to improve overall model performance. Copyright 2005 ACM.

  20. Algorithmic commonalities in the parallel environment

    NASA Technical Reports Server (NTRS)

    Mcanulty, Michael A.; Wainer, Michael S.

    1987-01-01

    The ultimate aim of this project was to analyze procedures from substantially different application areas to discover what is either common or peculiar in the process of conversion to the Massively Parallel Processor (MPP). Three areas were identified: molecular dynamic simulation, production systems (rule systems), and various graphics and vision algorithms. To date, only selected graphics procedures have been investigated. They are the most readily available, and produce the most visible results. These include simple polygon patch rendering, raycasting against a constructive solid geometric model, and stochastic or fractal based textured surface algorithms. Only the simplest of conversion strategies, mapping a major loop to the array, has been investigated so far. It is not entirely satisfactory.

  1. Parallel/distributed direct method for solving linear systems

    NASA Technical Reports Server (NTRS)

    Lin, Avi

    1990-01-01

    A new family of parallel schemes for directly solving linear systems is presented and analyzed. It is shown that these schemes exhibit a near optimal performance and enjoy several important features: (1) For large enough linear systems, the design of the appropriate paralleled algorithm is insensitive to the number of processors as its performance grows monotonically with them; (2) It is especially good for large matrices, with dimensions large relative to the number of processors in the system; (3) It can be used in both distributed parallel computing environments and tightly coupled parallel computing systems; and (4) This set of algorithms can be mapped onto any parallel architecture without any major programming difficulties or algorithmical changes.

  2. A parallel dynamic programming algorithm for multi-reservoir system optimization

    NASA Astrophysics Data System (ADS)

    Li, Xiang; Wei, Jiahua; Li, Tiejian; Wang, Guangqian; Yeh, William W.-G.

    2014-05-01

    This paper develops a parallel dynamic programming algorithm to optimize the joint operation of a multi-reservoir system. First, a multi-dimensional dynamic programming (DP) model is formulated for a multi-reservoir system. Second, the DP algorithm is parallelized using a peer-to-peer parallel paradigm. The parallelization is based on the distributed memory architecture and the message passing interface (MPI) protocol. We consider both the distributed computing and distributed computer memory in the parallelization. The parallel paradigm aims at reducing the computation time as well as alleviating the computer memory requirement associated with running a multi-dimensional DP model. Next, we test the parallel DP algorithm on the classic, benchmark four-reservoir problem on a high-performance computing (HPC) system with up to 350 cores. Results indicate that the parallel DP algorithm exhibits good performance in parallel efficiency; the parallel DP algorithm is scalable and will not be restricted by the number of cores. Finally, the parallel DP algorithm is applied to a real-world, five-reservoir system in China. The results demonstrate the parallel efficiency and practical utility of the proposed methodology.

  3. Parallel algorithm strategies for circuit simulation.

    SciTech Connect

    Thornquist, Heidi K.; Schiek, Richard Louis; Keiter, Eric Richard

    2010-01-01

    Circuit simulation tools (e.g., SPICE) have become invaluable in the development and design of electronic circuits. However, they have been pushed to their performance limits in addressing circuit design challenges that come from the technology drivers of smaller feature scales and higher integration. Improving the performance of circuit simulation tools through exploiting new opportunities in widely-available multi-processor architectures is a logical next step. Unfortunately, not all traditional simulation applications are inherently parallel, and quickly adapting mature application codes (even codes designed to parallel applications) to new parallel paradigms can be prohibitively difficult. In general, performance is influenced by many choices: hardware platform, runtime environment, languages and compilers used, algorithm choice and implementation, and more. In this complicated environment, the use of mini-applications small self-contained proxies for real applications is an excellent approach for rapidly exploring the parameter space of all these choices. In this report we present a multi-core performance study of Xyce, a transistor-level circuit simulation tool, and describe the future development of a mini-application for circuit simulation.

  4. Parallel technology for numerical modeling of fluid dynamics problems by high-accuracy algorithms

    NASA Astrophysics Data System (ADS)

    Gorobets, A. V.

    2015-04-01

    A parallel computation technology for modeling fluid dynamics problems by finite-volume and finite-difference methods of high accuracy is presented. The development of an algorithm, the design of a software implementation, and the creation of parallel programs for computations on large-scale computing systems are considered. The presented parallel technology is based on a multilevel parallel model combining various types of parallelism: with shared and distributed memory and with multiple and single instruction streams to multiple data flows.

  5. Parallel LU-factorization algorithms for dense matrices

    SciTech Connect

    Oppe, T.C.; Kincaid, D.R.

    1987-05-01

    Several serial and parallel algorithms for computing the LU-factorization of a dense matrix are investigated. Numerical experiments and programming considerations to reduce bank conflicts on the Cray X-MP4 parallel computer are presented. Speedup factors are given for the parallel algorithms. 15 refs., 6 tabs.

  6. Parallel Harmony Search Based Distributed Energy Resource Optimization

    SciTech Connect

    Ceylan, Oguzhan; Liu, Guodong; Tomsovic, Kevin

    2015-01-01

    This paper presents a harmony search based parallel optimization algorithm to minimize voltage deviations in three phase unbalanced electrical distribution systems and to maximize active power outputs of distributed energy resources (DR). The main contribution is to reduce the adverse impacts on voltage profile during a day as photovoltaics (PVs) output or electrical vehicles (EVs) charging changes throughout a day. The IEEE 123- bus distribution test system is modified by adding DRs and EVs under different load profiles. The simulation results show that by using parallel computing techniques, heuristic methods may be used as an alternative optimization tool in electrical power distribution systems operation.

  7. A parallel genetic algorithm for the set partitioning problem

    SciTech Connect

    Levine, D.

    1994-05-01

    In this dissertation the author reports on his efforts to develop a parallel genetic algorithm and apply it to the solution of set partitioning problem -- a difficult combinatorial optimization problem used by many airlines as a mathematical model for flight crew scheduling. He developed a distributed steady-state genetic algorithm in conjunction with a specialized local search heuristic for solving the set partitioning problem. The genetic algorithm is based on an island model where multiple independent subpopulations each run a steady-state genetic algorithm on their subpopulation and occasionally fit strings migrate between the subpopulations. Tests on forty real-world set partitioning problems were carried out on up to 128 nodes of an IBM SP1 parallel computer. The authors found that performance, as measured by the quality of the solution found and the iteration on which it was found, improved as additional subpopulation found and the iteration on which it was found, improved as additional subpopulations were added to the computation. With larger numbers of subpopulations the genetic algorithm was regularly able to find the optimal solution to problems having up to a few thousand integer variables. In two cases, high-quality integer feasible solutions were found for problems with 36,699 and 43,749 integer variables, respectively. A notable limitation they found was the difficulty solving problems with many constraints.

  8. A parallel QR algorithm for the nonsymmetric eigenvalue problem

    NASA Astrophysics Data System (ADS)

    Boley, Daniel; Maier, Robert; Kim, Joung

    1989-05-01

    This paper describes a prototype parallel algorithm for approximating eigenvalues of a dense nonsymmetric matrix on a linear, synchronous processor array. The algorithm is parallel implementation of the explicitly-shifted QR, employing n distributed-memory processors to deliver all eigenvalues in O( n 2) time. The algorithm uses Givens rotations to generate a series of unitary similarity transformations. The rotations are passed between neibouring processors and applied, in pipeline fashion, to columns of the matrix. The rotations are also accumulated in a unitary transformation matrix, enabling the solution of eigenvectors via back-substitution and back-transformation. The algorithm involves only local communication, and confronts the problems of convergence, splitting and updating the shift in a pipelined scheme. The algorithm is implemented on a hypercube, using a ring of processors to simulate a systolic array. Experimental results on the NCUBE/seven hypercube show O( n) speedup over competing sequential codes, despite the overhead of interprocessor communication. Speedup and efficiency are estimated by comparing with EISPACK performance.

  9. Massively Parallel Algorithms for Solution of Schrodinger Equation

    NASA Technical Reports Server (NTRS)

    Fijany, Amir; Barhen, Jacob; Toomerian, Nikzad

    1994-01-01

    In this paper massively parallel algorithms for solution of Schrodinger equation are developed. Our results clearly indicate that the Crank-Nicolson method, in addition to its excellent numerical properties, is also highly suitable for massively parallel computation.

  10. Towards Distributed Memory Parallel Program Analysis

    SciTech Connect

    Quinlan, D; Barany, G; Panas, T

    2008-06-17

    This paper presents a parallel attribute evaluation for distributed memory parallel computer architectures where previously only shared memory parallel support for this technique has been developed. Attribute evaluation is a part of how attribute grammars are used for program analysis within modern compilers. Within this work, we have extended ROSE, a open compiler infrastructure, with a distributed memory parallel attribute evaluation mechanism to support user defined global program analysis required for some forms of security analysis which can not be addressed by a file by file view of large scale applications. As a result, user defined security analyses may now run in parallel without the user having to specify the way data is communicated between processors. The automation of communication enables an extensible open-source parallel program analysis infrastructure.

  11. A parallel algorithm for the non-symmetric eigenvalue problem

    SciTech Connect

    Dongarra, J.; Sidani, M. |

    1991-12-01

    This paper describes a parallel algorithm for computing the eigenvalues and eigenvectors of a non-symmetric matrix. The algorithm is based on a divide-and-conquer procedure and uses an iterative refinement technique.

  12. Parallel implementation of the FETI-DPEM algorithm for general 3D EM simulations

    NASA Astrophysics Data System (ADS)

    Li, Yu-Jia; Jin, Jian-Ming

    2009-05-01

    A parallel implementation of the electromagnetic dual-primal finite element tearing and interconnecting algorithm (FETI-DPEM) is designed for general three-dimensional (3D) electromagnetic large-scale simulations. As a domain decomposition implementation of the finite element method, the FETI-DPEM algorithm provides fully decoupled subdomain problems and an excellent numerical scalability, and thus is well suited for parallel computation. The parallel implementation of the FETI-DPEM algorithm on a distributed-memory system using the message passing interface (MPI) is discussed in detail along with a few practical guidelines obtained from numerical experiments. Numerical examples are provided to demonstrate the efficiency of the parallel implementation.

  13. Differences Between Distributed and Parallel Systems

    SciTech Connect

    Brightwell, R.; Maccabe, A.B.; Rissen, R.

    1998-10-01

    Distributed systems have been studied for twenty years and are now coming into wider use as fast networks and powerful workstations become more readily available. In many respects a massively parallel computer resembles a network of workstations and it is tempting to port a distributed operating system to such a machine. However, there are significant differences between these two environments and a parallel operating system is needed to get the best performance out of a massively parallel system. This report characterizes the differences between distributed systems, networks of workstations, and massively parallel systems and analyzes the impact of these differences on operating system design. In the second part of the report, we introduce Puma, an operating system specifically developed for massively parallel systems. We describe Puma portals, the basic building blocks for message passing paradigms implemented on top of Puma, and show how the differences observed in the first part of the report have influenced the design and implementation of Puma.

  14. Parallelization of Nullspace Algorithm for the computation of metabolic pathways.

    PubMed

    Jevremović, Dimitrije; Trinh, Cong T; Srienc, Friedrich; Sosa, Carlos P; Boley, Daniel

    2011-06-01

    Elementary mode analysis is a useful metabolic pathway analysis tool in understanding and analyzing cellular metabolism, since elementary modes can represent metabolic pathways with unique and minimal sets of enzyme-catalyzed reactions of a metabolic network under steady state conditions. However, computation of the elementary modes of a genome- scale metabolic network with 100-1000 reactions is very expensive and sometimes not feasible with the commonly used serial Nullspace Algorithm. In this work, we develop a distributed memory parallelization of the Nullspace Algorithm to handle efficiently the computation of the elementary modes of a large metabolic network. We give an implementation in C++ language with the support of MPI library functions for the parallel communication. Our proposed algorithm is accompanied with an analysis of the complexity and identification of major bottlenecks during computation of all possible pathways of a large metabolic network. The algorithm includes methods to achieve load balancing among the compute-nodes and specific communication patterns to reduce the communication overhead and improve efficiency.

  15. A general construction for parallelizing Metropolis-Hastings algorithms.

    PubMed

    Calderhead, Ben

    2014-12-09

    Markov chain Monte Carlo methods (MCMC) are essential tools for solving many modern-day statistical and computational problems; however, a major limitation is the inherently sequential nature of these algorithms. In this paper, we propose a natural generalization of the Metropolis-Hastings algorithm that allows for parallelizing a single chain using existing MCMC methods. We do so by proposing multiple points in parallel, then constructing and sampling from a finite-state Markov chain on the proposed points such that the overall procedure has the correct target density as its stationary distribution. Our approach is generally applicable and straightforward to implement. We demonstrate how this construction may be used to greatly increase the computational speed and statistical efficiency of a variety of existing MCMC methods, including Metropolis-Adjusted Langevin Algorithms and Adaptive MCMC. Furthermore, we show how it allows for a principled way of using every integration step within Hamiltonian Monte Carlo methods; our approach increases robustness to the choice of algorithmic parameters and results in increased accuracy of Monte Carlo estimates with little extra computational cost.

  16. A general construction for parallelizing Metropolis−Hastings algorithms

    PubMed Central

    Calderhead, Ben

    2014-01-01

    Markov chain Monte Carlo methods (MCMC) are essential tools for solving many modern-day statistical and computational problems; however, a major limitation is the inherently sequential nature of these algorithms. In this paper, we propose a natural generalization of the Metropolis−Hastings algorithm that allows for parallelizing a single chain using existing MCMC methods. We do so by proposing multiple points in parallel, then constructing and sampling from a finite-state Markov chain on the proposed points such that the overall procedure has the correct target density as its stationary distribution. Our approach is generally applicable and straightforward to implement. We demonstrate how this construction may be used to greatly increase the computational speed and statistical efficiency of a variety of existing MCMC methods, including Metropolis-Adjusted Langevin Algorithms and Adaptive MCMC. Furthermore, we show how it allows for a principled way of using every integration step within Hamiltonian Monte Carlo methods; our approach increases robustness to the choice of algorithmic parameters and results in increased accuracy of Monte Carlo estimates with little extra computational cost. PMID:25422442

  17. Parallel Architectures and Parallel Algorithms for Integrated Vision Systems. Ph.D. Thesis

    NASA Technical Reports Server (NTRS)

    Choudhary, Alok Nidhi

    1989-01-01

    Computer vision is regarded as one of the most complex and computationally intensive problems. An integrated vision system (IVS) is a system that uses vision algorithms from all levels of processing to perform for a high level application (e.g., object recognition). An IVS normally involves algorithms from low level, intermediate level, and high level vision. Designing parallel architectures for vision systems is of tremendous interest to researchers. Several issues are addressed in parallel architectures and parallel algorithms for integrated vision systems.

  18. Parallel algorithms and architecture for computation of manipulator forward dynamics

    NASA Technical Reports Server (NTRS)

    Fijany, Amir; Bejczy, Antal K.

    1989-01-01

    Parallel computation of manipulator forward dynamics is investigated. Considering three classes of algorithms for the solution of the problem, that is, the O(n), the O(n exp 2), and the O(n exp 3) algorithms, parallelism in the problem is analyzed. It is shown that the problem belongs to the class of NC and that the time and processors bounds are of O(log2/2n) and O(n exp 4), respectively. However, the fastest stable parallel algorithms achieve the computation time of O(n) and can be derived by parallelization of the O(n exp 3) serial algorithms. Parallel computation of the O(n exp 3) algorithms requires the development of parallel algorithms for a set of fundamentally different problems, that is, the Newton-Euler formulation, the computation of the inertia matrix, decomposition of the symmetric, positive definite matrix, and the solution of triangular systems. Parallel algorithms for this set of problems are developed which can be efficiently implemented on a unique architecture, a triangular array of n(n+2)/2 processors with a simple nearest-neighbor interconnection. This architecture is particularly suitable for VLSI and WSI implementations. The developed parallel algorithm, compared to the best serial O(n) algorithm, achieves an asymptotic speedup of more than two orders-of-magnitude in the computation the forward dynamics.

  19. Parallel Breadth-First Search on Distributed Memory Systems

    SciTech Connect

    Computational Research Division; Buluc, Aydin; Madduri, Kamesh

    2011-04-15

    Data-intensive, graph-based computations are pervasive in several scientific applications, and are known to to be quite challenging to implement on distributed memory systems. In this work, we explore the design space of parallel algorithms for Breadth-First Search (BFS), a key subroutine in several graph algorithms. We present two highly-tuned par- allel approaches for BFS on large parallel systems: a level-synchronous strategy that relies on a simple vertex-based partitioning of the graph, and a two-dimensional sparse matrix- partitioning-based approach that mitigates parallel commu- nication overhead. For both approaches, we also present hybrid versions with intra-node multithreading. Our novel hybrid two-dimensional algorithm reduces communication times by up to a factor of 3.5, relative to a common vertex based approach. Our experimental study identifies execu- tion regimes in which these approaches will be competitive, and we demonstrate extremely high performance on lead- ing distributed-memory parallel systems. For instance, for a 40,000-core parallel execution on Hopper, an AMD Magny- Cours based system, we achieve a BFS performance rate of 17.8 billion edge visits per second on an undirected graph of 4.3 billion vertices and 68.7 billion edges with skewed degree distribution.

  20. Parallel optimization algorithms and their implementation in VLSI design

    NASA Technical Reports Server (NTRS)

    Lee, G.; Feeley, J. J.

    1991-01-01

    Two new parallel optimization algorithms based on the simplex method are described. They may be executed by a SIMD parallel processor architecture and be implemented in VLSI design. Several VLSI design implementations are introduced. An application example is reported to demonstrate that the algorithms are effective.

  1. Applications and accuracy of the parallel diagonal dominant algorithm

    NASA Technical Reports Server (NTRS)

    Sun, Xian-He

    1993-01-01

    The Parallel Diagonal Dominant (PDD) algorithm is a highly efficient, ideally scalable tridiagonal solver. In this paper, a detailed study of the PDD algorithm is given. First the PDD algorithm is introduced. Then the algorithm is extended to solve periodic tridiagonal systems. A variant, the reduced PDD algorithm, is also proposed. Accuracy analysis is provided for a class of tridiagonal systems, the symmetric, and anti-symmetric Toeplitz tridiagonal systems. Implementation results show that the analysis gives a good bound on the relative error, and the algorithm is a good candidate for the emerging massively parallel machines.

  2. Distributed Minimum Hop Algorithms

    DTIC Science & Technology

    1982-01-01

    acknowledgement), node d starts iteration i+1, and otherwise the algorithm terminates. A detailed description of the algorithm is given in pidgin algol...precise behavior of the algorithm under these circumstances is described by the pidgin algol program in the appendix which is executed by each node. The...l) < N!(2) for each neighbor j, and thus by induction,J -1 N!(2-1) < n-i + (Z-1) + N!(Z-1), completing the proof. Algorithm Dl in Pidgin Algol It is

  3. An efficient parallel algorithm for accelerating computational protein design

    PubMed Central

    Zhou, Yichao; Xu, Wei; Donald, Bruce R.; Zeng, Jianyang

    2014-01-01

    Motivation: Structure-based computational protein design (SCPR) is an important topic in protein engineering. Under the assumption of a rigid backbone and a finite set of discrete conformations of side-chains, various methods have been proposed to address this problem. A popular method is to combine the dead-end elimination (DEE) and A* tree search algorithms, which provably finds the global minimum energy conformation (GMEC) solution. Results: In this article, we improve the efficiency of computing A* heuristic functions for protein design and propose a variant of A* algorithm in which the search process can be performed on a single GPU in a massively parallel fashion. In addition, we make some efforts to address the memory exceeding problem in A* search. As a result, our enhancements can achieve a significant speedup of the A*-based protein design algorithm by four orders of magnitude on large-scale test data through pre-computation and parallelization, while still maintaining an acceptable memory overhead. We also show that our parallel A* search algorithm could be successfully combined with iMinDEE, a state-of-the-art DEE criterion, for rotamer pruning to further improve SCPR with the consideration of continuous side-chain flexibility. Availability: Our software is available and distributed open-source under the GNU Lesser General License Version 2.1 (GNU, February 1999). The source code can be downloaded from http://www.cs.duke.edu/donaldlab/osprey.php or http://iiis.tsinghua.edu.cn/∼compbio/software.html. Contact: zengjy321@tsinghua.edu.cn Supplementary information: Supplementary data are available at Bioinformatics online. PMID:24931991

  4. A Parallel Algorithm for Contact in a Finite Element Hydrocode

    SciTech Connect

    Pierce, Timothy G.

    2003-06-01

    A parallel algorithm is developed for contact/impact of multiple three dimensional bodies undergoing large deformation. As time progresses the relative positions of contact between the multiple bodies changes as collision and sliding occurs. The parallel algorithm is capable of tracking these changes and enforcing an impenetrability constraint and momentum transfer across the surfaces in contact. Portions of the various surfaces of the bodies are assigned to the processors of a distributed-memory parallel machine in an arbitrary fashion, known as the primary decomposition. A secondary, dynamic decomposition is utilized to bring opposing sections of the contacting surfaces together on the same processors, so that opposing forces may be balanced and the resultant deformation of the bodies calculated. The secondary decomposition is accomplished and updated using only local communication with a limited subset of neighbor processors. Each processor represents both a domain of the primary decomposition and a domain of the secondary, or contact, decomposition. Thus each processor has four sets of neighbor processors: (a) those processors which represent regions adjacent to it in the primary decomposition, (b) those processors which represent regions adjacent to it in the contact decomposition, (c) those processors which send it the data from which it constructs its contact domain, and (d) those processors to which it sends its primary domain data, from which they construct their contact domains. The latter three of these neighbor sets change dynamically as the simulation progresses. By constraining all communication to these sets of neighbors, all global communication, with its attendant nonscalable performance, is avoided. A set of tests are provided to measure the degree of scalability achieved by this algorithm on up to 1024 processors. Issues related to the operating system of the test platform which lead to some degradation of the results are analyzed. This algorithm

  5. Parallel transformation of K-SVD solar image denoising algorithm

    NASA Astrophysics Data System (ADS)

    Liang, Youwen; Tian, Yu; Li, Mei

    2017-02-01

    The images obtained by observing the sun through a large telescope always suffered with noise due to the low SNR. K-SVD denoising algorithm can effectively remove Gauss white noise. Training dictionaries for sparse representations is a time consuming task, due to the large size of the data involved and to the complexity of the training algorithms. In this paper, an OpenMP parallel programming language is proposed to transform the serial algorithm to the parallel version. Data parallelism model is used to transform the algorithm. Not one atom but multiple atoms updated simultaneously is the biggest change. The denoising effect and acceleration performance are tested after completion of the parallel algorithm. Speedup of the program is 13.563 in condition of using 16 cores. This parallel version can fully utilize the multi-core CPU hardware resources, greatly reduce running time and easily to transplant in multi-core platform.

  6. AN ALGORITHM FOR PARALLEL SN SWEEPS ON UNSTRUCTURED MESHES

    SciTech Connect

    S. D. PAUTZ

    2000-12-01

    We develop a new algorithm for performing parallel S{sub n} sweeps on unstructured meshes. The algorithm uses a low-complexity list ordering heuristic to determine a sweep ordering on any partitioned mesh. For typical problems and with ''normal'' mesh partitionings we have observed nearly linear speedups on up to 126 processors. This is an important and desirable result, since although analyses of structured meshes indicate that parallel sweeps will not scale with normal partitioning approaches, we do not observe any severe asymptotic degradation in the parallel efficiency with modest ({le}100) levels of parallelism. This work is a fundamental step in the development of parallel S{sub n} methods.

  7. Sort-First, Distributed Memory Parallel Visualization and Rendering

    SciTech Connect

    Bethel, E. Wes; Humphreys, Greg; Paul, Brian; Brederson, J. Dean

    2003-07-15

    While commodity computing and graphics hardware has increased in capacity and dropped in cost, it is still quite difficult to make effective use of such systems for general-purpose parallel visualization and graphics. We describe the results of a recent project that provides a software infrastructure suitable for general-purpose use by parallel visualization and graphics applications. Our work combines and extends two technologies: Chromium, a stream-oriented framework that implements the OpenGL programming interface; and OpenRM Scene Graph, a pipelined-parallel scene graph interface for graphics data management. Using this combination, we implement a sort-first, distributed memory, parallel volume rendering application. We describe the performance characteristics in terms of bandwidth requirements and highlight key algorithmic considerations needed to implement the sort-first system. We characterize system performance using a distributed memory parallel volume rendering application, a nd present performance gains realized by using scene specific knowledge to accelerate rendering through reduced network bandwidth. The contribution of this work is an exploration of general-purpose, sort-first architecture performance characteristics as applied to distributed memory, commodity hardware, along with a description of the algorithmic support needed to realize parallel, sort-first implementations.

  8. A Parallel Algorithm for the Vehicle Routing Problem

    SciTech Connect

    Groer, Christopher S; Golden, Bruce; Edward, Wasil

    2011-01-01

    The vehicle routing problem (VRP) is a dicult and well-studied combinatorial optimization problem. We develop a parallel algorithm for the VRP that combines a heuristic local search improvement procedure with integer programming. We run our parallel algorithm with as many as 129 processors and are able to quickly nd high-quality solutions to standard benchmark problems. We assess the impact of parallelism by analyzing our procedure's performance under a number of dierent scenarios.

  9. A new scheduling algorithm for parallel sparse LU factorization with static pivoting

    SciTech Connect

    Grigori, Laura; Li, Xiaoye S.

    2002-08-20

    In this paper we present a static scheduling algorithm for parallel sparse LU factorization with static pivoting. The algorithm is divided into mapping and scheduling phases, using the symmetric pruned graphs of L' and U to represent dependencies. The scheduling algorithm is designed for driving the parallel execution of the factorization on a distributed-memory architecture. Experimental results and comparisons with SuperLU{_}DIST are reported after applying this algorithm on real world application matrices on an IBM SP RS/6000 distributed memory machine.

  10. Algorithm Calculates Cumulative Poisson Distribution

    NASA Technical Reports Server (NTRS)

    Bowerman, Paul N.; Nolty, Robert C.; Scheuer, Ernest M.

    1992-01-01

    Algorithm calculates accurate values of cumulative Poisson distribution under conditions where other algorithms fail because numbers are so small (underflow) or so large (overflow) that computer cannot process them. Factors inserted temporarily to prevent underflow and overflow. Implemented in CUMPOIS computer program described in "Cumulative Poisson Distribution Program" (NPO-17714).

  11. Parallel Algorithms for Least Squares and Related Computations.

    DTIC Science & Technology

    1991-03-22

    with K. Gallivan and A. Sameh at the University of Illinois, with the development of a comprehensive treatise (publications 7, 9) on parallel algorithms...algorithms. This is joint work with K. Gallivan and A. Sameh from the University of Illinois Center for Supercomputing Research and Development. (See...633 (with D. James). 7. Parallel algorithms for dense linear algebra computations, SIAM Review, 32 (1990), pp. 54- 135 (with K. Gallivan and A. Sameh

  12. Algorithmically Specialized Parallel Architecture For Robotics

    NASA Technical Reports Server (NTRS)

    Fijany, Amir; Bejczy, Antal K.

    1991-01-01

    Computing system called Robot Mathematics Processor (RMP) contains large number of processor elements (PE's) connected in various parallel and serial combinations reconfigurable via software. Special-purpose architecture designed for solving diverse computational problems in robot control, simulation, trajectory generation, workspace analysis, and like. System an MIMD-SIMD parallel architecture capable of exploiting parallelism in different forms and at several computational levels. Major advantage lies in design of cells, which provides flexibility and reconfigurability superior to previous SIMD processors.

  13. Parallelization and automatic data distribution for nuclear reactor simulations

    SciTech Connect

    Liebrock, L.M.

    1997-07-01

    Detailed attempts at realistic nuclear reactor simulations currently take many times real time to execute on high performance workstations. Even the fastest sequential machine can not run these simulations fast enough to ensure that the best corrective measure is used during a nuclear accident to prevent a minor malfunction from becoming a major catastrophe. Since sequential computers have nearly reached the speed of light barrier, these simulations will have to be run in parallel to make significant improvements in speed. In physical reactor plants, parallelism abounds. Fluids flow, controls change, and reactions occur in parallel with only adjacent components directly affecting each other. These do not occur in the sequentialized manner, with global instantaneous effects, that is often used in simulators. Development of parallel algorithms that more closely approximate the real-world operation of a reactor may, in addition to speeding up the simulations, actually improve the accuracy and reliability of the predictions generated. Three types of parallel architecture (shared memory machines, distributed memory multicomputers, and distributed networks) are briefly reviewed as targets for parallelization of nuclear reactor simulation. Various parallelization models (loop-based model, shared memory model, functional model, data parallel model, and a combined functional and data parallel model) are discussed along with their advantages and disadvantages for nuclear reactor simulation. A variety of tools are introduced for each of the models. Emphasis is placed on the data parallel model as the primary focus for two-phase flow simulation. Tools to support data parallel programming for multiple component applications and special parallelization considerations are also discussed.

  14. A Parallel Prefix Algorithm for Almost Toeplitz Tridiagonal Systems

    NASA Technical Reports Server (NTRS)

    Sun, Xian-He; Joslin, Ronald D.

    1995-01-01

    A compact scheme is a discretization scheme that is advantageous in obtaining highly accurate solutions. However, the resulting systems from compact schemes are tridiagonal systems that are difficult to solve efficiently on parallel computers. Considering the almost symmetric Toeplitz structure, a parallel algorithm, simple parallel prefix (SPP), is proposed. The SPP algorithm requires less memory than the conventional LU decomposition and is efficient on parallel machines. It consists of a prefix communication pattern and AXPY operations. Both the computation and the communication can be truncated without degrading the accuracy when the system is diagonally dominant. A formal accuracy study has been conducted to provide a simple truncation formula. Experimental results have been measured on a MasPar MP-1 SIMD machine and on a Cray 2 vector machine. Experimental results show that the simple parallel prefix algorithm is a good algorithm for symmetric, almost symmetric Toeplitz tridiagonal systems and for the compact scheme on high-performance computers.

  15. Distributed parallel messaging for multiprocessor systems

    DOEpatents

    Chen, Dong; Heidelberger, Philip; Salapura, Valentina; Senger, Robert M; Steinmacher-Burrow, Burhard; Sugawara, Yutaka

    2013-06-04

    A method and apparatus for distributed parallel messaging in a parallel computing system. The apparatus includes, at each node of a multiprocessor network, multiple injection messaging engine units and reception messaging engine units, each implementing a DMA engine and each supporting both multiple packet injection into and multiple reception from a network, in parallel. The reception side of the messaging unit (MU) includes a switch interface enabling writing of data of a packet received from the network to the memory system. The transmission side of the messaging unit, includes switch interface for reading from the memory system when injecting packets into the network.

  16. Distributed Parallel Particle Advection using Work Requesting

    SciTech Connect

    Muller, Cornelius; Camp, David; Hentschel, Bernd; Garth, Christoph

    2013-09-30

    Particle advection is an important vector field visualization technique that is difficult to apply to very large data sets in a distributed setting due to scalability limitations in existing algorithms. In this paper, we report on several experiments using work requesting dynamic scheduling which achieves balanced work distribution on arbitrary problems with minimal communication overhead. We present a corresponding prototype implementation, provide and analyze benchmark results, and compare our results to an existing algorithm.

  17. An efficient parallel algorithm for matrix-vector multiplication

    SciTech Connect

    Hendrickson, B.; Leland, R.; Plimpton, S.

    1993-03-01

    The multiplication of a vector by a matrix is the kernel computation of many algorithms in scientific computation. A fast parallel algorithm for this calculation is therefore necessary if one is to make full use of the new generation of parallel supercomputers. This paper presents a high performance, parallel matrix-vector multiplication algorithm that is particularly well suited to hypercube multiprocessors. For an n x n matrix on p processors, the communication cost of this algorithm is O(n/[radical]p + log(p)), independent of the matrix sparsity pattern. The performance of the algorithm is demonstrated by employing it as the kernel in the well-known NAS conjugate gradient benchmark, where a run time of 6.09 seconds was observed. This is the best published performance on this benchmark achieved to date using a massively parallel supercomputer.

  18. Parallelization of the Implicit RPLUS Algorithm

    NASA Technical Reports Server (NTRS)

    Orkwis, Paul D.

    1994-01-01

    The multiblock reacting Navier-Stokes flow-solver RPLUS2D was modified for parallel implementation. Results for non-reacting flow calculations of this code indicate parallelization efficiencies greater than 84% are possible for a typical test problem. Results tend to improve as the size of the problem increases. The convergence rate of the scheme is degraded slightly when additional artificial block boundaries are included for the purpose of parallelization. However, this degradation virtually disappears if the solution is converged near to machine zero. Recommendations are made for further code improvements to increase efficiency, correct bugs in the original version, and study decomposition effectiveness.

  19. Parallelization of the Implicit RPLUS Algorithm

    NASA Technical Reports Server (NTRS)

    Orkwis, Paul D.

    1997-01-01

    The multiblock reacting Navier-Stokes flow solver RPLUS2D was modified for parallel implementation. Results for non-reacting flow calculations of this code indicate parallelization efficiencies greater than 84% are possible for a typical test problem. Results tend to improve as the size of the problem increases. The convergence rate of the scheme is degraded slightly when additional artificial block boundaries are included for the purpose of parallelization. However, this degradation virtually disappears if the solution is converged near to machine zero. Recommendations are made for further code improvements to increase efficiency, correct bugs in the original version, and study decomposition effectiveness.

  20. Asynchronous Distributed Flow Control Algorithms.

    DTIC Science & Technology

    1984-10-01

    SCHEDULE IS. DISTRIBUTION STATEMENT (of this Report) Approved for public release; distribution unlimited. I?. DISTRIBUTION STATEMENT (of the abstract...model for asynchronous computation developed by Bertsekas [14] to get some results relating to general-asynchronous distributed algo- rithms with update...to get some results relating to general asynchronous distributed algorithms with update protocols. These results are used to give an alternate proof of

  1. Design and Analysis of Scalable Parallel Algorithms

    DTIC Science & Technology

    1993-11-15

    Journal of Parallel Programming, 20(2), 1991. 8 Conference Proceedings "* Anshul Gupta, Vipin Kumar and Ahmed Sameh . Performance and Scalability of Precon...Science, University of Minnesota, Minneapolis, 1993. o Anshul Gupta, Vipin Kumar and Ahmed Sameh . Performance and Scalability of Precondi- tioned...Ahmed Sameh . Performance and scalability of precondi- tioned conjugate gradient methods on parallel computers. Technical Report TR 92-64, Uni- versity

  2. A Parallel Particle Swarm Optimization Algorithm Accelerated by Asynchronous Evaluations

    NASA Technical Reports Server (NTRS)

    Venter, Gerhard; Sobieszczanski-Sobieski, Jaroslaw

    2005-01-01

    A parallel Particle Swarm Optimization (PSO) algorithm is presented. Particle swarm optimization is a fairly recent addition to the family of non-gradient based, probabilistic search algorithms that is based on a simplified social model and is closely tied to swarming theory. Although PSO algorithms present several attractive properties to the designer, they are plagued by high computational cost as measured by elapsed time. One approach to reduce the elapsed time is to make use of coarse-grained parallelization to evaluate the design points. Previous parallel PSO algorithms were mostly implemented in a synchronous manner, where all design points within a design iteration are evaluated before the next iteration is started. This approach leads to poor parallel speedup in cases where a heterogeneous parallel environment is used and/or where the analysis time depends on the design point being analyzed. This paper introduces an asynchronous parallel PSO algorithm that greatly improves the parallel e ciency. The asynchronous algorithm is benchmarked on a cluster assembled of Apple Macintosh G5 desktop computers, using the multi-disciplinary optimization of a typical transport aircraft wing as an example.

  3. Exact parallel maximum clique algorithm for general and protein graphs.

    PubMed

    Depolli, Matjaž; Konc, Janez; Rozman, Kati; Trobec, Roman; Janežič, Dušanka

    2013-09-23

    A new exact parallel maximum clique algorithm MaxCliquePara, which finds the maximum clique (the fully connected subgraph) in undirected general and protein graphs, is presented. First, a new branch and bound algorithm for finding a maximum clique on a single computer core, which builds on ideas presented in two published state of the art sequential algorithms is implemented. The new sequential MaxCliqueSeq algorithm is faster than the reference algorithms on both DIMACS benchmark graphs as well as on protein-derived product graphs used for protein structural comparisons. Next, the MaxCliqueSeq algorithm is parallelized by splitting the branch-and-bound search tree to multiple cores, resulting in MaxCliquePara algorithm. The ability to exploit all cores efficiently makes the new parallel MaxCliquePara algorithm markedly superior to other tested algorithms. On a 12-core computer, the parallelization provides up to 2 orders of magnitude faster execution on the large DIMACS benchmark graphs and up to an order of magnitude faster execution on protein product graphs. The algorithms are freely accessible on http://commsys.ijs.si/~matjaz/maxclique.

  4. Parallel algorithms for interactive manipulation of digital terrain models

    NASA Technical Reports Server (NTRS)

    Davis, E. W.; Mcallister, D. F.; Nagaraj, V.

    1988-01-01

    Interactive three-dimensional graphics applications, such as terrain data representation and manipulation, require extensive arithmetic processing. Massively parallel machines are attractive for this application since they offer high computational rates, and grid connected architectures provide a natural mapping for grid based terrain models. Presented here are algorithms for data movement on the massive parallel processor (MPP) in support of pan and zoom functions over large data grids. It is an extension of earlier work that demonstrated real-time performance of graphics functions on grids that were equal in size to the physical dimensions of the MPP. When the dimensions of a data grid exceed the processing array size, data is packed in the array memory. Windows of the total data grid are interactively selected for processing. Movement of packed data is needed to distribute items across the array for efficient parallel processing. Execution time for data movement was found to exceed that for arithmetic aspects of graphics functions. Performance figures are given for routines written in MPP Pascal.

  5. Parallel optimization of pixel purity index algorithm for massive hyperspectral images in cloud computing environment

    NASA Astrophysics Data System (ADS)

    Chen, Yufeng; Wu, Zebin; Sun, Le; Wei, Zhihui; Li, Yonglong

    2016-04-01

    With the gradual increase in the spatial and spectral resolution of hyperspectral images, the size of image data becomes larger and larger, and the complexity of processing algorithms is growing, which poses a big challenge to efficient massive hyperspectral image processing. Cloud computing technologies distribute computing tasks to a large number of computing resources for handling large data sets without the limitation of memory and computing resource of a single machine. This paper proposes a parallel pixel purity index (PPI) algorithm for unmixing massive hyperspectral images based on a MapReduce programming model for the first time in the literature. According to the characteristics of hyperspectral images, we describe the design principle of the algorithm, illustrate the main cloud unmixing processes of PPI, and analyze the time complexity of serial and parallel algorithms. Experimental results demonstrate that the parallel implementation of the PPI algorithm on the cloud can effectively process big hyperspectral data and accelerate the algorithm.

  6. Parallel algorithms and architectures for the manipulator inertia matrix

    SciTech Connect

    Amin-Javaheri, M.

    1989-01-01

    Several parallel algorithms and architectures to compute the manipulator inertia matrix in real time are proposed. An O(N) and an O(log{sub 2}N) parallel algorithm based upon recursive computation of the inertial parameters of sets of composite rigid bodies are formulated. One- and two-dimensional systolic architectures are presented to implement the O(N) parallel algorithm. A cube architecture is employed to implement the diagonal element of the inertia matrix in O(log{sub 2}N) time and the upper off-diagonal elements in O(N) time. The resulting K{sub 1}O(N) + K{sub 2}O(log{sub 2}N) parallel algorithm is more efficient for a cube network implementation. All the architectural configurations are based upon a VLSI Robotics Processor exploiting fine-grain parallelism. In evaluation all the architectural configurations, significant performance parameters such as I/O time and idle time due to processor synchronization as well as CPU utilization and on-chip memory size are fully included. The O(N) and O(log{sub 2}N) parallel algorithms adhere to the precedence relationships among the processors. In order to achieve a higher speedup factor; however, parallel algorithms in conjunction with Non-Strict Computational Models are devised to relax interprocess precedence, and as a result, to decrease the effective computational delays. The effectiveness of the Non-strict Computational Algorithms is verified by computer simulations, based on a PUMA 560 robot manipulator. It is demonstrated that a combination of parallel algorithms and architectures results in a very effective approach to achieve real-time response for computing the manipulator inertia matrix.

  7. Ray tracing on distributed memory parallel systems

    NASA Technical Reports Server (NTRS)

    Jensen, David W.; Reed, Daniel A.

    1990-01-01

    Among the many techniques in computer graphics, ray tracing is prized because it can render realistic images, albeit at great computational expense. In this note, the performance of several approaches to ray tracing on a distributed memory parallel system is evaluated. A set of performance instrumentation tools and their associated visualization software are used to identify the underlying causes of performance differences.

  8. Algorithms for parallel and vector computations

    NASA Technical Reports Server (NTRS)

    Ortega, James M.

    1995-01-01

    This is a final report on work performed under NASA grant NAG-1-1112-FOP during the period March, 1990 through February 1995. Four major topics are covered: (1) solution of nonlinear poisson-type equations; (2) parallel reduced system conjugate gradient method; (3) orderings for conjugate gradient preconditioners, and (4) SOR as a preconditioner.

  9. Algorithmic support for commodity-based parallel computing systems.

    SciTech Connect

    Leung, Vitus Joseph; Bender, Michael A.; Bunde, David P.; Phillips, Cynthia Ann

    2003-10-01

    The Computational Plant or Cplant is a commodity-based distributed-memory supercomputer under development at Sandia National Laboratories. Distributed-memory supercomputers run many parallel programs simultaneously. Users submit their programs to a job queue. When a job is scheduled to run, it is assigned to a set of available processors. Job runtime depends not only on the number of processors but also on the particular set of processors assigned to it. Jobs should be allocated to localized clusters of processors to minimize communication costs and to avoid bandwidth contention caused by overlapping jobs. This report introduces new allocation strategies and performance metrics based on space-filling curves and one dimensional allocation strategies. These algorithms are general and simple. Preliminary simulations and Cplant experiments indicate that both space-filling curves and one-dimensional packing improve processor locality compared to the sorted free list strategy previously used on Cplant. These new allocation strategies are implemented in Release 2.0 of the Cplant System Software that was phased into the Cplant systems at Sandia by May 2002. Experimental results then demonstrated that the average number of communication hops between the processors allocated to a job strongly correlates with the job's completion time. This report also gives processor-allocation algorithms for minimizing the average number of communication hops between the assigned processors for grid architectures. The associated clustering problem is as follows: Given n points in {Re}d, find k points that minimize their average pairwise L{sub 1} distance. Exact and approximate algorithms are given for these optimization problems. One of these algorithms has been implemented on Cplant and will be included in Cplant System Software, Version 2.1, to be released. In more preliminary work, we suggest improvements to the scheduler separate from the allocator.

  10. An improved spectral graph partitioning algorithm for mapping parallel computations

    SciTech Connect

    Hendrickson, B.; Leland, R.

    1992-09-01

    Efficient use of a distributed memory parallel computer requires that the computational load be balanced across processors in a way that minimizes interprocessor communication. We present a new domain mapping algorithm that extends recent work in which ideas from spectral graph theory have been applied to this problem. Our generalization of spectral graph bisection involves a novel use of multiple eigenvectors to allow for division of a computation into four or eight parts at each stage of a recursive decomposition. The resulting method is suitable for scientific computations like irregular finite elements or differences performed on hypercube or mesh architecture machines. Experimental results confirm that the new method provides better decompositions arrived at more economically and robustly than with previous spectral methods. We have also improved upon the known spectral lower bound for graph bisection.

  11. A Programming Environment for Parallel Vision Algorithms

    DTIC Science & Technology

    1990-04-11

    linear parallel speedup. Many appli- cations for the image processing pipeline (including tracking, color histograrmning, feature detection, frame-rate...pure logic. For example, a language based on algebra of real numbers might treat constraints such as "X = Y + Z", "X = Y x Z", and so on as primitives. A...however, time for a more usable version of the language. A front end processor is therefore being written to parse expressions written in an algebraic

  12. A Parallel Algorithm for the Two-Dimensional Time Fractional Diffusion Equation with Implicit Difference Method

    PubMed Central

    Bao, Weimin; Tang, Guojian; Jiang, Yuewen; Liu, Jie

    2014-01-01

    It is very time consuming to solve fractional differential equations. The computational complexity of two-dimensional fractional differential equation (2D-TFDE) with iterative implicit finite difference method is O(M x M y N 2). In this paper, we present a parallel algorithm for 2D-TFDE and give an in-depth discussion about this algorithm. A task distribution model and data layout with virtual boundary are designed for this parallel algorithm. The experimental results show that the parallel algorithm compares well with the exact solution. The parallel algorithm on single Intel Xeon X5540 CPU runs 3.16–4.17 times faster than the serial algorithm on single CPU core. The parallel efficiency of 81 processes is up to 88.24% compared with 9 processes on a distributed memory cluster system. We do think that the parallel computing technology will become a very basic method for the computational intensive fractional applications in the near future. PMID:24744680

  13. A parallel algorithm for the two-dimensional time fractional diffusion equation with implicit difference method.

    PubMed

    Gong, Chunye; Bao, Weimin; Tang, Guojian; Jiang, Yuewen; Liu, Jie

    2014-01-01

    It is very time consuming to solve fractional differential equations. The computational complexity of two-dimensional fractional differential equation (2D-TFDE) with iterative implicit finite difference method is O(M(x)M(y)N(2)). In this paper, we present a parallel algorithm for 2D-TFDE and give an in-depth discussion about this algorithm. A task distribution model and data layout with virtual boundary are designed for this parallel algorithm. The experimental results show that the parallel algorithm compares well with the exact solution. The parallel algorithm on single Intel Xeon X5540 CPU runs 3.16-4.17 times faster than the serial algorithm on single CPU core. The parallel efficiency of 81 processes is up to 88.24% compared with 9 processes on a distributed memory cluster system. We do think that the parallel computing technology will become a very basic method for the computational intensive fractional applications in the near future.

  14. Multimodal Estimation of Distribution Algorithms.

    PubMed

    Yang, Qiang; Chen, Wei-Neng; Li, Yun; Chen, C L Philip; Xu, Xiang-Min; Zhang, Jun

    2016-02-15

    Taking the advantage of estimation of distribution algorithms (EDAs) in preserving high diversity, this paper proposes a multimodal EDA. Integrated with clustering strategies for crowding and speciation, two versions of this algorithm are developed, which operate at the niche level. Then these two algorithms are equipped with three distinctive techniques: 1) a dynamic cluster sizing strategy; 2) an alternative utilization of Gaussian and Cauchy distributions to generate offspring; and 3) an adaptive local search. The dynamic cluster sizing affords a potential balance between exploration and exploitation and reduces the sensitivity to the cluster size in the niching methods. Taking advantages of Gaussian and Cauchy distributions, we generate the offspring at the niche level through alternatively using these two distributions. Such utilization can also potentially offer a balance between exploration and exploitation. Further, solution accuracy is enhanced through a new local search scheme probabilistically conducted around seeds of niches with probabilities determined self-adaptively according to fitness values of these seeds. Extensive experiments conducted on 20 benchmark multimodal problems confirm that both algorithms can achieve competitive performance compared with several state-of-the-art multimodal algorithms, which is supported by nonparametric tests. Especially, the proposed algorithms are very promising for complex problems with many local optima.

  15. Hadoop neural network for parallel and distributed feature selection.

    PubMed

    Hodge, Victoria J; O'Keefe, Simon; Austin, Jim

    2016-06-01

    In this paper, we introduce a theoretical basis for a Hadoop-based neural network for parallel and distributed feature selection in Big Data sets. It is underpinned by an associative memory (binary) neural network which is highly amenable to parallel and distributed processing and fits with the Hadoop paradigm. There are many feature selectors described in the literature which all have various strengths and weaknesses. We present the implementation details of five feature selection algorithms constructed using our artificial neural network framework embedded in Hadoop YARN. Hadoop allows parallel and distributed processing. Each feature selector can be divided into subtasks and the subtasks can then be processed in parallel. Multiple feature selectors can also be processed simultaneously (in parallel) allowing multiple feature selectors to be compared. We identify commonalities among the five features selectors. All can be processed in the framework using a single representation and the overall processing can also be greatly reduced by only processing the common aspects of the feature selectors once and propagating these aspects across all five feature selectors as necessary. This allows the best feature selector and the actual features to select to be identified for large and high dimensional data sets through exploiting the efficiency and flexibility of embedding the binary associative-memory neural network in Hadoop.

  16. Totally parallel multilevel algorithms for sparse elliptic systems

    NASA Technical Reports Server (NTRS)

    Frederickson, Paul O.

    1989-01-01

    The fastest known algorithms for the solution of a large elliptic boundary value problem on a massively parallel hypercube all require O(log(n)) floating point operations and O(log(n)) distance-1 communications, if massively parallel is defined to mean a number of processors proportional to the size n of the problem. The Totally Parallel Multilevel Algorithm (TPMA) that has, as special cases, four of these fast algorithms is described. These four algorithms are Parallel Superconvergent Multigrid (PSMG), Robust Multigrid, the Fast Fourier Transformation (FFT) based Spectral Algorithm, and Parallel Cyclic Reduction. The algorithm TPMA, when described recursively, has four steps: (1) project to a collection of interlaced, coarser problems at the next lower level; (2) apply TPMA, recursively, to each of these lower level problems, solving directly at the lowest level; (3) interpolate these approximate solutions to the finer grid, and to verage them to form an approximate solution on this grid; and (4) refine this approximate solution with a defect-correction step, using a local approximate inverse. Choice of the projection operator (P), the interpolation operator (Q), and the smoother (S) determines the class of problems on which TPMA is most effective. There are special cases in which the first three steps produce an exact solution, and the smoother is not needed (e.g., constant coefficient operators).

  17. Fast parallel algorithm for CT image reconstruction.

    PubMed

    Flores, Liubov A; Vidal, Vicent; Mayo, Patricia; Rodenas, Francisco; Verdú, Gumersindo

    2012-01-01

    In X-ray computed tomography (CT) the X rays are used to obtain the projection data needed to generate an image of the inside of an object. The image can be generated with different techniques. Iterative methods are more suitable for the reconstruction of images with high contrast and precision in noisy conditions and from a small number of projections. Their use may be important in portable scanners for their functionality in emergency situations. However, in practice, these methods are not widely used due to the high computational cost of their implementation. In this work we analyze iterative parallel image reconstruction with the Portable Extensive Toolkit for Scientific computation (PETSc).

  18. Designing a parallel evolutionary algorithm for inferring gene networks on the cloud computing environment

    PubMed Central

    2014-01-01

    Background To improve the tedious task of reconstructing gene networks through testing experimentally the possible interactions between genes, it becomes a trend to adopt the automated reverse engineering procedure instead. Some evolutionary algorithms have been suggested for deriving network parameters. However, to infer large networks by the evolutionary algorithm, it is necessary to address two important issues: premature convergence and high computational cost. To tackle the former problem and to enhance the performance of traditional evolutionary algorithms, it is advisable to use parallel model evolutionary algorithms. To overcome the latter and to speed up the computation, it is advocated to adopt the mechanism of cloud computing as a promising solution: most popular is the method of MapReduce programming model, a fault-tolerant framework to implement parallel algorithms for inferring large gene networks. Results This work presents a practical framework to infer large gene networks, by developing and parallelizing a hybrid GA-PSO optimization method. Our parallel method is extended to work with the Hadoop MapReduce programming model and is executed in different cloud computing environments. To evaluate the proposed approach, we use a well-known open-source software GeneNetWeaver to create several yeast S. cerevisiae sub-networks and use them to produce gene profiles. Experiments have been conducted and the results have been analyzed. They show that our parallel approach can be successfully used to infer networks with desired behaviors and the computation time can be largely reduced. Conclusions Parallel population-based algorithms can effectively determine network parameters and they perform better than the widely-used sequential algorithms in gene network inference. These parallel algorithms can be distributed to the cloud computing environment to speed up the computation. By coupling the parallel model population-based optimization method and the parallel

  19. Designing a parallel evolutionary algorithm for inferring gene networks on the cloud computing environment.

    PubMed

    Lee, Wei-Po; Hsiao, Yu-Ting; Hwang, Wei-Che

    2014-01-16

    To improve the tedious task of reconstructing gene networks through testing experimentally the possible interactions between genes, it becomes a trend to adopt the automated reverse engineering procedure instead. Some evolutionary algorithms have been suggested for deriving network parameters. However, to infer large networks by the evolutionary algorithm, it is necessary to address two important issues: premature convergence and high computational cost. To tackle the former problem and to enhance the performance of traditional evolutionary algorithms, it is advisable to use parallel model evolutionary algorithms. To overcome the latter and to speed up the computation, it is advocated to adopt the mechanism of cloud computing as a promising solution: most popular is the method of MapReduce programming model, a fault-tolerant framework to implement parallel algorithms for inferring large gene networks. This work presents a practical framework to infer large gene networks, by developing and parallelizing a hybrid GA-PSO optimization method. Our parallel method is extended to work with the Hadoop MapReduce programming model and is executed in different cloud computing environments. To evaluate the proposed approach, we use a well-known open-source software GeneNetWeaver to create several yeast S. cerevisiae sub-networks and use them to produce gene profiles. Experiments have been conducted and the results have been analyzed. They show that our parallel approach can be successfully used to infer networks with desired behaviors and the computation time can be largely reduced. Parallel population-based algorithms can effectively determine network parameters and they perform better than the widely-used sequential algorithms in gene network inference. These parallel algorithms can be distributed to the cloud computing environment to speed up the computation. By coupling the parallel model population-based optimization method and the parallel computational framework, high

  20. High-Performance Psychometrics: The Parallel-E Parallel-M Algorithm for Generalized Latent Variable Models. Research Report. ETS RR-16-34

    ERIC Educational Resources Information Center

    von Davier, Matthias

    2016-01-01

    This report presents results on a parallel implementation of the expectation-maximization (EM) algorithm for multidimensional latent variable models. The developments presented here are based on code that parallelizes both the E step and the M step of the parallel-E parallel-M algorithm. Examples presented in this report include item response…

  1. FRPA: A Framework for Recursive Parallel Algorithms

    DTIC Science & Technology

    2015-05-01

    merge() did not have a signif- icant effect on performance . We therefore removed this optimization in the final version of our code. Fig. 1...Precision Fig. 3: Strassen-Winograd’s performance for a selection of BFS/DFS interleavings on two machines. Effective GFlops is the number of floating...multiplication algorithm would perform if it completed the multiplication in the same amount of time. For MKL, effective GFlops = actual GFlops because

  2. Graphical representation of parallel algorithmic processes. Master's thesis

    SciTech Connect

    Williams, E.M.

    1990-12-01

    Algorithm animation is a visualization method used to enhance understanding of functioning of an algorithm or program. Visualization is used for many purposes, including education, algorithm research, performance analysis, and program debugging. This research applies algorithm animation techniques to programs developed for parallel architectures, with specific on the Intel iPSC/2 hypercube. While both P-time and NP-time algorithms can potentially benefit from using visualization techniques, the set of NP-complete problems provides fertile ground for developing parallel applications, since the combinatoric nature of the problems makes finding the optimum solution impractical. The primary goals for this visualization system are: Data should be displayed as it is generated. The interface to the targe program should be transparent, allowing the animation of existing programs. Flexibility - the system should be able to animate any algorithm. The resulting system incorporates and extends two AFIT products: the AFIT Algorithm Animation Research Facility (AAARF) and the Parallel Resource Analysis Software Environment (PRASE). AAARF is an algorithm animation system developed primarily for sequential programs, but is easily adaptable for use with parallel programs. PRASE is an instrumentation package that extracts system performance data from programs on the Intel hypercubes. Since performance data is an essential part of analyzing any parallel program, views of the performance data are provided as an elementary part of the system. Custom software is designed to interface these systems and to display the program data. The program chosen as the example for this study is a member of the NP-complete problem set; it is a parallel implementation of a general.

  3. Efficient sequential and parallel algorithms for record linkage.

    PubMed

    Mamun, Abdullah-Al; Mi, Tian; Aseltine, Robert; Rajasekaran, Sanguthevar

    2014-01-01

    Integrating data from multiple sources is a crucial and challenging problem. Even though there exist numerous algorithms for record linkage or deduplication, they suffer from either large time needs or restrictions on the number of datasets that they can integrate. In this paper we report efficient sequential and parallel algorithms for record linkage which handle any number of datasets and outperform previous algorithms. Our algorithms employ hierarchical clustering algorithms as the basis. A key idea that we use is radix sorting on certain attributes to eliminate identical records before any further processing. Another novel idea is to form a graph that links similar records and find the connected components. Our sequential and parallel algorithms have been tested on a real dataset of 1,083,878 records and synthetic datasets ranging in size from 50,000 to 9,000,000 records. Our sequential algorithm runs at least two times faster, for any dataset, than the previous best-known algorithm, the two-phase algorithm using faster computation of the edit distance (TPA (FCED)). The speedups obtained by our parallel algorithm are almost linear. For example, we get a speedup of 7.5 with 8 cores (residing in a single node), 14.1 with 16 cores (residing in two nodes), and 26.4 with 32 cores (residing in four nodes). We have compared the performance of our sequential algorithm with TPA (FCED) and found that our algorithm outperforms the previous one. The accuracy is the same as that of this previous best-known algorithm.

  4. Efficient sequential and parallel algorithms for record linkage

    PubMed Central

    Mamun, Abdullah-Al; Mi, Tian; Aseltine, Robert; Rajasekaran, Sanguthevar

    2014-01-01

    Background and objective Integrating data from multiple sources is a crucial and challenging problem. Even though there exist numerous algorithms for record linkage or deduplication, they suffer from either large time needs or restrictions on the number of datasets that they can integrate. In this paper we report efficient sequential and parallel algorithms for record linkage which handle any number of datasets and outperform previous algorithms. Methods Our algorithms employ hierarchical clustering algorithms as the basis. A key idea that we use is radix sorting on certain attributes to eliminate identical records before any further processing. Another novel idea is to form a graph that links similar records and find the connected components. Results Our sequential and parallel algorithms have been tested on a real dataset of 1 083 878 records and synthetic datasets ranging in size from 50 000 to 9 000 000 records. Our sequential algorithm runs at least two times faster, for any dataset, than the previous best-known algorithm, the two-phase algorithm using faster computation of the edit distance (TPA (FCED)). The speedups obtained by our parallel algorithm are almost linear. For example, we get a speedup of 7.5 with 8 cores (residing in a single node), 14.1 with 16 cores (residing in two nodes), and 26.4 with 32 cores (residing in four nodes). Conclusions We have compared the performance of our sequential algorithm with TPA (FCED) and found that our algorithm outperforms the previous one. The accuracy is the same as that of this previous best-known algorithm. PMID:24154837

  5. Resource Management for Distributed Parallel Systems

    NASA Technical Reports Server (NTRS)

    Neuman, B. Clifford; Rao, Santosh

    1993-01-01

    Multiprocessor systems should exist in the the larger context of distributed systems, allowing multiprocessor resources to be shared by those that need them. Unfortunately, typical multiprocessor resource management techniques do not scale to large networks. The Prospero Resource Manager (PRM) is a scalable resource allocation system that supports the allocation of processing resources in large networks and multiprocessor systems. To manage resources in such distributed parallel systems, PRM employs three types of managers: system managers, job managers, and node managers. There exist multiple independent instances of each type of manager, reducing bottlenecks. The complexity of each manager is further reduced because each is designed to utilize information at an appropriate level of abstraction.

  6. Resource Management for Distributed Parallel Systems

    NASA Technical Reports Server (NTRS)

    Neuman, B. Clifford; Rao, Santosh

    1993-01-01

    Multiprocessor systems should exist in the the larger context of distributed systems, allowing multiprocessor resources to be shared by those that need them. Unfortunately, typical multiprocessor resource management techniques do not scale to large networks. The Prospero Resource Manager (PRM) is a scalable resource allocation system that supports the allocation of processing resources in large networks and multiprocessor systems. To manage resources in such distributed parallel systems, PRM employs three types of managers: system managers, job managers, and node managers. There exist multiple independent instances of each type of manager, reducing bottlenecks. The complexity of each manager is further reduced because each is designed to utilize information at an appropriate level of abstraction.

  7. Cloud identification using genetic algorithms and massively parallel computation

    NASA Technical Reports Server (NTRS)

    Buckles, Bill P.; Petry, Frederick E.

    1996-01-01

    As a Guest Computational Investigator under the NASA administered component of the High Performance Computing and Communication Program, we implemented a massively parallel genetic algorithm on the MasPar SIMD computer. Experiments were conducted using Earth Science data in the domains of meteorology and oceanography. Results obtained in these domains are competitive with, and in most cases better than, similar problems solved using other methods. In the meteorological domain, we chose to identify clouds using AVHRR spectral data. Four cloud speciations were used although most researchers settle for three. Results were remarkedly consistent across all tests (91% accuracy). Refinements of this method may lead to more timely and complete information for Global Circulation Models (GCMS) that are prevalent in weather forecasting and global environment studies. In the oceanographic domain, we chose to identify ocean currents from a spectrometer having similar characteristics to AVHRR. Here the results were mixed (60% to 80% accuracy). Given that one is willing to run the experiment several times (say 10), then it is acceptable to claim the higher accuracy rating. This problem has never been successfully automated. Therefore, these results are encouraging even though less impressive than the cloud experiment. Successful conclusion of an automated ocean current detection system would impact coastal fishing, naval tactics, and the study of micro-climates. Finally we contributed to the basic knowledge of GA (genetic algorithm) behavior in parallel environments. We developed better knowledge of the use of subpopulations in the context of shared breeding pools and the migration of individuals. Rigorous experiments were conducted based on quantifiable performance criteria. While much of the work confirmed current wisdom, for the first time we were able to submit conclusive evidence. The software developed under this grant was placed in the public domain. An extensive user

  8. A scalable parallel algorithm for multiple objective linear programs

    NASA Technical Reports Server (NTRS)

    Wiecek, Malgorzata M.; Zhang, Hong

    1994-01-01

    This paper presents an ADBASE-based parallel algorithm for solving multiple objective linear programs (MOLP's). Job balance, speedup and scalability are of primary interest in evaluating efficiency of the new algorithm. Implementation results on Intel iPSC/2 and Paragon multiprocessors show that the algorithm significantly speeds up the process of solving MOLP's, which is understood as generating all or some efficient extreme points and unbounded efficient edges. The algorithm gives specially good results for large and very large problems. Motivation and justification for solving such large MOLP's are also included.

  9. A Parallel Saturation Algorithm on Shared Memory Architectures

    NASA Technical Reports Server (NTRS)

    Ezekiel, Jonathan; Siminiceanu

    2007-01-01

    Symbolic state-space generators are notoriously hard to parallelize. However, the Saturation algorithm implemented in the SMART verification tool differs from other sequential symbolic state-space generators in that it exploits the locality of ring events in asynchronous system models. This paper explores whether event locality can be utilized to efficiently parallelize Saturation on shared-memory architectures. Conceptually, we propose to parallelize the ring of events within a decision diagram node, which is technically realized via a thread pool. We discuss the challenges involved in our parallel design and conduct experimental studies on its prototypical implementation. On a dual-processor dual core PC, our studies show speed-ups for several example models, e.g., of up to 50% for a Kanban model, when compared to running our algorithm only on a single core.

  10. General upper bounds on the runtime of parallel evolutionary algorithms.

    PubMed

    Lässig, Jörg; Sudholt, Dirk

    2014-01-01

    We present a general method for analyzing the runtime of parallel evolutionary algorithms with spatially structured populations. Based on the fitness-level method, it yields upper bounds on the expected parallel runtime. This allows for a rigorous estimate of the speedup gained by parallelization. Tailored results are given for common migration topologies: ring graphs, torus graphs, hypercubes, and the complete graph. Example applications for pseudo-Boolean optimization show that our method is easy to apply and that it gives powerful results. In our examples the performance guarantees improve with the density of the topology. Surprisingly, even sparse topologies such as ring graphs lead to a significant speedup for many functions while not increasing the total number of function evaluations by more than a constant factor. We also identify which number of processors lead to the best guaranteed speedups, thus giving hints on how to parameterize parallel evolutionary algorithms.

  11. Singular value decomposition utilizing parallel algorithms on graphical processors

    SciTech Connect

    Kotas, Charlotte W; Barhen, Jacob

    2011-01-01

    transformations, and then diagonalizes the intermediate bidiagonal matrix through implicit QR shifts. This is similar to that implemented for real matrices by Lahabar and Narayanan ("Singular Value Decomposition on GPU using CUDA", IEEE International Parallel Distributed Processing Symposium 2009). The implementation is done in a hybrid manner, with the bidiagonalization stage done using the GPU while the diagonalization stage is done using the CPU, with the GPU used to update the U and V matrices. The second algorithm is based on a one-sided Jacobi scheme utilizing a sequence of pair-wise column orthogonalizations such that A is replaced by AV until the resulting matrix is sufficiently orthogonal (that is, equal to U ). V is obtained from the sequence of orthogonalizations, while can be found from the square root of the diagonal elements of AH A and, once is known, U can be found from column scaling the resulting matrix. These implementations utilize CUDA Fortran and NVIDIA's CUB LAS library. The primary goal of this study is to quantify the comparative performance of these two techniques against themselves and other standard implementations (for example, MATLAB). Considering that there is significant overhead associated with transferring data to the GPU and with synchronization between the GPU and the host CPU, it is also important to understand when it is worthwhile to use the GPU in terms of the matrix size and number of concurrent SVDs to be calculated.

  12. A communication-less parallel algorithm for tridiagonal Toeplitz systems

    NASA Astrophysics Data System (ADS)

    McNally, Jeffrey M.; Garey, L. E.; Shaw, R. E.

    2008-03-01

    Diagonally dominant tridiagonal Toeplitz systems of linear equations arise in many application areas and have been well studied in the past. Modern interest in numerical linear algebra is often focusing on solving classic problems in parallel. In McNally [Fast parallel algorithms for tri-diagonal symmetric Toeplitz systems, MCS Thesis, University of New Brunswick, Saint John, 1999], an m processor Split & Correct algorithm was presented for approximating the solution to a symmetric tridiagonal Toeplitz linear system of equations. Nemani [Perturbation methods for circulant-banded systems and their parallel implementation, Ph.D. Thesis, University of New Brunswick, Saint John, 2001] and McNally (2003) adapted the works of Rojo [A new method for solving symmetric circulant tri-diagonal system of linear equations, Comput. Math. Appl. 20 (1990) 61-67], Yan and Chung [A fast algorithm for solving special tri-diagonal systems, Computing 52 (1994) 203-211] and McNally et al. [A split-correct parallel algorithm for solving tri-diagonal symmetric Toeplitz systems, Internat. J. Comput. Math. 75 (2000) 303-313] to the non-symmetric case. In this paper we present relevant background from these methods and then introduce an m processor scalable communication-less approximation algorithm for solving a diagonally dominant tridiagonal Toeplitz system of linear equations.

  13. A biconjugate gradient type algorithm on massively parallel architectures

    NASA Technical Reports Server (NTRS)

    Freund, Roland W.; Hochbruck, Marlis

    1991-01-01

    The biconjugate gradient (BCG) method is the natural generalization of the classical conjugate gradient algorithm for Hermitian positive definite matrices to general non-Hermitian linear systems. Unfortunately, the original BCG algorithm is susceptible to possible breakdowns and numerical instabilities. Recently, Freund and Nachtigal have proposed a novel BCG type approach, the quasi-minimal residual method (QMR), which overcomes the problems of BCG. Here, an implementation is presented of QMR based on an s-step version of the nonsymmetric look-ahead Lanczos algorithm. The main feature of the s-step Lanczos algorithm is that, in general, all inner products, except for one, can be computed in parallel at the end of each block; this is unlike the other standard Lanczos process where inner products are generated sequentially. The resulting implementation of QMR is particularly attractive on massively parallel SIMD architectures, such as the Connection Machine.

  14. Parallel Detection Algorithm for Fast Frequency Hopping OFDM

    NASA Astrophysics Data System (ADS)

    Kun, Xu; Xiao-xin, Yi

    2011-05-01

    Fast frequency hopping OFDM (FFH-OFDM) exploits frequency diversity in one OFDM symbol to enhance conventional OFDM performance without using channel coding. Zero-forcing (ZF) and minimum mean square error (MMSE) equalization were first used to detect FFH-OFDM signal with a relatively poor bit error rate (BER) performance compared to QR-based detection algorithm. This paper proposes a parallel detection algorithm (PDA) to further improve the BER performance with parallel interference cancelation (PIC) based on MMSE criterion. Our proposed PDA not only improves the BER performance at high signal to noise ratio (SNR) regime but also possesses lower decoding delay property with respect to QR-based detection algorithm while maintaining comparable computation complexity. Simulation results indicate that at BER = 10-3 the PDA achieves 5 dB SNR gain over QR-based detection algorithm and more as SNR increases.

  15. Parallel algorithms for computation of the manipulator inertia matrix

    NASA Technical Reports Server (NTRS)

    Amin-Javaheri, Masoud; Orin, David E.

    1989-01-01

    The development of an O(log2N) parallel algorithm for the manipulator inertia matrix is presented. It is based on the most efficient serial algorithm which uses the composite rigid body method. Recursive doubling is used to reformulate the linear recurrence equations which are required to compute the diagonal elements of the matrix. It results in O(log2N) levels of computation. Computation of the off-diagonal elements involves N linear recurrences of varying-size and a new method, which avoids redundant computation of position and orientation transforms for the manipulator, is developed. The O(log2N) algorithm is presented in both equation and graphic forms which clearly show the parallelism inherent in the algorithm.

  16. Parallel processors and nonlinear structural dynamics algorithms and software

    NASA Technical Reports Server (NTRS)

    Belytschko, T.

    1986-01-01

    A nonlinear structural dynamics program with an element library that exploits parallel processing is under development. The aim is to exploit scheduling-allocation so that parallel processing and vectorization can effectively be treated in a general purpose program. As a byproduct an automatic scheme for assigning time steps was devised. A rudimentary form of the program is complete and has been tested; it shows substantial advantage can be taken of parallelism. In addition, a stability proof for the subcycling algorithm has been developed.

  17. Parallel AFSA algorithm accelerating based on MIC architecture

    NASA Astrophysics Data System (ADS)

    Zhou, Junhao; Xiao, Hong; Huang, Yifan; Li, Yongzhao; Xu, Yuanrui

    2017-05-01

    Analysis AFSA past for solving the traveling salesman problem, the algorithm efficiency is often a big problem, and the algorithm processing method, it does not fully responsive to the characteristics of the traveling salesman problem to deal with, and therefore proposes a parallel join improved AFSA process. The simulation with the current TSP known optimal solutions were analyzed, the results showed that the AFSA iterations improved less, on the MIC cards doubled operating efficiency, efficiency significantly.

  18. Highly parallel consistent labeling algorithm suitable for optoelectronic implementation.

    PubMed

    Marsden, G C; Kiamilev, F; Esener, S; Lee, S H

    1991-01-10

    Constraint satisfaction problems require a search through a large set of possibilities. Consistent labeling is a method by which search spaces can be drastically reduced. We present a highly parallel consistent labeling algorithm, which achieves strong k-consistency for any value k and which can include higher-order constraints. The algorithm uses vector outer product, matrix summation, and matrix intersection operations. These operations require local computation with global communication and, therefore, are well suited to a optoelectronic implementation.

  19. Parallel implementation of an algorithm for Delaunay triangulation

    NASA Technical Reports Server (NTRS)

    Merriam, Marshal L.

    1992-01-01

    The theory and practice of implementing Tanemura's algorithm for 3D Delaunay triangulation on Intel's Gamma prototype, a 128 processor MIMD computer, is described. Efficient implementation of Tanemura's algorithm on a conventional, vector processing supercomputer is problematic. It does not vectorize to any significant degree and requires indirect addressing. Efficient implementation on a parallel architecture is possible, however. Speeds in excess of 20 times a single processor Cray Y-MP are realized on 128 processors of the Intel Gamma prototype.

  20. Parallel implementation of an algorithm for Delaunay triangulation

    NASA Technical Reports Server (NTRS)

    Merriam, Marshall L.

    1992-01-01

    This work concerns the theory and practice of implementing Tanemura's algorithm for 3D Delaunay triangulation on Intel's Gamma prototype, a 128 processor MIMD computer. Tanemura's algorithm does not vectorize to any significant degree and requires indirect addressing. Efficient implementation on a conventional, vector processing, supercomputer is problematic. Efficient implementation on a parallel architecture is possible, however. In this work, speeds in excess of 8 times a single processor Cray Y-mp are realized on 128 processors of the Intel Gamma prototype.

  1. Applications of Parallelism to Current Algorithms for Intelligence Analysis

    DTIC Science & Technology

    1987-07-10

    ALGORITHMS FOR INTELLIGENCE ANALYSIS Martha Ann Griesel * J. Steven Hughes Beth R. Moore 10 July 1987 National Aeronautics and Space Administration...INTELLIGENCE CENTER AND SCHOOL Software Analysis and Management System Applications of Parallelism to Current Algorithms for Intelligence Analysis 10 July 1987...rates and a growing diversity of IEW information sources create a void in current intelligence analysis methods. New ways are needed to quickly

  2. CRBLASTER: A Parallel-Processing Computational Framework for Embarrassingly-Parallel Image-Analysis Algorithms

    NASA Astrophysics Data System (ADS)

    Mighell, Kenneth John

    2011-11-01

    The development of parallel-processing image-analysis codes is generally a challenging task that requires complicated choreography of interprocessor communications. If, however, the image-analysis algorithm is embarrassingly parallel, then the development of a parallel-processing implementation of that algorithm can be a much easier task to accomplish because, by definition, there is little need for communication between the compute processes. I describe the design, implementation, and performance of a parallel-processing image-analysis application, called CRBLASTER, which does cosmic-ray rejection of CCD (charge-coupled device) images using the embarrassingly-parallel L.A.COSMIC algorithm. CRBLASTER is written in C using the high-performance computing industry standard Message Passing Interface (MPI) library. The code has been designed to be used by research scientists who are familiar with C as a parallel-processing computational framework that enables the easy development of parallel-processing image-analysis programs based on embarrassingly-parallel algorithms. The CRBLASTER source code is freely available at the official application website at the National Optical Astronomy Observatory. Removing cosmic rays from a single 800x800 pixel Hubble Space Telescope WFPC2 image takes 44 seconds with the IRAF script lacos_im.cl running on a single core of an Apple Mac Pro computer with two 2.8-GHz quad-core Intel Xeon processors. CRBLASTER is 7.4 times faster processing the same image on a single core on the same machine. Processing the same image with CRBLASTER simultaneously on all 8 cores of the same machine takes 0.875 seconds -- which is a speedup factor of 50.3 times faster than the IRAF script. A detailed analysis is presented of the performance of CRBLASTER using between 1 and 57 processors on a low-power Tilera 700-MHz 64-core TILE64 processor.

  3. Efficient parallel algorithms for optical computing with the discrete Fourier transform (DFT) primitive

    NASA Astrophysics Data System (ADS)

    Reif, John H.; Tyagi, Akhilesh

    1997-10-01

    Optical-computing technology offers new challenges to algorithm designers since it can perform an n -point discrete Fourier transform (DFT) computation in only unit time. Note that the DFT is a nontrivial computation in the parallel random-access machine model, a model of computing commonly used by parallel-algorithm designers. We develop two new models, the DFT VLSIO (very-large-scale integrated optics) and the DFT circuit, to capture this characteristic of optical computing. We also provide two paradigms for developing parallel algorithms in these models. Efficient parallel algorithms for many problems, including polynomial and matrix computations, sorting, and string matching, are presented. The sorting and string-matching algorithms are particularly noteworthy. Almost all these algorithms are within a polylog factor of the optical-computing (VLSIO) lower bounds derived by Barakat and Reif Appl. Opt. 26, 1015 (1987) and by Tyagi and Reif Proceedings of the Second IEEE Symposium on Parallel and Distributed Processing (Institute of Electrical and Electronics Engineers, New York, 1990) p. 14 .

  4. A parallel simulated annealing algorithm for standard cell placement on a hypercube computer

    NASA Technical Reports Server (NTRS)

    Jones, Mark Howard

    1987-01-01

    A parallel version of a simulated annealing algorithm is presented which is targeted to run on a hypercube computer. A strategy for mapping the cells in a two dimensional area of a chip onto processors in an n-dimensional hypercube is proposed such that both small and large distance moves can be applied. Two types of moves are allowed: cell exchanges and cell displacements. The computation of the cost function in parallel among all the processors in the hypercube is described along with a distributed data structure that needs to be stored in the hypercube to support parallel cost evaluation. A novel tree broadcasting strategy is used extensively in the algorithm for updating cell locations in the parallel environment. Studies on the performance of the algorithm on example industrial circuits show that it is faster and gives better final placement results than the uniprocessor simulated annealing algorithms. An improved uniprocessor algorithm is proposed which is based on the improved results obtained from parallelization of the simulated annealing algorithm.

  5. Accelerated parallel algorithm for gene network reverse engineering.

    PubMed

    He, Jing; Zhou, Zhou; Reed, Michael; Califano, Andrea

    2017-09-21

    The Algorithm for the Reconstruction of Accurate Cellular Networks (ARACNE) represents one of the most effective tools to reconstruct gene regulatory networks from large-scale molecular profile datasets. However, previous implementations require intensive computing resources and, in some cases, restrict the number of samples that can be used. These issues can be addressed elegantly in a GPU computing framework, where repeated mathematical computation can be done efficiently, but requires extensive redesign to apply parallel computing techniques to the original serial algorithm, involving detailed optimization efforts based on a deep understanding of both hardware and software architecture. Here, we present an accelerated parallel implementation of ARACNE (GPU-ARACNE). By taking advantage of multi-level parallelism and the Compute Unified Device Architecture (CUDA) parallel kernel-call library, GPU-ARACNE successfully parallelizes a serial algorithm and simplifies the user experience from multi-step operations to one step. Using public datasets on comparable hardware configurations, we showed that GPU-ARACNE is faster than previous implementations and is able to reconstruct equally valid gene regulatory networks. Given that previous versions of ARACNE are extremely resource demanding, either in computational time or in hardware investment, GPU-ARACNE is remarkably valuable for researchers who need to build complex regulatory networks from large expression datasets, but with limited budget on computational resources. In addition, our GPU-centered optimization of adaptive partitioning for Mutual Information (MI) estimation provides lessons that are applicable to other domains.

  6. NavP: Structured and Multithreaded Distributed Parallel Programming

    NASA Technical Reports Server (NTRS)

    Pan, Lei

    2007-01-01

    We present Navigational Programming (NavP) -- a distributed parallel programming methodology based on the principles of migrating computations and multithreading. The four major steps of NavP are: (1) Distribute the data using the data communication pattern in a given algorithm; (2) Insert navigational commands for the computation to migrate and follow large-sized distributed data; (3) Cut the sequential migrating thread and construct a mobile pipeline; and (4) Loop back for refinement. NavP is significantly different from the current prevailing Message Passing (MP) approach. The advantages of NavP include: (1) NavP is structured distributed programming and it does not change the code structure of an original algorithm. This is in sharp contrast to MP as MP implementations in general do not resemble the original sequential code; (2) NavP implementations are always competitive with the best MPI implementations in terms of performance. Approaches such as DSM or HPF have failed to deliver satisfying performance as of today in contrast, even if they are relatively easy to use compared to MP; (3) NavP provides incremental parallelization, which is beyond the reach of MP; and (4) NavP is a unifying approach that allows us to exploit both fine- (multithreading on shared memory) and coarse- (pipelined tasks on distributed memory) grained parallelism. This is in contrast to the currently popular hybrid use of MP+OpenMP, which is known to be complex to use. We present experimental results that demonstrate the effectiveness of NavP.

  7. NavP: Structured and Multithreaded Distributed Parallel Programming

    NASA Technical Reports Server (NTRS)

    Pan, Lei

    2007-01-01

    We present Navigational Programming (NavP) -- a distributed parallel programming methodology based on the principles of migrating computations and multithreading. The four major steps of NavP are: (1) Distribute the data using the data communication pattern in a given algorithm; (2) Insert navigational commands for the computation to migrate and follow large-sized distributed data; (3) Cut the sequential migrating thread and construct a mobile pipeline; and (4) Loop back for refinement. NavP is significantly different from the current prevailing Message Passing (MP) approach. The advantages of NavP include: (1) NavP is structured distributed programming and it does not change the code structure of an original algorithm. This is in sharp contrast to MP as MP implementations in general do not resemble the original sequential code; (2) NavP implementations are always competitive with the best MPI implementations in terms of performance. Approaches such as DSM or HPF have failed to deliver satisfying performance as of today in contrast, even if they are relatively easy to use compared to MP; (3) NavP provides incremental parallelization, which is beyond the reach of MP; and (4) NavP is a unifying approach that allows us to exploit both fine- (multithreading on shared memory) and coarse- (pipelined tasks on distributed memory) grained parallelism. This is in contrast to the currently popular hybrid use of MP+OpenMP, which is known to be complex to use. We present experimental results that demonstrate the effectiveness of NavP.

  8. A Parallel Genetic Algorithm for Automated Electronic Circuit Design

    NASA Technical Reports Server (NTRS)

    Lohn, Jason D.; Colombano, Silvano P.; Haith, Gary L.; Stassinopoulos, Dimitris; Norvig, Peter (Technical Monitor)

    2000-01-01

    We describe a parallel genetic algorithm (GA) that automatically generates circuit designs using evolutionary search. A circuit-construction programming language is introduced and we show how evolution can generate practical analog circuit designs. Our system allows circuit size (number of devices), circuit topology, and device values to be evolved. We present experimental results as applied to analog filter and amplifier design tasks.

  9. Parallel processors and nonlinear structural dynamics algorithms and software

    NASA Technical Reports Server (NTRS)

    Belytschko, Ted; Gilbertsen, Noreen D.; Neal, Mark O.; Plaskacz, Edward J.

    1989-01-01

    The adaptation of a finite element program with explicit time integration to a massively parallel SIMD (single instruction multiple data) computer, the CONNECTION Machine is described. The adaptation required the development of a new algorithm, called the exchange algorithm, in which all nodal variables are allocated to the element with an exchange of nodal forces at each time step. The architectural and C* programming language features of the CONNECTION Machine are also summarized. Various alternate data structures and associated algorithms for nonlinear finite element analysis are discussed and compared. Results are presented which demonstrate that the CONNECTION Machine is capable of outperforming the CRAY XMP/14.

  10. Parallel algorithm of VLBI software correlator under multiprocessor environment

    NASA Astrophysics Data System (ADS)

    Zheng, Weimin; Zhang, Dong

    2007-11-01

    The correlator is the key signal processing equipment of a Very Lone Baseline Interferometry (VLBI) synthetic aperture telescope. It receives the mass data collected by the VLBI observatories and produces the visibility function of the target, which can be used to spacecraft position, baseline length measurement, synthesis imaging, and other scientific applications. VLBI data correlation is a task of data intensive and computation intensive. This paper presents the algorithms of two parallel software correlators under multiprocessor environments. A near real-time correlator for spacecraft tracking adopts the pipelining and thread-parallel technology, and runs on the SMP (Symmetric Multiple Processor) servers. Another high speed prototype correlator using the mixed Pthreads and MPI (Massage Passing Interface) parallel algorithm is realized on a small Beowulf cluster platform. Both correlators have the characteristic of flexible structure, scalability, and with 10-station data correlating abilities.

  11. The delayed coupling method: An algorithm for solving banded diagonal matrix problems in parallel

    SciTech Connect

    Mattor, N.; Williams, T.J.; Hewett, D.W.; Dimits, A.M.

    1997-09-01

    We present a new algorithm for solving banded diagonal matrix problems efficiently on distributed-memory parallel computers, designed originally for use in dynamic alternating-direction implicit partial differential equation solvers. The algorithm optimizes efficiency with respect to the number of numerical operations and to the amount of interprocessor communication. This is called the ``delayed coupling method`` because the communication is deferred until needed. We focus here on tridiagonal and periodic tridiagonal systems.

  12. Technical Report: Scalable Parallel Algorithms for High Dimensional Numerical Integration

    SciTech Connect

    Masalma, Yahya; Jiao, Yu

    2010-10-01

    We implemented a scalable parallel quasi-Monte Carlo numerical high-dimensional integration for tera-scale data points. The implemented algorithm uses the Sobol s quasi-sequences to generate random samples. Sobol s sequence was used to avoid clustering effects in the generated random samples and to produce low-discrepancy random samples which cover the entire integration domain. The performance of the algorithm was tested. Obtained results prove the scalability and accuracy of the implemented algorithms. The implemented algorithm could be used in different applications where a huge data volume is generated and numerical integration is required. We suggest using the hyprid MPI and OpenMP programming model to improve the performance of the algorithms. If the mixed model is used, attention should be paid to the scalability and accuracy.

  13. A Computational Fluid Dynamics Algorithm on a Massively Parallel Computer

    NASA Technical Reports Server (NTRS)

    Jespersen, Dennis C.; Levit, Creon

    1989-01-01

    The discipline of computational fluid dynamics is demanding ever-increasing computational power to deal with complex fluid flow problems. We investigate the performance of a finite-difference computational fluid dynamics algorithm on a massively parallel computer, the Connection Machine. Of special interest is an implicit time-stepping algorithm; to obtain maximum performance from the Connection Machine, it is necessary to use a nonstandard algorithm to solve the linear systems that arise in the implicit algorithm. We find that the Connection Machine ran achieve very high computation rates on both explicit and implicit algorithms. The performance of the Connection Machine puts it in the same class as today's most powerful conventional supercomputers.

  14. Fast parallel algorithms: from images to level sets and labels

    NASA Astrophysics Data System (ADS)

    Nguyen, H. T.; Jung, Ken K.; Raghavan, Raghu

    1990-07-01

    Decomposition into level sets refers to assigning a code with respect to intensity or elevation while labeling refers to assigning a code with respect to disconnected regions. We present a sequence of parallel algorithms for these two processes. The process of labeling includes re-assign labels into a natural sequence and compare different labeling algorithm. We discuss the difference between edge-based and region-based labeling. The speed improvements in this labeling scheme come from the collective efficiency of different techniques. We have implemented these algorithms on an in-house built Geometric Single Instruction Multiple Data (GSIMD) parallel machine with global buses and a Multiple Instruction Multiple Data (MIMD) controller. This allows real time image interpretation on live data at a rate that is much higher than video rate. The performance figures will be shown.

  15. A parallel stereo reconstruction algorithm with applications in entomology (APSRA)

    NASA Astrophysics Data System (ADS)

    Bhasin, Rajesh; Jang, Won Jun; Hart, John C.

    2012-03-01

    We propose a fast parallel algorithm for the reconstruction of 3-Dimensional point clouds of insects from binocular stereo image pairs using a hierarchical approach for disparity estimation. Entomologists study various features of insects to classify them, build their distribution maps, and discover genetic links between specimens among various other essential tasks. This information is important to the pesticide and the pharmaceutical industries among others. When considering the large collections of insects entomologists analyze, it becomes difficult to physically handle the entire collection and share the data with researchers across the world. With the method presented in our work, Entomologists can create an image database for their collections and use the 3D models for studying the shape and structure of the insects thus making it easier to maintain and share. Initial feedback shows that the reconstructed 3D models preserve the shape and size of the specimen. We further optimize our results to incorporate multiview stereo which produces better overall structure of the insects. Our main contribution is applying stereoscopic vision techniques to entomology to solve the problems faced by entomologists.

  16. Parallel global optimization with the particle swarm algorithm.

    PubMed

    Schutte, J F; Reinbolt, J A; Fregly, B J; Haftka, R T; George, A D

    2004-12-07

    Present day engineering optimization problems often impose large computational demands, resulting in long solution times even on a modern high-end processor. To obtain enhanced computational throughput and global search capability, we detail the coarse-grained parallelization of an increasingly popular global search method, the particle swarm optimization (PSO) algorithm. Parallel PSO performance was evaluated using two categories of optimization problems possessing multiple local minima-large-scale analytical test problems with computationally cheap function evaluations and medium-scale biomechanical system identification problems with computationally expensive function evaluations. For load-balanced analytical test problems formulated using 128 design variables, speedup was close to ideal and parallel efficiency above 95% for up to 32 nodes on a Beowulf cluster. In contrast, for load-imbalanced biomechanical system identification problems with 12 design variables, speedup plateaued and parallel efficiency decreased almost linearly with increasing number of nodes. The primary factor affecting parallel performance was the synchronization requirement of the parallel algorithm, which dictated that each iteration must wait for completion of the slowest fitness evaluation. When the analytical problems were solved using a fixed number of swarm iterations, a single population of 128 particles produced a better convergence rate than did multiple independent runs performed using sub-populations (8 runs with 16 particles, 4 runs with 32 particles, or 2 runs with 64 particles). These results suggest that (1) parallel PSO exhibits excellent parallel performance under load-balanced conditions, (2) an asynchronous implementation would be valuable for real-life problems subject to load imbalance, and (3) larger population sizes should be considered when multiple processors are available.

  17. Time parallelization of plasma simulations using the parareal algorithm

    SciTech Connect

    Samaddar, D.; Houlberg, Wayne A; Berry, Lee A; Elwasif, Wael R; Huysmans, G; Batchelor, Donald B

    2011-01-01

    Simulation of fusion plasmas involve a broad range of timescales. In magnetically confined plasmas, such as in ITER, the timescale associated with the microturbulence responsible for transport and confinement timescales vary by an order of 10^6 10^9. Simulating this entire range of timescales is currently impossible, even on the most powerful supercomputers available. Space parallelization has so far been the most common approach to solve partial differential equations. Space parallelization alone has led to computational saturation for fluid codes, which means that the walltime for computaion does not linearly decrease with the increasing number of processors used. The application of the parareal algorithm to simulations of fusion plasmas ushers in a new avenue of parallelization, namely temporal parallelization. The algorithm has been successfully applied to plasma turbulence simulations, prior to which it has been applied to other relatively simpler problems. This work explores the extension of the applicability of the parareal algorithm to ITER relevant problems, starting with a diffusion-convection model.

  18. Efficient parallel implementation of active appearance model fitting algorithm on GPU.

    PubMed

    Wang, Jinwei; Ma, Xirong; Zhu, Yuanping; Sun, Jizhou

    2014-01-01

    The active appearance model (AAM) is one of the most powerful model-based object detecting and tracking methods which has been widely used in various situations. However, the high-dimensional texture representation causes very time-consuming computations, which makes the AAM difficult to apply to real-time systems. The emergence of modern graphics processing units (GPUs) that feature a many-core, fine-grained parallel architecture provides new and promising solutions to overcome the computational challenge. In this paper, we propose an efficient parallel implementation of the AAM fitting algorithm on GPUs. Our design idea is fine grain parallelism in which we distribute the texture data of the AAM, in pixels, to thousands of parallel GPU threads for processing, which makes the algorithm fit better into the GPU architecture. We implement our algorithm using the compute unified device architecture (CUDA) on the Nvidia's GTX 650 GPU, which has the latest Kepler architecture. To compare the performance of our algorithm with different data sizes, we built sixteen face AAM models of different dimensional textures. The experiment results show that our parallel AAM fitting algorithm can achieve real-time performance for videos even on very high-dimensional textures.

  19. A domain decomposition parallel processing algorithm for molecular dynamics simulations of polymers

    NASA Astrophysics Data System (ADS)

    Brown, David; Clarke, Julian H. R.; Okuda, Motoi; Yamazaki, Takao

    1994-10-01

    We describe in this paper a domain decomposition molecular dynamics algorithm for use on distributed memory parallel computers which is capable of handling systems containing rigid bond constraints and three- and four-body potentials as well as non-bonded potentials. The algorithm has been successfully implemented on the Fujitsu 1024 processor element AP1000 machine. The performance has been compared with and benchmarked against the alternative cloning method of parallel processing [D. Brown, J.H.R. Clarke, M. Okuda and T. Yamazaki, J. Chem. Phys., 100 (1994) 1684] and results obtained using other scalar and vector machines. Two parallel versions of the SHAKE algorithm, which solves the bond length constraints problem, have been compared with regard to optimising the performance of this procedure.

  20. Aligning multiple protein sequences by parallel hybrid genetic algorithm.

    PubMed

    Nguyen, Hung Dinh; Yoshihara, Ikuo; Yamamori, Kunihito; Yasunaga, Moritoshi

    2002-01-01

    This paper presents a parallel hybrid genetic algorithm (GA) for solving the sum-of-pairs multiple protein sequence alignment. A new chromosome representation and its corresponding genetic operators are proposed. A multi-population GENITOR-type GA is combined with local search heuristics. It is then extended to run in parallel on a multiprocessor system for speeding up. Experimental results of benchmarks from the BAliBASE show that the proposed method is superior to MSA, OMA, and SAGA methods with regard to quality of solution and running time. It can be used for finding multiple sequence alignment as well as testing cost functions.

  1. Fault Tolerant Statistical Signal Processing Algorithms for Parallel Architectures.

    DTIC Science & Technology

    2014-09-26

    AD-fi57 393 FAULT TOLERANT STATISTICAL SIGNAL PROCESSING ALGORITHMS i/i FOR PARALLEL ARCH U) JOHNS HOPKINS UNIV BALTIMORE MD DEPT OF ELECTRICAL...COVERED * ’ Fault Tolerant Statistical Signal Processing Technical A l g o r i t h m s f o r P a r a l l e l A r c h i t e c t u r e s a ._ P E R F O R M I...Identify by block number) , Fault Tolerance, Signal Processing, Parallel Architecture 0 20. ABSTRACT (Continue on reveree side It neceseary and identify by

  2. Approximation algorithms for scheduling unrelated parallel machines with release dates

    NASA Astrophysics Data System (ADS)

    Avdeenko, T. V.; Mesentsev, Y. A.; Estraykh, I. V.

    2017-01-01

    In this paper we propose approaches to optimal scheduling of unrelated parallel machines with release dates. One approach is based on the scheme of dynamic programming modified with adaptive narrowing of search domain ensuring its computational effectiveness. We discussed complexity of the exact schedules synthesis and compared it with approximate, close to optimal, solutions. Also we explain how the algorithm works for the example of two unrelated parallel machines and five jobs with release dates. Performance results that show the efficiency of the proposed approach have been given.

  3. a Distributed Polygon Retrieval Algorithm Using Mapreduce

    NASA Astrophysics Data System (ADS)

    Guo, Q.; Palanisamy, B.; Karimi, H. A.

    2015-07-01

    The burst of large-scale spatial terrain data due to the proliferation of data acquisition devices like 3D laser scanners poses challenges to spatial data analysis and computation. Among many spatial analyses and computations, polygon retrieval is a fundamental operation which is often performed under real-time constraints. However, existing sequential algorithms fail to meet this demand for larger sizes of terrain data. Motivated by the MapReduce programming model, a well-adopted large-scale parallel data processing technique, we present a MapReduce-based polygon retrieval algorithm designed with the objective of reducing the IO and CPU loads of spatial data processing. By indexing the data based on a quad-tree approach, a significant amount of unneeded data is filtered in the filtering stage and it reduces the IO overhead. The indexed data also facilitates querying the relationship between the terrain data and query area in shorter time. The results of the experiments performed in our Hadoop cluster demonstrate that our algorithm performs significantly better than the existing distributed algorithms.

  4. CRBLASTER: A Parallel-Processing Computational Framework for Embarrassingly Parallel Image-Analysis Algorithms

    NASA Astrophysics Data System (ADS)

    Mighell, Kenneth John

    2010-10-01

    The development of parallel-processing image-analysis codes is generally a challenging task that requires complicated choreography of interprocessor communications. If, however, the image-analysis algorithm is embarrassingly parallel, then the development of a parallel-processing implementation of that algorithm can be a much easier task to accomplish because, by definition, there is little need for communication between the compute processes. I describe the design, implementation, and performance of a parallel-processing image-analysis application, called crblaster, which does cosmic-ray rejection of CCD images using the embarrassingly parallel l.a.cosmic algorithm. crblaster is written in C using the high-performance computing industry standard Message Passing Interface (MPI) library. crblaster uses a two-dimensional image partitioning algorithm that partitions an input image into N rectangular subimages of nearly equal area; the subimages include sufficient additional pixels along common image partition edges such that the need for communication between computer processes is eliminated. The code has been designed to be used by research scientists who are familiar with C as a parallel-processing computational framework that enables the easy development of parallel-processing image-analysis programs based on embarrassingly parallel algorithms. The crblaster source code is freely available at the official application Web site at the National Optical Astronomy Observatory. Removing cosmic rays from a single 800 × 800 pixel Hubble Space Telescope WFPC2 image takes 44 s with the IRAF script lacos_im.cl running on a single core of an Apple Mac Pro computer with two 2.8 GHz quad-core Intel Xeon processors. crblaster is 7.4 times faster when processing the same image on a single core on the same machine. Processing the same image with crblaster simultaneously on all eight cores of the same machine takes 0.875 s—which is a speedup factor of 50.3 times faster than the

  5. Generalization and Parallelization of Messy Genetic Algorithms and Communication in Parallel Genetic Algorithms.

    DTIC Science & Technology

    1992-12-01

    model of schema growth for solution sharing(36) is refined and extended to predict the behavior of three solution sharing strategies. Experiments...complexity. GAs are inspired by and modeled after the processes of natural selection. The most commonly implemented GAs are "simple" GAs, which use three...solution. Efficiency is the al- gorithmic complexity of the algorithm. Current theory of genetic algorithm behavior is based on the assumptions of zero

  6. An improved coarse-grained parallel algorithm for computational acceleration of ordinary Kriging interpolation

    NASA Astrophysics Data System (ADS)

    Hu, Hongda; Shu, Hong

    2015-05-01

    Heavy computation limits the use of Kriging interpolation methods in many real-time applications, especially with the ever-increasing problem size. Many researchers have realized that parallel processing techniques are critical to fully exploit computational resources and feasibly solve computation-intensive problems like Kriging. Much research has addressed the parallelization of traditional approach to Kriging, but this computation-intensive procedure may not be suitable for high-resolution interpolation of spatial data. On the basis of a more effective serial approach, we propose an improved coarse-grained parallel algorithm to accelerate ordinary Kriging interpolation. In particular, the interpolation task of each unobserved point is considered as a basic parallel unit. To reduce time complexity and memory consumption, the large right hand side matrix in the Kriging linear system is transformed and fixed at only two columns and therefore no longer directly relevant to the number of unobserved points. The MPI (Message Passing Interface) model is employed to implement our parallel programs in a homogeneous distributed memory system. Experimentally, the improved parallel algorithm performs better than the traditional one in spatial interpolation of annual average precipitation in Victoria, Australia. For example, when the number of processors is 24, the improved algorithm keeps speed-up at 20.8 while the speed-up of the traditional algorithm only reaches 9.3. Likewise, the weak scaling efficiency of the improved algorithm is nearly 90% while that of the traditional algorithm almost drops to 40% with 16 processors. Experimental results also demonstrate that the performance of the improved algorithm is enhanced by increasing the problem size.

  7. Parallel and Grid-Based Data Mining - Algorithms, Models and Systems for High-Performance KDD

    NASA Astrophysics Data System (ADS)

    Congiusta, Antonio; Talia, Domenico; Trunfio, Paolo

    Data Mining often is a computing intensive and time requiring process. For this reason, several Data Mining systems have been implemented on parallel computing platforms to achieve high performance in the analysis of large data sets. Moreover, when large data repositories are coupled with geographical distribution of data, users and systems, more sophisticated technologies are needed to implement high-performance distributed KDD systems. Since computational Grids emerged as privileged platforms for distributed computing, a growing number of Grid-based KDD systems has been proposed. In this chapter we first discuss different ways to exploit parallelism in the main Data Mining techniques and algorithms, then we discuss Grid-based KDD systems. Finally, we introduce the Knowledge Grid, an environment which makes use of standard Grid middleware to support the development of parallel and distributed knowledge discovery applications.

  8. Pathfinder: A parallel search algorithm for concerted atomistic events

    NASA Astrophysics Data System (ADS)

    Nakano, Aiichiro

    2007-02-01

    An algorithm has been designed to search for the escape paths with the lowest activation barriers when starting from a local minimum-energy configuration of a many-atom system. The pathfinder algorithm combines: (1) a steered eigenvector-following method that guides a constrained escape from the convex region and subsequently climbs to a transition state tangentially to the eigenvector corresponding to the lowest negative Hessian eigenvalue; (2) discrete abstraction of the atomic configuration to systematically enumerate concerted events as linear combinations of atomistic events; (3) evolutionary control of the population dynamics of low activation-barrier events; and (4) hybrid task + spatial decompositions to implement massive search for complex events on parallel computers. The program exhibits good scalability on parallel computers and has been used to study concerted bond-breaking events in the fracture of alumina.

  9. Parallel Algorithms for Graph Optimization using Tree Decompositions

    SciTech Connect

    Sullivan, Blair D; Weerapurage, Dinesh P; Groer, Christopher S

    2012-06-01

    Although many $\\cal{NP}$-hard graph optimization problems can be solved in polynomial time on graphs of bounded tree-width, the adoption of these techniques into mainstream scientific computation has been limited due to the high memory requirements of the necessary dynamic programming tables and excessive runtimes of sequential implementations. This work addresses both challenges by proposing a set of new parallel algorithms for all steps of a tree decomposition-based approach to solve the maximum weighted independent set problem. A hybrid OpenMP/MPI implementation includes a highly scalable parallel dynamic programming algorithm leveraging the MADNESS task-based runtime, and computational results demonstrate scaling. This work enables a significant expansion of the scale of graphs on which exact solutions to maximum weighted independent set can be obtained, and forms a framework for solving additional graph optimization problems with similar techniques.

  10. Feed-forward volume rendering algorithm for moderately parallel MIMD machines

    NASA Technical Reports Server (NTRS)

    Yagel, Roni

    1993-01-01

    Algorithms for direct volume rendering on parallel and vector processors are investigated. Volumes are transformed efficiently on parallel processors by dividing the data into slices and beams of voxels. Equal sized sets of slices along one axis are distributed to processors. Parallelism is achieved at two levels. Because each slice can be transformed independently of others, processors transform their assigned slices with no communication, thus providing maximum possible parallelism at the first level. Within each slice, consecutive beams are incrementally transformed using coherency in the transformation computation. Also, coherency across slices can be exploited to further enhance performance. This coherency yields the second level of parallelism through the use of the vector processing or pipelining. Other ongoing efforts include investigations into image reconstruction techniques, load balancing strategies, and improving performance.

  11. High Performance Parallel Algorithms for Improved Reduced-Order Modeling

    DTIC Science & Technology

    2008-05-04

    HIGH PERFORMANCE PARALLEL ALGORITHMS FOR IMPROVED REDUCED-ORDER MODELING AFOSR FA9550-05-1-0449 FINAL REPORT Chris Beattie, Jeff Borggaard, Serkan ... Serkan Gugercin and Traian Iliescu (co-PIs) Post-Docs Andrew Duggelby, Alexander Hay and Sonja Schlaugh Students Weston Hunter, Denis Kovacs, Miroslav...internship to discuss his research. [Contacts: Chris Camphouse (937) 255-6326, James Myatt (937) 255-8498] Synergistic Activities 1. Serkan Gugerin, with

  12. A hybrid algorithm for parallel molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Mangiardi, Chris M.; Meyer, R.

    2017-10-01

    This article describes algorithms for the hybrid parallelization and SIMD vectorization of molecular dynamics simulations with short-range forces. The parallelization method combines domain decomposition with a thread-based parallelization approach. The goal of the work is to enable efficient simulations of very large (tens of millions of atoms) and inhomogeneous systems on many-core processors with hundreds or thousands of cores and SIMD units with large vector sizes. In order to test the efficiency of the method, simulations of a variety of configurations with up to 74 million atoms have been performed. Results are shown that were obtained on multi-core systems with Sandy Bridge and Haswell processors as well as systems with Xeon Phi many-core processors.

  13. HPC-NMF: A High-Performance Parallel Algorithm for Nonnegative Matrix Factorization

    SciTech Connect

    Kannan, Ramakrishnan; Sukumar, Sreenivas R.; Ballard, Grey M.; Park, Haesun

    2016-08-22

    NMF is a useful tool for many applications in different domains such as topic modeling in text mining, background separation in video analysis, and community detection in social networks. Despite its popularity in the data mining community, there is a lack of efficient distributed algorithms to solve the problem for big data sets. We propose a high-performance distributed-memory parallel algorithm that computes the factorization by iteratively solving alternating non-negative least squares (NLS) subproblems for $\\WW$ and $\\HH$. It maintains the data and factor matrices in memory (distributed across processors), uses MPI for interprocessor communication, and, in the dense case, provably minimizes communication costs (under mild assumptions). As opposed to previous implementation, our algorithm is also flexible: It performs well for both dense and sparse matrices, and allows the user to choose any one of the multiple algorithms for solving the updates to low rank factors $\\WW$ and $\\HH$ within the alternating iterations.

  14. A parallel algorithm for the eigenvalues and eigenvectors for a general complex matrix

    NASA Technical Reports Server (NTRS)

    Shroff, Gautam

    1989-01-01

    A new parallel Jacobi-like algorithm is developed for computing the eigenvalues of a general complex matrix. Most parallel methods for this parallel typically display only linear convergence. Sequential norm-reducing algorithms also exit and they display quadratic convergence in most cases. The new algorithm is a parallel form of the norm-reducing algorithm due to Eberlein. It is proven that the asymptotic convergence rate of this algorithm is quadratic. Numerical experiments are presented which demonstrate the quadratic convergence of the algorithm and certain situations where the convergence is slow are also identified. The algorithm promises to be very competitive on a variety of parallel architectures.

  15. Superelement model based parallel algorithm for vehicle dynamics

    NASA Astrophysics Data System (ADS)

    Agrawal, O. P.; Danhof, K. J.; Kumar, R.

    1994-05-01

    This paper presents a superelement model based parallel algorithm for a planar vehicle dynamics. The vehicle model is made up of a chassis and two suspension systems each of which consists of an axle-wheel assembly and two trailing arms. In this model, the chassis is treated as a Cartesian element and each suspension system is treated as a superelement. The parameters associated with the superelements are computed using an inverse dynamics technique. Suspension shock absorbers and the tires are modeled by nonlinear springs and dampers. The Euler-Lagrange approach is used to develop the system equations of motion. This leads to a system of differential and algebraic equations in which the constraints internal to superelements appear only explicitly. The above formulation is implemented on a multiprocessor machine. The numerical flow chart is divided into modules and the computation of several modules is performed in parallel to gain computational efficiency. In this implementation, the master (parent processor) creates a pool of slaves (child processors) at the beginning of the program. The slaves remain in the pool until they are needed to perform certain tasks. Upon completion of a particular task, a slave returns to the pool. This improves the overall response time of the algorithm. The formulation presented is general which makes it attractive for a general purpose code development. Speedups obtained in the different modules of the dynamic analysis computation are also presented. Results show that the superelement model based parallel algorithm can significantly reduce the vehicle dynamics simulation time.

  16. NETRA: A parallel architecture for integrated vision systems 2: Algorithms and performance evaluation

    NASA Technical Reports Server (NTRS)

    Choudhary, Alok N.; Patel, Janak H.; Ahuja, Narendra

    1989-01-01

    In part 1 architecture of NETRA is presented. A performance evaluation of NETRA using several common vision algorithms is also presented. Performance of algorithms when they are mapped on one cluster is described. It is shown that SIMD, MIMD, and systolic algorithms can be easily mapped onto processor clusters, and almost linear speedups are possible. For some algorithms, analytical performance results are compared with implementation performance results. It is observed that the analysis is very accurate. Performance analysis of parallel algorithms when mapped across clusters is presented. Mappings across clusters illustrate the importance and use of shared as well as distributed memory in achieving high performance. The parameters for evaluation are derived from the characteristics of the parallel algorithms, and these parameters are used to evaluate the alternative communication strategies in NETRA. Furthermore, the effect of communication interference from other processors in the system on the execution of an algorithm is studied. Using the analysis, performance of many algorithms with different characteristics is presented. It is observed that if communication speeds are matched with the computation speeds, good speedups are possible when algorithms are mapped across clusters.

  17. Load Balancing and Data Locality in the Parallelization of the Fast Multipole Algorithm

    NASA Astrophysics Data System (ADS)

    Banicescu, Ioana

    Scientific problems are often irregular, large and computationally intensive. Efficient parallel implementations of algorithms that are employed in finding solutions to these problems play an important role in the development of science. This thesis studies the parallelization of a certain class of irregular scientific problems, the N -body problem, using a classical hierarchical algorithm: the Fast Multipole Algorithm (FMA). Hierarchical N-body algorithms in general, and the FMA in particular, are amenable to parallel execution. However, performance gains are difficult to obtain, due to load imbalances that are primarily caused by the irregular distribution of bodies and of computation domains. Understanding application characteristics is essential for obtaining high performance implementations on parallel machines. After surveying the available parallelism in the FMA, we address the problem of exploiting this parallelism with partitioning and scheduling techniques that optimally map it onto a parallel machine, the KSR1. The KSR1 is a parallel shared address-space machine with a hierarchical cache-only architecture. The tension between maintaining data locality and balancing processor loads requires a scheduling scheme that combines static techniques (that exploit data locality) with dynamic techniques (that improve load balancing). An effective combined scheduling scheme that balances processor loads and maintains locality, by exploiting self-similarity properties of fractals, is Fractiling. Fractiling is based on a probabilistic analysis. It thus accommodates load imbalances caused by predictable events (such as irregular data) as well as unpredictable events (such as data access latency). Fractiling adapts to algorithmic and system induced load imbalances while maximizing data locality. We used Fractiling to schedule a parallel FMA on the KSR1. Our parallel 2-d and 3-d FMA implementations were run using uniform and nonuniform data set distributions under a

  18. ParaKMeans: Implementation of a parallelized K-means algorithm suitable for general laboratory use.

    PubMed

    Kraj, Piotr; Sharma, Ashok; Garge, Nikhil; Podolsky, Robert; McIndoe, Richard A

    2008-04-16

    During the last decade, the use of microarrays to assess the transcriptome of many biological systems has generated an enormous amount of data. A common technique used to organize and analyze microarray data is to perform cluster analysis. While many clustering algorithms have been developed, they all suffer a significant decrease in computational performance as the size of the dataset being analyzed becomes very large. For example, clustering 10000 genes from an experiment containing 200 microarrays can be quite time consuming and challenging on a desktop PC. One solution to the scalability problem of clustering algorithms is to distribute or parallelize the algorithm across multiple computers. The software described in this paper is a high performance multithreaded application that implements a parallelized version of the K-means Clustering algorithm. Most parallel processing applications are not accessible to the general public and require specialized software libraries (e.g. MPI) and specialized hardware configurations. The parallel nature of the application comes from the use of a web service to perform the distance calculations and cluster assignments. Here we show our parallel implementation provides significant performance gains over a wide range of datasets using as little as seven nodes. The software was written in C# and was designed in a modular fashion to provide both deployment flexibility as well as flexibility in the user interface. ParaKMeans was designed to provide the general scientific community with an easy and manageable client-server application that can be installed on a wide variety of Windows operating systems.

  19. A parallel genetic algorithm for the set partitioning problem

    SciTech Connect

    Levine, D.

    1996-12-31

    This paper describes a parallel genetic algorithm developed for the solution of the set partitioning problem- a difficult combinatorial optimization problem used by many airlines as a mathematical model for flight crew scheduling. The genetic algorithm is based on an island model where multiple independent subpopulations each run a steady-state genetic algorithm on their own subpopulation and occasionally fit strings migrate between the subpopulations. Tests on forty real-world set partitioning problems were carried out on up to 128 nodes of an IBM SP1 parallel computer. We found that performance, as measured by the quality of the solution found and the iteration on which it was found, improved as additional subpopulations were added to the computation. With larger numbers of subpopulations the genetic algorithm was regularly able to find the optimal solution to problems having up to a few thousand integer variables. In two cases, high- quality integer feasible solutions were found for problems with 36, 699 and 43,749 integer variables, respectively. A notable limitation we found was the difficulty solving problems with many constraints.

  20. A novel highly parallel algorithm for linearly unmixing hyperspectral images

    NASA Astrophysics Data System (ADS)

    Guerra, Raúl; López, Sebastián.; Callico, Gustavo M.; López, Jose F.; Sarmiento, Roberto

    2014-10-01

    Endmember extraction and abundances calculation represent critical steps within the process of linearly unmixing a given hyperspectral image because of two main reasons. The first one is due to the need of computing a set of accurate endmembers in order to further obtain confident abundance maps. The second one refers to the huge amount of operations involved in these time-consuming processes. This work proposes an algorithm to estimate the endmembers of a hyperspectral image under analysis and its abundances at the same time. The main advantage of this algorithm is its high parallelization degree and the mathematical simplicity of the operations implemented. This algorithm estimates the endmembers as virtual pixels. In particular, the proposed algorithm performs the descent gradient method to iteratively refine the endmembers and the abundances, reducing the mean square error, according with the linear unmixing model. Some mathematical restrictions must be added so the method converges in a unique and realistic solution. According with the algorithm nature, these restrictions can be easily implemented. The results obtained with synthetic images demonstrate the well behavior of the algorithm proposed. Moreover, the results obtained with the well-known Cuprite dataset also corroborate the benefits of our proposal.

  1. Potts-model grain growth simulations: Parallel algorithms and applications

    SciTech Connect

    Wright, S.A.; Plimpton, S.J.; Swiler, T.P.

    1997-08-01

    Microstructural morphology and grain boundary properties often control the service properties of engineered materials. This report uses the Potts-model to simulate the development of microstructures in realistic materials. Three areas of microstructural morphology simulations were studied. They include the development of massively parallel algorithms for Potts-model grain grow simulations, modeling of mass transport via diffusion in these simulated microstructures, and the development of a gradient-dependent Hamiltonian to simulate columnar grain growth. Potts grain growth models for massively parallel supercomputers were developed for the conventional Potts-model in both two and three dimensions. Simulations using these parallel codes showed self similar grain growth and no finite size effects for previously unapproachable large scale problems. In addition, new enhancements to the conventional Metropolis algorithm used in the Potts-model were developed to accelerate the calculations. These techniques enable both the sequential and parallel algorithms to run faster and use essentially an infinite number of grain orientation values to avoid non-physical grain coalescence events. Mass transport phenomena in polycrystalline materials were studied in two dimensions using numerical diffusion techniques on microstructures generated using the Potts-model. The results of the mass transport modeling showed excellent quantitative agreement with one dimensional diffusion problems, however the results also suggest that transient multi-dimension diffusion effects cannot be parameterized as the product of the grain boundary diffusion coefficient and the grain boundary width. Instead, both properties are required. Gradient-dependent grain growth mechanisms were included in the Potts-model by adding an extra term to the Hamiltonian. Under normal grain growth, the primary driving term is the curvature of the grain boundary, which is included in the standard Potts-model Hamiltonian.

  2. Space complexity of estimation of distribution algorithms.

    PubMed

    Gao, Yong; Culberson, Joseph

    2005-01-01

    In this paper, we investigate the space complexity of the Estimation of Distribution Algorithms (EDAs), a class of sampling-based variants of the genetic algorithm. By analyzing the nature of EDAs, we identify criteria that characterize the space complexity of two typical implementation schemes of EDAs, the factorized distribution algorithm and Bayesian network-based algorithms. Using random additive functions as the prototype, we prove that the space complexity of the factorized distribution algorithm and Bayesian network-based algorithms is exponential in the problem size even if the optimization problem has a very sparse interaction structure.

  3. Parallel Newton-Krylov-Schwarz algorithms for the transonic full potential equation

    NASA Technical Reports Server (NTRS)

    Cai, Xiao-Chuan; Gropp, William D.; Keyes, David E.; Melvin, Robin G.; Young, David P.

    1996-01-01

    We study parallel two-level overlapping Schwarz algorithms for solving nonlinear finite element problems, in particular, for the full potential equation of aerodynamics discretized in two dimensions with bilinear elements. The overall algorithm, Newton-Krylov-Schwarz (NKS), employs an inexact finite-difference Newton method and a Krylov space iterative method, with a two-level overlapping Schwarz method as a preconditioner. We demonstrate that NKS, combined with a density upwinding continuation strategy for problems with weak shocks, is robust and, economical for this class of mixed elliptic-hyperbolic nonlinear partial differential equations, with proper specification of several parameters. We study upwinding parameters, inner convergence tolerance, coarse grid density, subdomain overlap, and the level of fill-in in the incomplete factorization, and report their effect on numerical convergence rate, overall execution time, and parallel efficiency on a distributed-memory parallel computer.

  4. MM Algorithms for Some Discrete Multivariate Distributions.

    PubMed

    Zhou, Hua; Lange, Kenneth

    2010-09-01

    The MM (minorization-maximization) principle is a versatile tool for constructing optimization algorithms. Every EM algorithm is an MM algorithm but not vice versa. This article derives MM algorithms for maximum likelihood estimation with discrete multivariate distributions such as the Dirichlet-multinomial and Connor-Mosimann distributions, the Neerchal-Morel distribution, the negative-multinomial distribution, certain distributions on partitions, and zero-truncated and zero-inflated distributions. These MM algorithms increase the likelihood at each iteration and reliably converge to the maximum from well-chosen initial values. Because they involve no matrix inversion, the algorithms are especially pertinent to high-dimensional problems. To illustrate the performance of the MM algorithms, we compare them to Newton's method on data used to classify handwritten digits.

  5. Parallel hybrid algorithm for solution in electrical impedance equation

    NASA Astrophysics Data System (ADS)

    Ponomaryov, Volodymyr; Robles-Gonzalez, Marco; Bucio-Ramirez, Ariana; Ramirez-Tachiquin, Marco; Ramos-Diaz, Eduardo

    2015-02-01

    This work is dedicated to the analysis of the forward and the inverse problem to obtain a better approximation to the Electrical Impedance Tomography equation. In this case, we employ for the forward problem the numerical method based on the Taylor series in formal power and for the inverse problem the Finite Element Method. For the analysis of the forward problem, we proposed a novel algorithm, which employs a regularization technique for the stability, additionally the parallel computing is used to obtain the solution faster; this modification permits to obtain an efficient solution of the forward problem. Then, the found solution is used in the inverse problem for the approximation employing the Finite Element Method. The algorithms employed in this work are developed in structural programming paradigm in C++, including parallel processing; the time run analysis is performed only in the forward problem because the Finite Element Method due to their high recursive does not accept parallelism. Some examples are performed for this analysis, in which several conductivity functions are employed for two different cases: for the analytical cases: the exponential and sinusoidal functions are used, and for the geometrical cases the circle at center and five disk structure are revised as conductivity functions. The Lebesgue measure is used as metric for error estimation in the forward problem, meanwhile, in the inverse problem PSNR, SSIM, MSE criteria are applied, to determine the convergence of both methods.

  6. Serial Order: A Parallel Distributed Processing Approach.

    ERIC Educational Resources Information Center

    Jordan, Michael I.

    Human behavior shows a variety of serially ordered action sequences. This paper presents a theory of serial order which describes how sequences of actions might be learned and performed. In this theory, parallel interactions across time (coarticulation) and parallel interactions across space (dual-task interference) are viewed as two aspects of a…

  7. Enhanced animation of parallel algorithms. Volume 1. Master's thesis

    SciTech Connect

    Lack, M.D.

    1991-12-01

    Algorithm animation is a visualization method used to enhance understanding of the functioning of an algorithm or program. Visualization is used for many purposes, including education, algorithm research, performance analysis, and program debugging. This research, which follows from previous work, examines algorithm animation requirements for the various visualization purposes and extends the capabilities of an existing facility, the AFIT Algorithm Animation Research Facility (AAARF). The structure of AAARF is summarised and its visualization capabilities presented, analysed and compared with other similar packages. This research focuses on the parallel data requirements of the AAARF users, and the meaningful display of large amounts of data. This paper discusses a series of refined animations suitable for a variety of purposes which are capable of conveying detailed information in a concise and timely manner and the development and implementation of a new performance animation type is presented. These animations are built upon pedagogical efforts in a classroom environment. To assist novice users in efficiently using AAARF, an expert system interface has been implemented to advise on optimizing environment configuration. Considerable effort has been devoted to porting AAARF to the X Windows environment and the lessons learned and progress made are discussed.

  8. Parallel computer graphics algorithms for the Connection Machine

    SciTech Connect

    Richardson, J.F.

    1990-01-01

    Many of the classes of computer graphics algorithms and polygon storage schemes can be adapted for parallel execution on various parallel architectures. The connection machine is one such architecture that should be thought of as a multiprocessor grid that can be reconfigured into standard 2-dimensional mesh and n-dimensional hypercube architectures. The classes of algorithms considered in this paper are SPLINES; POLYGON STORAGE; TRIANGULARIZATION; and SYMBOLIC INPUT. The target Connection Machine (hearafter designated as CM) for the algorithms of this paper has 8192 physical processors. Each physical processor has 8 kilobytes of local memory plus an arithmetic-logic unit. All processors can communicate with any other processor through a router. Thus this CM has a shared memory of 64 megabytes when used as a standard multiprocessor (MIMD) architecture. In addition, the CM interconnection structure can simulate a 2-dimensional mesh and n-dimensional hypercube (SIMD) architecture with the mesh being the default architecture. The front end for the CM is a Symbolics and the high level language is LISP or FORTRAN.

  9. BMI optimization by using parallel UNDX real-coded genetic algorithm with Beowulf cluster

    NASA Astrophysics Data System (ADS)

    Handa, Masaya; Kawanishi, Michihiro; Kanki, Hiroshi

    2007-12-01

    This paper deals with the global optimization algorithm of the Bilinear Matrix Inequalities (BMIs) based on the Unimodal Normal Distribution Crossover (UNDX) GA. First, analyzing the structure of the BMIs, the existence of the typical difficult structures is confirmed. Then, in order to improve the performance of algorithm, based on results of the problem structures analysis and consideration of BMIs characteristic properties, we proposed the algorithm using primary search direction with relaxed Linear Matrix Inequality (LMI) convex estimation. Moreover, in these algorithms, we propose two types of evaluation methods for GA individuals based on LMI calculation considering BMI characteristic properties more. In addition, in order to reduce computational time, we proposed parallelization of RCGA algorithm, Master-Worker paradigm with cluster computing technique.

  10. Distributed and parallel Ada and the Ada 9X recommendations

    NASA Technical Reports Server (NTRS)

    Volz, Richard A.; Goldsack, Stephen J.; Theriault, R.; Waldrop, Raymond S.; Holzbacher-Valero, A. A.

    1992-01-01

    Recently, the DoD has sponsored work towards a new version of Ada, intended to support the construction of distributed systems. The revised version, often called Ada 9X, will become the new standard sometimes in the 1990s. It is intended that Ada 9X should provide language features giving limited support for distributed system construction. The requirements for such features are given. Many of the most advanced computer applications involve embedded systems that are comprised of parallel processors or networks of distributed computers. If Ada is to become the widely adopted language envisioned by many, it is essential that suitable compilers and tools be available to facilitate the creation of distributed and parallel Ada programs for these applications. The major languages issues impacting distributed and parallel programming are reviewed, and some principles upon which distributed/parallel language systems should be built are suggested. Based upon these, alternative language concepts for distributed/parallel programming are analyzed.

  11. Distributed and parallel Ada and the Ada 9X recommendations

    SciTech Connect

    Volz, R.A.; Goldsack, S.J.; Theriault, R.; Waldrop, R.S.; Holzbacher-Valero, A.A.

    1992-04-01

    Recently, the DoD has sponsored work towards a new version of Ada, intended to support the construction of distributed systems. The revised version, often called Ada9x, will become the new standard sometimes in the 1990s. It is intended that Ada9x should provide language features giving limited support for distributed system construction. The requirements for such features are given. Many of the most advanced computer applications involve embedded systems that are comprised of parallel processors or networks of distributed computers. If Ada is to become the widely adopted language envisioned by many, it is essential that suitable compilers and tools be available to facilitate the creation of distributed and parallel Ada programs for these applications. The major languages issues impacting distributed and parallel programming are reviewed, and some principles upon which distributed/parallel language systems should be built are suggested. Based upon these, alternative language concepts for distributed/parallel programming are analyzed.

  12. Parallel Algorithms for Computational Models of Geophysical Systems

    NASA Astrophysics Data System (ADS)

    Carrillo Ledesma, A.; Herrera, I.; de la Cruz, L. M.; Hernández, G.; Grupo de Modelacion Matematica y Computacional

    2013-05-01

    Mathematical models of many systems of interest, including very important continuous systems of Earth Sciences and Engineering, lead to a great variety of partial differential equations (PDEs) whose solution methods are based on the computational processing of large-scale algebraic systems. Furthermore, the incredible expansion experienced by the existing computational hardware and software has made amenable to effective treatment problems of an ever increasing diversity and complexity, posed by scientific and engineering applications. Parallel computing is outstanding among the new computational tools and, in order to effectively use the most advanced computers available today, massively parallel software is required. Domain decomposition methods (DDMs) have been developed precisely for effectively treating PDEs in paralle. Ideally, the main objective of domain decomposition research is to produce algorithms capable of 'obtaining the global solution by exclusively solving local problems', but up-to-now this has only been an aspiration; that is, a strong desire for achieving such a property and so we call it 'the DDM-paradigm'. In recent times, numerically competitive DDM-algorithms are non-overlapping, preconditioned and necessarily incorporate constraints which pose an additional challenge for achieving the DDM-paradigm. Recently a group of four algorithms, referred to as the 'DVS-algorithms', which fulfill the DDM-paradigm, was developed. To derive them a new discretization method, which uses a non-overlapping system of nodes (the derived-nodes), was introduced. This discretization procedure can be applied to any boundary-value problem, or system of such equations. In turn, the resulting system of discrete equations can be treated using any available DDM-algorithm. In particular, two of the four DVS-algorithms mentioned above were obtained by application of the well-known and very effective algorithms BDDC and FETI-DP; these will be referred to as the DVS

  13. Automatic Management of Parallel and Distributed System Resources

    NASA Technical Reports Server (NTRS)

    Yan, Jerry; Ngai, Tin Fook; Lundstrom, Stephen F.

    1990-01-01

    Viewgraphs on automatic management of parallel and distributed system resources are presented. Topics covered include: parallel applications; intelligent management of multiprocessing systems; performance evaluation of parallel architecture; dynamic concurrent programs; compiler-directed system approach; lattice gaseous cellular automata; and sparse matrix Cholesky factorization.

  14. A Simple Physical Optics Algorithm Perfect for Parallel Computing

    NASA Technical Reports Server (NTRS)

    Imbriale, W. A.; Cwik, T.

    1993-01-01

    One of the simplest reflector antenna computer programs is based upon a discrete approximation of the radiation integral. This calculation replaces the actual reflector surface with a triangular facet representation so that the reflector resembles a geodesic dome. The Physical Optics (PO) current is assumed to be constant in magnitude and phase over each facet so the radiation integral is reduced to a simple summation. This program has proven to be surprisingly robust and useful for the analysis of arbitrary reflectors, particularly when the near-field is desired and surface derivatives are not known. Because of its simplicity, the algorithm has proven to be extremely easy to adapt to the parallel computing architecture of a modest number of large-grain computing elements such as are used in the Intel iPSC and Touchstone Delta parallel machines.

  15. A parallel algorithm for solving the 3d Schroedinger equation

    SciTech Connect

    Strickland, Michael; Yager-Elorriaga, David

    2010-08-20

    We describe a parallel algorithm for solving the time-independent 3d Schroedinger equation using the finite difference time domain (FDTD) method. We introduce an optimized parallelization scheme that reduces communication overhead between computational nodes. We demonstrate that the compute time, t, scales inversely with the number of computational nodes as t {proportional_to} (N{sub nodes}){sup -0.95} {sup {+-} 0.04}. This makes it possible to solve the 3d Schroedinger equation on extremely large spatial lattices using a small computing cluster. In addition, we present a new method for precisely determining the energy eigenvalues and wavefunctions of quantum states based on a symmetry constraint on the FDTD initial condition. Finally, we discuss the usage of multi-resolution techniques in order to speed up convergence on extremely large lattices.

  16. Adaptive Mesh Refinement Algorithms for Parallel Unstructured Finite Element Codes

    SciTech Connect

    Parsons, I D; Solberg, J M

    2006-02-03

    This project produced algorithms for and software implementations of adaptive mesh refinement (AMR) methods for solving practical solid and thermal mechanics problems on multiprocessor parallel computers using unstructured finite element meshes. The overall goal is to provide computational solutions that are accurate to some prescribed tolerance, and adaptivity is the correct path toward this goal. These new tools will enable analysts to conduct more reliable simulations at reduced cost, both in terms of analyst and computer time. Previous academic research in the field of adaptive mesh refinement has produced a voluminous literature focused on error estimators and demonstration problems; relatively little progress has been made on producing efficient implementations suitable for large-scale problem solving on state-of-the-art computer systems. Research issues that were considered include: effective error estimators for nonlinear structural mechanics; local meshing at irregular geometric boundaries; and constructing efficient software for parallel computing environments.

  17. A Simple Physical Optics Algorithm Perfect for Parallel Computing

    NASA Technical Reports Server (NTRS)

    Imbriale, W. A.; Cwik, T.

    1993-01-01

    One of the simplest reflector antenna computer programs is based upon a discrete approximation of the radiation integral. This calculation replaces the actual reflector surface with a triangular facet representation so that the reflector resembles a geodesic dome. The Physical Optics (PO) current is assumed to be constant in magnitude and phase over each facet so the radiation integral is reduced to a simple summation. This program has proven to be surprisingly robust and useful for the analysis of arbitrary reflectors, particularly when the near-field is desired and surface derivatives are not known. Because of its simplicity, the algorithm has proven to be extremely easy to adapt to the parallel computing architecture of a modest number of large-grain computing elements such as are used in the Intel iPSC and Touchstone Delta parallel machines.

  18. Parallelization of an Adaptive Multigrid Algorithm for Fast Solution of Finite Element Structural Problems

    SciTech Connect

    Crane, N K; Parsons, I D; Hjelmstad, K D

    2002-03-21

    Adaptive mesh refinement selectively subdivides the elements of a coarse user supplied mesh to produce a fine mesh with reduced discretization error. Effective use of adaptive mesh refinement coupled with an a posteriori error estimator can produce a mesh that solves a problem to a given discretization error using far fewer elements than uniform refinement. A geometric multigrid solver uses increasingly finer discretizations of the same geometry to produce a very fast and numerically scalable solution to a set of linear equations. Adaptive mesh refinement is a natural method for creating the different meshes required by the multigrid solver. This paper describes the implementation of a scalable adaptive multigrid method on a distributed memory parallel computer. Results are presented that demonstrate the parallel performance of the methodology by solving a linear elastic rocket fuel deformation problem on an SGI Origin 3000. Two challenges must be met when implementing adaptive multigrid algorithms on massively parallel computing platforms. First, although the fine mesh for which the solution is desired may be large and scaled to the number of processors, the multigrid algorithm must also operate on much smaller fixed-size data sets on the coarse levels. Second, the mesh must be repartitioned as it is adapted to maintain good load balancing. In an adaptive multigrid algorithm, separate mesh levels may require separate partitioning, further complicating the load balance problem. This paper shows that, when the proper optimizations are made, parallel adaptive multigrid algorithms perform well on machines with several hundreds of processors.

  19. Parallel supercomputing: Advanced methods, algorithms, and software for large-scale linear and nonlinear problems

    SciTech Connect

    Carey, G.F.; Young, D.M.

    1993-12-31

    The program outlined here is directed to research on methods, algorithms, and software for distributed parallel supercomputers. Of particular interest are finite element methods and finite difference methods together with sparse iterative solution schemes for scientific and engineering computations of very large-scale systems. Both linear and nonlinear problems will be investigated. In the nonlinear case, applications with bifurcation to multiple solutions will be considered using continuation strategies. The parallelizable numerical methods of particular interest are a family of partitioning schemes embracing domain decomposition, element-by-element strategies, and multi-level techniques. The methods will be further developed incorporating parallel iterative solution algorithms with associated preconditioners in parallel computer software. The schemes will be implemented on distributed memory parallel architectures such as the CRAY MPP, Intel Paragon, the NCUBE3, and the Connection Machine. We will also consider other new architectures such as the Kendall-Square (KSQ) and proposed machines such as the TERA. The applications will focus on large-scale three-dimensional nonlinear flow and reservoir problems with strong convective transport contributions. These are legitimate grand challenge class computational fluid dynamics (CFD) problems of significant practical interest to DOE. The methods developed and algorithms will, however, be of wider interest.

  20. Algorithms for parallel flow solvers on message passing architectures

    NASA Technical Reports Server (NTRS)

    Vanderwijngaart, Rob F.

    1995-01-01

    The purpose of this project has been to identify and test suitable technologies for implementation of fluid flow solvers -- possibly coupled with structures and heat equation solvers -- on MIMD parallel computers. In the course of this investigation much attention has been paid to efficient domain decomposition strategies for ADI-type algorithms. Multi-partitioning derives its efficiency from the assignment of several blocks of grid points to each processor in the parallel computer. A coarse-grain parallelism is obtained, and a near-perfect load balance results. In uni-partitioning every processor receives responsibility for exactly one block of grid points instead of several. This necessitates fine-grain pipelined program execution in order to obtain a reasonable load balance. Although fine-grain parallelism is less desirable on many systems, especially high-latency networks of workstations, uni-partition methods are still in wide use in production codes for flow problems. Consequently, it remains important to achieve good efficiency with this technique that has essentially been superseded by multi-partitioning for parallel ADI-type algorithms. Another reason for the concentration on improving the performance of pipeline methods is their applicability in other types of flow solver kernels with stronger implied data dependence. Analytical expressions can be derived for the size of the dynamic load imbalance incurred in traditional pipelines. From these it can be determined what is the optimal first-processor retardation that leads to the shortest total completion time for the pipeline process. Theoretical predictions of pipeline performance with and without optimization match experimental observations on the iPSC/860 very well. Analysis of pipeline performance also highlights the effect of uncareful grid partitioning in flow solvers that employ pipeline algorithms. If grid blocks at boundaries are not at least as large in the wall-normal direction as those

  1. Parallel algorithms for finding cliques in a graph

    NASA Astrophysics Data System (ADS)

    Szabó, S.

    2011-01-01

    A clique is a subgraph in a graph that is complete in the sense that each two of its nodes are connected by an edge. Finding cliques in a given graph is an important procedure in discrete mathematical modeling. The paper will show how concepts such as splitting partitions, quasi coloring, node and edge dominance are related to clique search problems. In particular we will discuss the connection with parallel clique search algorithms. These concepts also suggest practical guide lines to inspect a given graph before starting a large scale search.

  2. An experimental APL compiler for a distributed memory parallel machine

    SciTech Connect

    Ching, W.M.; Katz, A.

    1994-12-31

    The authors developed an experimental APL compiler for the IBM SP1 distributed memory parallel machine. It accepts classical APL programs, without additional directives, and generates parallelized C code for execution on the SP1 machine. The compiler exploits data parallelism in APL programs based on parallel high level primitives. Program variables are either replicated or partitioned. They also present performance data for five moderate size programs running on the SP1.

  3. Parallel simulations of Grover's algorithm for closest match search in neutron monitor data

    NASA Astrophysics Data System (ADS)

    Kussainov, Arman; White, Yelena

    We are studying the parallel implementations of Grover's closest match search algorithm for neutron monitor data analysis. This includes data formatting, and matching quantum parameters to a conventional structure of a chosen programming language and selected experimental data type. We have employed several workload distribution models based on acquired data and search parameters. As a result of these simulations, we have an understanding of potential problems that may arise during configuration of real quantum computational devices and the way they could run tasks in parallel. The work was supported by the Science Committee of the Ministry of Science and Education of the Republic of Kazakhstan Grant #2532/GF3.

  4. Efficient parallel algorithms for string editing and related problems

    NASA Technical Reports Server (NTRS)

    Apostolico, Alberto; Atallah, Mikhail J.; Larmore, Lawrence; Mcfaddin, H. S.

    1988-01-01

    The string editing problem for input strings x and y consists of transforming x into y by performing a series of weighted edit operations on x of overall minimum cost. An edit operation on x can be the deletion of a symbol from x, the insertion of a symbol in x or the substitution of a symbol x with another symbol. This problem has a well known O((absolute value of x)(absolute value of y)) time sequential solution (25). The efficient Program Requirements Analysis Methods (PRAM) parallel algorithms for the string editing problem are given. If m = ((absolute value of x),(absolute value of y)) and n = max((absolute value of x),(absolute value of y)), then the CREW bound is O (log m log n) time with O (mn/log m) processors. In all algorithms, space is O (mn).

  5. Embedded diagonally implicit Runge-Kutta algorithms on parallel computers

    NASA Astrophysics Data System (ADS)

    van der Houwen, P. J.; Sommeijer, B. P.; Couzy, W.

    1992-01-01

    This paper investigates diagonally implicit Runge-Kutta methods in which the implicit relations can be solved in parallel and are singly diagonal-implicit on each processor. The algorithms are based on diagonally implicit iteration of fully implicit Runge-Kutta methods of high order. The iteration scheme is chosen in such a way that the resulting algorithm is A(α ) -stable or L(α ) -stable with α equal or very close to π /2 . In this way, highly stable, singly diagonal-implicit Runge-Kutta methods of orders up to 10 can be constructed. Because of the iterative nature of the methods, embedded formulas of lower orders are automatically available, allowing a strategy for step and order variation.

  6. An intrinsic algorithm for parallel Poisson disk sampling on arbitrary surfaces.

    PubMed

    Ying, Xiang; Xin, Shi-Qing; Sun, Qian; He, Ying

    2013-09-01

    Poisson disk sampling has excellent spatial and spectral properties, and plays an important role in a variety of visual computing. Although many promising algorithms have been proposed for multidimensional sampling in euclidean space, very few studies have been reported with regard to the problem of generating Poisson disks on surfaces due to the complicated nature of the surface. This paper presents an intrinsic algorithm for parallel Poisson disk sampling on arbitrary surfaces. In sharp contrast to the conventional parallel approaches, our method neither partitions the given surface into small patches nor uses any spatial data structure to maintain the voids in the sampling domain. Instead, our approach assigns each sample candidate a random and unique priority that is unbiased with regard to the distribution. Hence, multiple threads can process the candidates simultaneously and resolve conflicts by checking the given priority values. Our algorithm guarantees that the generated Poisson disks are uniformly and randomly distributed without bias. It is worth noting that our method is intrinsic and independent of the embedding space. This intrinsic feature allows us to generate Poisson disk patterns on arbitrary surfaces in IR(n). To our knowledge, this is the first intrinsic, parallel, and accurate algorithm for surface Poisson disk sampling. Furthermore, by manipulating the spatially varying density function, we can obtain adaptive sampling easily.

  7. Parallel pipeline algorithm of real time star map preprocessing

    NASA Astrophysics Data System (ADS)

    Wang, Hai-yong; Qin, Tian-mu; Liu, Jia-qi; Li, Zhi-feng; Li, Jian-hua

    2016-03-01

    To improve the preprocessing speed of star map and reduce the resource consumption of embedded system of star tracker, a parallel pipeline real-time preprocessing algorithm is presented. The two characteristics, the mean and the noise standard deviation of the background gray of a star map, are firstly obtained dynamically by the means that the intervene of the star image itself to the background is removed in advance. The criterion on whether or not the following noise filtering is needed is established, then the extraction threshold value is assigned according to the level of background noise, so that the centroiding accuracy is guaranteed. In the processing algorithm, as low as two lines of pixel data are buffered, and only 100 shift registers are used to record the connected domain label, by which the problems of resources wasting and connected domain overflow are solved. The simulating results show that the necessary data of the selected bright stars could be immediately accessed in a delay time as short as 10us after the pipeline processing of a 496×496 star map in 50Mb/s is finished, and the needed memory and registers resource total less than 80kb. To verify the accuracy performance of the algorithm proposed, different levels of background noise are added to the processed ideal star map, and the statistic centroiding error is smaller than 1/23 pixel under the condition that the signal to noise ratio is greater than 1. The parallel pipeline algorithm of real time star map preprocessing helps to increase the data output speed and the anti-dynamic performance of star tracker.

  8. A Parallel Genetic Algorithm for Automated Electronic Circuit Design

    NASA Technical Reports Server (NTRS)

    Long, Jason D.; Colombano, Silvano P.; Haith, Gary L.; Stassinopoulos, Dimitris

    2000-01-01

    Parallelized versions of genetic algorithms (GAs) are popular primarily for three reasons: the GA is an inherently parallel algorithm, typical GA applications are very compute intensive, and powerful computing platforms, especially Beowulf-style computing clusters, are becoming more affordable and easier to implement. In addition, the low communication bandwidth required allows the use of inexpensive networking hardware such as standard office ethernet. In this paper we describe a parallel GA and its use in automated high-level circuit design. Genetic algorithms are a type of trial-and-error search technique that are guided by principles of Darwinian evolution. Just as the genetic material of two living organisms can intermix to produce offspring that are better adapted to their environment, GAs expose genetic material, frequently strings of 1s and Os, to the forces of artificial evolution: selection, mutation, recombination, etc. GAs start with a pool of randomly-generated candidate solutions which are then tested and scored with respect to their utility. Solutions are then bred by probabilistically selecting high quality parents and recombining their genetic representations to produce offspring solutions. Offspring are typically subjected to a small amount of random mutation. After a pool of offspring is produced, this process iterates until a satisfactory solution is found or an iteration limit is reached. Genetic algorithms have been applied to a wide variety of problems in many fields, including chemistry, biology, and many engineering disciplines. There are many styles of parallelism used in implementing parallel GAs. One such method is called the master-slave or processor farm approach. In this technique, slave nodes are used solely to compute fitness evaluations (the most time consuming part). The master processor collects fitness scores from the nodes and performs the genetic operators (selection, reproduction, variation, etc.). Because of dependency

  9. Multi-jagged: A scalable parallel spatial partitioning algorithm

    DOE PAGES

    Deveci, Mehmet; Rajamanickam, Sivasankaran; Devine, Karen D.; ...

    2015-03-18

    Geometric partitioning is fast and effective for load-balancing dynamic applications, particularly those requiring geometric locality of data (particle methods, crash simulations). We present, to our knowledge, the first parallel implementation of a multidimensional-jagged geometric partitioner. In contrast to the traditional recursive coordinate bisection algorithm (RCB), which recursively bisects subdomains perpendicular to their longest dimension until the desired number of parts is obtained, our algorithm does recursive multi-section with a given number of parts in each dimension. By computing multiple cut lines concurrently and intelligently deciding when to migrate data while computing the partition, we minimize data movement compared to efficientmore » implementations of recursive bisection. We demonstrate the algorithm's scalability and quality relative to the RCB implementation in Zoltan on both real and synthetic datasets. Our experiments show that the proposed algorithm performs and scales better than RCB in terms of run-time without degrading the load balance. Lastly, our implementation partitions 24 billion points into 65,536 parts within a few seconds and exhibits near perfect weak scaling up to 6K cores.« less

  10. Multi-jagged: A scalable parallel spatial partitioning algorithm

    SciTech Connect

    Deveci, Mehmet; Rajamanickam, Sivasankaran; Devine, Karen D.; Catalyurek, Umit V.

    2015-03-18

    Geometric partitioning is fast and effective for load-balancing dynamic applications, particularly those requiring geometric locality of data (particle methods, crash simulations). We present, to our knowledge, the first parallel implementation of a multidimensional-jagged geometric partitioner. In contrast to the traditional recursive coordinate bisection algorithm (RCB), which recursively bisects subdomains perpendicular to their longest dimension until the desired number of parts is obtained, our algorithm does recursive multi-section with a given number of parts in each dimension. By computing multiple cut lines concurrently and intelligently deciding when to migrate data while computing the partition, we minimize data movement compared to efficient implementations of recursive bisection. We demonstrate the algorithm's scalability and quality relative to the RCB implementation in Zoltan on both real and synthetic datasets. Our experiments show that the proposed algorithm performs and scales better than RCB in terms of run-time without degrading the load balance. Lastly, our implementation partitions 24 billion points into 65,536 parts within a few seconds and exhibits near perfect weak scaling up to 6K cores.

  11. A class of parallel algorithms for computation of the manipulator inertia matrix

    NASA Technical Reports Server (NTRS)

    Fijany, Amir; Bejczy, Antal K.

    1989-01-01

    Parallel and parallel/pipeline algorithms for computation of the manipulator inertia matrix are presented. An algorithm based on composite rigid-body spatial inertia method, which provides better features for parallelization, is used for the computation of the inertia matrix. Two parallel algorithms are developed which achieve the time lower bound in computation. Also described is the mapping of these algorithms with topological variation on a two-dimensional processor array, with nearest-neighbor connection, and with cardinality variation on a linear processor array. An efficient parallel/pipeline algorithm for the linear array was also developed, but at significantly higher efficiency.

  12. Vascular system modeling in parallel environment - distributed and shared memory approaches.

    PubMed

    Jurczuk, Krzysztof; Kretowski, Marek; Bezy-Wendling, Johanne

    2011-07-01

    This paper presents two approaches in parallel modeling of vascular system development in internal organs. In the first approach, new parts of tissue are distributed among processors and each processor is responsible for perfusing its assigned parts of tissue to all vascular trees. Communication between processors is accomplished by passing messages, and therefore, this algorithm is perfectly suited for distributed memory architectures. The second approach is designed for shared memory machines. It parallelizes the perfusion process during which individual processing units perform calculations concerning different vascular trees. The experimental results, performed on a computing cluster and multicore machines, show that both algorithms provide a significant speedup.

  13. Privacy Preservation in Distributed Subgradient Optimization Algorithms.

    PubMed

    Lou, Youcheng; Yu, Lean; Wang, Shouyang; Yi, Peng

    2017-07-31

    In this paper, some privacy-preserving features for distributed subgradient optimization algorithms are considered. Most of the existing distributed algorithms focus mainly on the algorithm design and convergence analysis, but not the protection of agents' privacy. Privacy is becoming an increasingly important issue in applications involving sensitive information. In this paper, we first show that the distributed subgradient synchronous homogeneous-stepsize algorithm is not privacy preserving in the sense that the malicious agent can asymptotically discover other agents' subgradients by transmitting untrue estimates to its neighbors. Then a distributed subgradient asynchronous heterogeneous-stepsize projection algorithm is proposed and accordingly its convergence and optimality is established. In contrast to the synchronous homogeneous-stepsize algorithm, in the new algorithm agents make their optimization updates asynchronously with heterogeneous stepsizes. The introduced two mechanisms of projection operation and asynchronous heterogeneous-stepsize optimization can guarantee that agents' privacy can be effectively protected.

  14. An Intrinsic Algorithm for Parallel Poisson Disk Sampling on Arbitrary Surfaces.

    PubMed

    Ying, Xiang; Xin, Shi-Qing; Sun, Qian; He, Ying

    2013-03-08

    Poisson disk sampling plays an important role in a variety of visual computing, due to its useful statistical property in distribution and the absence of aliasing artifacts. While many effective techniques have been proposed to generate Poisson disk distribution in Euclidean space, relatively few work has been reported to the surface counterpart. This paper presents an intrinsic algorithm for parallel Poisson disk sampling on arbitrary surfaces. We propose a new technique for parallelizing the dart throwing. Rather than the conventional approaches that explicitly partition the spatial domain to generate the samples in parallel, our approach assigns each sample candidate a random and unique priority that is unbiased with regard to the distribution. Hence, multiple threads can process the candidates simultaneously and resolve conflicts by checking the given priority values. It is worth noting that our algorithm is accurate as the generated Poisson disks are uniformly and randomly distributed without bias. Our method is intrinsic in that all the computations are based on the intrinsic metric and are independent of the embedding space. This intrinsic feature allows us to generate Poisson disk distributions on arbitrary surfaces. Furthermore, by manipulating the spatially varying density function, we can obtain adaptive sampling easily.

  15. Parallel radiation transport algorithms and associated architectural requirements

    SciTech Connect

    Morel, J. E.; Baker, R. S.; Warsa, J. S.

    2004-01-01

    The radiation transport equation is a seven-dimensional equation that can be extremely expensive to solve. In general, transport can be expected to completely dominate the memory and CPU time requirements for the ASCI codes. Both traditional iterative transport solution methods and modern Krylov-subspace solution methods require the inversion of a large number of block lower-diagonal matrices. While such inversions are easily done in serial, a high level of sophistication is needed for implementations on massively parallel platforms. Rectangular-mesh methods are well-established and generally quite efficient but unstructured-mesh methods remain a research topic. Nonetheless, considerable progress has been made in unstructured-mesh methods over the last several years. In general, the efficiency of transport solution algorithms are quite sensitive to communication latencies and bandwidth, but there are other significant considerations as well. Some new parallel algorithms have recently been defined that may be significantly better than existing methods for time-dependent problems, but will be significantly less effective for steady-state problems in some circumstances. Transport methods would benefit from a machine architecture with low latencies, high bandwidth, and on the order of one thousand very fast, large-memory processors, as opposed to an architecture that consists of a very large number of slower processors with less memory. In addition, a lightweight operating system is highly desirable.

  16. Efficient parallel algorithms for elastic plastic finite element analysis

    NASA Astrophysics Data System (ADS)

    Ding, K. Z.; Qin, Q.-H.; Cardew-Hall, M.; Kalyanasundaram, S.

    2008-03-01

    This paper presents our new development of parallel finite element algorithms for elastic plastic problems. The proposed method is based on dividing the original structure under consideration into a number of substructures which are treated as isolated finite element models via the interface conditions. Throughout the analysis, each processor stores only the information relevant to its substructure and generates the local stiffness matrix. A parallel substructure oriented preconditioned conjugate gradient method, which is combined with MR smoothing and diagonal storage scheme are employed to solve linear systems of equations. After having obtained the displacements of the problem under consideration, a substepping scheme is used to integrate elastic plastic stress strain relations. The procedure outlined controls the error of the computed stress by choosing each substep size automatically according to a prescribed tolerance. The combination of these algorithms shows a good speedup when increasing the number of processors and the effective solution of 3D elastic plastic problems whose size is much too large for a single workstation becomes possible.

  17. Full tensor gravity gradiometry data inversion: Performance analysis of parallel computing algorithms

    NASA Astrophysics Data System (ADS)

    Hou, Zhen-Long; Wei, Xiao-Hui; Huang, Da-Nian; Sun, Xu

    2015-09-01

    We apply reweighted inversion focusing to full tensor gravity gradiometry data using message-passing interface (MPI) and compute unified device architecture (CUDA) parallel computing algorithms, and then combine MPI with CUDA to formulate a hybrid algorithm. Parallel computing performance metrics are introduced to analyze and compare the performance of the algorithms. We summarize the rules for the performance evaluation of parallel algorithms. We use model and real data from the Vinton salt dome to test the algorithms. We find good match between model and real density data, and verify the high efficiency and feasibility of parallel computing algorithms in the inversion of full tensor gravity gradiometry data.

  18. An Evaluation of Biosurveillance Grid—Dynamic Algorithm Distribution Across Multiple Computer Nodes

    PubMed Central

    Tsai, Ming-Chi; Tsui, Fu-Chiang; Wagner, Michael M.

    2007-01-01

    Performing fast data analysis to detect disease outbreaks plays a critical role in real-time biosurveillance. In this paper, we described and evaluated an Algorithm Distribution Manager Service (ADMS) based on grid technologies, which dynamically partition and distribute detection algorithms across multiple computers. We compared the execution time to perform the analysis on a single computer and on a grid network (3 computing nodes) with and without using dynamic algorithm distribution. We found that algorithms with long runtime completed approximately three times earlier in distributed environment than in a single computer while short runtime algorithms performed worse in distributed environment. A dynamic algorithm distribution approach also performed better than static algorithm distribution approach. This pilot study shows a great potential to reduce lengthy analysis time through dynamic algorithm partitioning and parallel processing, and provides the opportunity of distributing algorithms from a client to remote computers in a grid network. PMID:18693936

  19. An evaluation of biosurveillance grid--dynamic algorithm distribution across multiple computer nodes.

    PubMed

    Tsai, Ming-Chi; Tsui, Fu-Chiang; Wagner, Michael M

    2007-10-11

    Performing fast data analysis to detect disease outbreaks plays a critical role in real-time biosurveillance. In this paper, we described and evaluated an Algorithm Distribution Manager Service (ADMS) based on grid technologies, which dynamically partition and distribute detection algorithms across multiple computers. We compared the execution time to perform the analysis on a single computer and on a grid network (3 computing nodes) with and without using dynamic algorithm distribution. We found that algorithms with long runtime completed approximately three times earlier in distributed environment than in a single computer while short runtime algorithms performed worse in distributed environment. A dynamic algorithm distribution approach also performed better than static algorithm distribution approach. This pilot study shows a great potential to reduce lengthy analysis time through dynamic algorithm partitioning and parallel processing, and provides the opportunity of distributing algorithms from a client to remote computers in a grid network.

  20. Hierarchical fractional-step approximations and parallel kinetic Monte Carlo algorithms

    SciTech Connect

    Arampatzis, Giorgos; Katsoulakis, Markos A.; Plechac, Petr; Taufer, Michela; Xu, Lifan

    2012-10-01

    We present a mathematical framework for constructing and analyzing parallel algorithms for lattice kinetic Monte Carlo (KMC) simulations. The resulting algorithms have the capacity to simulate a wide range of spatio-temporal scales in spatially distributed, non-equilibrium physiochemical processes with complex chemistry and transport micro-mechanisms. Rather than focusing on constructing exactly the stochastic trajectories, our approach relies on approximating the evolution of observables, such as density, coverage, correlations and so on. More specifically, we develop a spatial domain decomposition of the Markov operator (generator) that describes the evolution of all observables according to the kinetic Monte Carlo algorithm. This domain decomposition corresponds to a decomposition of the Markov generator into a hierarchy of operators and can be tailored to specific hierarchical parallel architectures such as multi-core processors or clusters of Graphical Processing Units (GPUs). Based on this operator decomposition, we formulate parallel Fractional step kinetic Monte Carlo algorithms by employing the Trotter Theorem and its randomized variants; these schemes, (a) are partially asynchronous on each fractional step time-window, and (b) are characterized by their communication schedule between processors. The proposed mathematical framework allows us to rigorously justify the numerical and statistical consistency of the proposed algorithms, showing the convergence of our approximating schemes to the original serial KMC. The approach also provides a systematic evaluation of different processor communicating schedules. We carry out a detailed benchmarking of the parallel KMC schemes using available exact solutions, for example, in Ising-type systems and we demonstrate the capabilities of the method to simulate complex spatially distributed reactions at very large scales on GPUs. Finally, we discuss work load balancing between processors and propose a re

  1. Implementation of Novel Parallel Cyclic Convolution Algorithms in Clusters and Multi-Core Architectures

    DTIC Science & Technology

    2014-07-31

    Parallel Cyclic Convolution, Parallel Circular Correlators, Parallel One-Dimensional DFT, SDR GPS REPORT DOCUMENTATION PAGE 11. SPONSOR/MONITOR’S REPORT...of the MIT developed Quicksynch algorithm for fast circular correlation in GPS SDR systems. The algorithm is based on the sparsity of the...parallel correlator constructs that we are proposing. We also did a MATLAB implementation of an algorithm developed at MIT (Quicksynch) for GPS SDR

  2. NPAC Distributed-Parallel System Feasibility Study

    DTIC Science & Technology

    1993-08-01

    Syracuse, New York, and Rome Laboratory, 2 located in Rome, New York, using the Cronus Distributed Operating System.* 2. Design and specify a distributed...distributed operating system chosen for this platform was the Cronus distributed programming environment from BBN. While this system is widely...available as a het- erogeneous distributed system, this project was one of the first to make use a new " Cronus is a product of BBN Systems and Technologies

  3. Massively parallel algorithms for trace-driven cache simulations

    NASA Technical Reports Server (NTRS)

    Nicol, David M.; Greenberg, Albert G.; Lubachevsky, Boris D.

    1991-01-01

    Trace driven cache simulation is central to computer design. A trace is a very long sequence of reference lines from main memory. At the t(exp th) instant, reference x sub t is hashed into a set of cache locations, the contents of which are then compared with x sub t. If at the t sup th instant x sub t is not present in the cache, then it is said to be a miss, and is loaded into the cache set, possibly forcing the replacement of some other memory line, and making x sub t present for the (t+1) sup st instant. The problem of parallel simulation of a subtrace of N references directed to a C line cache set is considered, with the aim of determining which references are misses and related statistics. A simulation method is presented for the Least Recently Used (LRU) policy, which regradless of the set size C runs in time O(log N) using N processors on the exclusive read, exclusive write (EREW) parallel model. A simpler LRU simulation algorithm is given that runs in O(C log N) time using N/log N processors. Timings are presented of the second algorithm's implementation on the MasPar MP-1, a machine with 16384 processors. A broad class of reference based line replacement policies are considered, which includes LRU as well as the Least Frequently Used and Random replacement policies. A simulation method is presented for any such policy that on any trace of length N directed to a C line set runs in the O(C log N) time with high probability using N processors on the EREW model. The algorithms are simple, have very little space overhead, and are well suited for SIMD implementation.

  4. The high performance parallel algorithm for Unified Gas-Kinetic Scheme

    NASA Astrophysics Data System (ADS)

    Li, Shiyi; Li, Qibing; Fu, Song; Xu, Jinxiu

    2016-11-01

    A high performance parallel algorithm for UGKS is developed to simulate three-dimensional flows internal and external on arbitrary grid system. The physical domain and velocity domain are divided into different blocks and distributed according to the two-dimensional Cartesian topology with intra-communicators in physical domain for data exchange and other intra-communicators in velocity domain for sum reduction to moment integrals. Numerical results of three-dimensional cavity flow and flow past a sphere agree well with the results from the existing studies and validate the applicability of the algorithm. The scalability of the algorithm is tested both on small (1-16) and large (729-5832) scale processors. The tested speed-up ratio is near linear ashind thus the efficiency is around 1, which reveals the good scalability of the present algorithm.

  5. Parallel algorithm for computing points on a computation front hyperplane

    NASA Astrophysics Data System (ADS)

    Krasnov, M. M.

    2015-01-01

    A parallel algorithm for computing points on a computation front hyperplane is described. This task arises in the computation of a quantity defined on a multidimensional rectangular domain. Three-dimensional domains are usually discussed, but the material is given in the general form when the number of measurements is at least two. When the values of a quantity at different points are internally independent (which is frequently the case), the corresponding computations are independent as well and can be performed in parallel. However, if there are internal dependences (as, for example, in the Gauss-Seidel method for systems of linear equations), then the order of scanning points of the domain is an important issue. A conventional approach in this case is to form a computation front hyperplane (a usual plane in the three-dimensional case and a line in the two-dimensional case) that moves linearly across the domain at a certain angle. At every step in the course of motion of this hyperplane, its intersection points with the domain can be treated independently and, hence, in parallel, but the steps themselves are executed sequentially. At different steps, the intersection of the hyperplane with the entire domain can have a rather complex geometry and the search for all points of the domain lying on the hyperplane at a given step is a nontrivial problem. This problem (i.e., the computation of the coordinates of points lying in the intersection of the domain with the hyperplane at a given step in the course of hyperplane motion) is addressed below. The computations over the points of the hyperplane can be executed in parallel.

  6. A Parallel Algorithm for Connected Component Labelling of Gray-scale Images on Homogeneous Multicore Architectures

    NASA Astrophysics Data System (ADS)

    Niknam, Mehdi; Thulasiraman, Parimala; Camorlinga, Sergio

    2010-11-01

    Connected component labelling is an essential step in image processing. We provide a parallel version of Suzuki's sequential connected component algorithm in order to speed up the labelling process. Also, we modify the algorithm to enable labelling gray-scale images. Due to the data dependencies in the algorithm we used a method similar to pipeline to exploit parallelism. The parallel algorithm method achieved a speedup of 2.5 for image size of 256 × 256 pixels using 4 processing threads.

  7. Distributed sensor data compression algorithm

    NASA Astrophysics Data System (ADS)

    Ambrose, Barry; Lin, Freddie

    2006-04-01

    Theoretically it is possible for two sensors to reliably send data at rates smaller than the sum of the necessary data rates for sending the data independently, essentially taking advantage of the correlation of sensor readings to reduce the data rate. In 2001, Caltech researchers Michelle Effros and Qian Zhao developed new techniques for data compression code design for correlated sensor data, which were published in a paper at the 2001 Data Compression Conference (DCC 2001). These techniques take advantage of correlations between two or more closely positioned sensors in a distributed sensor network. Given two signals, X and Y, the X signal is sent using standard data compression. The goal is to design a partition tree for the Y signal. The Y signal is sent using a code based on the partition tree. At the receiving end, if ambiguity arises when using the partition tree to decode the Y signal, the X signal is used to resolve the ambiguity. We have extended this work to increase the efficiency of the code search algorithms. Our results have shown that development of a highly integrated sensor network protocol that takes advantage of a correlation in sensor readings can result in 20-30% sensor data transport cost savings. In contrast, the best possible compression using state-of-the-art compression techniques that did not take into account the correlation of the incoming data signals achieved only 9-10% compression at most. This work was sponsored by MDA, but has very widespread applicability to ad hoc sensor networks, hyperspectral imaging sensors and vehicle health monitoring sensors for space applications.

  8. Application of hybrid clustering using parallel k-means algorithm and DIANA algorithm

    NASA Astrophysics Data System (ADS)

    Umam, Khoirul; Bustamam, Alhadi; Lestari, Dian

    2017-03-01

    DNA is one of the carrier of genetic information of living organisms. Encoding, sequencing, and clustering DNA sequences has become the key jobs and routine in the world of molecular biology, in particular on bioinformatics application. There are two type of clustering, hierarchical clustering and partitioning clustering. In this paper, we combined two type clustering i.e. K-Means (partitioning clustering) and DIANA (hierarchical clustering), therefore it called Hybrid clustering. Application of hybrid clustering using Parallel K-Means algorithm and DIANA algorithm used to clustering DNA sequences of Human Papillomavirus (HPV). The clustering process is started with Collecting DNA sequences of HPV are obtained from NCBI (National Centre for Biotechnology Information), then performing characteristics extraction of DNA sequences. The characteristics extraction result is store in a matrix form, then normalize this matrix using Min-Max normalization and calculate genetic distance using Euclidian Distance. Furthermore, the hybrid clustering is applied by using implementation of Parallel K-Means algorithm and DIANA algorithm. The aim of using Hybrid Clustering is to obtain better clusters result. For validating the resulted clusters, to get optimum number of clusters, we use Davies-Bouldin Index (DBI). In this study, the result of implementation of Parallel K-Means clustering is data clustered become 5 clusters with minimal IDB value is 0.8741, and Hybrid Clustering clustered data become 13 sub-clusters with minimal IDB values = 0.8216, 0.6845, 0.3331, 0.1994 and 0.3952. The IDB value of hybrid clustering less than IBD value of Parallel K-Means clustering only that perform at 1ts stage. Its means clustering using Hybrid Clustering have the better result to clustered DNA sequence of HPV than perform parallel K-Means Clustering only.

  9. MPI/OpenMP Hybrid Parallel Algorithm of Resolution of Identity Second-Order Møller-Plesset Perturbation Calculation for Massively Parallel Multicore Supercomputers.

    PubMed

    Katouda, Michio; Nakajima, Takahito

    2013-12-10

    A new algorithm for massively parallel calculations of electron correlation energy of large molecules based on the resolution of identity second-order Møller-Plesset perturbation (RI-MP2) technique is developed and implemented into the quantum chemistry software NTChem. In this algorithm, a Message Passing Interface (MPI) and Open Multi-Processing (OpenMP) hybrid parallel programming model is applied to attain efficient parallel performance on massively parallel supercomputers. An in-core storage scheme of intermediate data of three-center electron repulsion integrals utilizing the distributed memory is developed to eliminate input/output (I/O) overhead. The parallel performance of the algorithm is tested on massively parallel supercomputers such as the K computer (using up to 45 992 central processing unit (CPU) cores) and a commodity Intel Xeon cluster (using up to 8192 CPU cores). The parallel RI-MP2/cc-pVTZ calculation of two-layer nanographene sheets (C150H30)2 (number of atomic orbitals is 9640) is performed using 8991 node and 71 288 CPU cores of the K computer.

  10. Parallel contact detection algorithm for transient solid dynamics simulations using PRONTO3D

    SciTech Connect

    Attaway, S.W.; Hendrickson, B.A.; Plimpton, S.J.

    1996-09-01

    An efficient, scalable, parallel algorithm for treating material surface contacts in solid mechanics finite element programs has been implemented in a modular way for MIMD parallel computers. The serial contact detection algorithm that was developed previously for the transient dynamics finite element code PRONTO3D has been extended for use in parallel computation by devising a dynamic (adaptive) processor load balancing scheme.

  11. Parallel-vector algorithms for particle simulations on shared-memory multiprocessors

    SciTech Connect

    Nishiura, Daisuke; Sakaguchi, Hide

    2011-03-01

    Over the last few decades, the computational demands of massive particle-based simulations for both scientific and industrial purposes have been continuously increasing. Hence, considerable efforts are being made to develop parallel computing techniques on various platforms. In such simulations, particles freely move within a given space, and so on a distributed-memory system, load balancing, i.e., assigning an equal number of particles to each processor, is not guaranteed. However, shared-memory systems achieve better load balancing for particle models, but suffer from the intrinsic drawback of memory access competition, particularly during (1) paring of contact candidates from among neighboring particles and (2) force summation for each particle. Here, novel algorithms are proposed to overcome these two problems. For the first problem, the key is a pre-conditioning process during which particle labels are sorted by a cell label in the domain to which the particles belong. Then, a list of contact candidates is constructed by pairing the sorted particle labels. For the latter problem, a table comprising the list indexes of the contact candidate pairs is created and used to sum the contact forces acting on each particle for all contacts according to Newton's third law. With just these methods, memory access competition is avoided without additional redundant procedures. The parallel efficiency and compatibility of these two algorithms were evaluated in discrete element method (DEM) simulations on four types of shared-memory parallel computers: a multicore multiprocessor computer, scalar supercomputer, vector supercomputer, and graphics processing unit. The computational efficiency of a DEM code was found to be drastically improved with our algorithms on all but the scalar supercomputer. Thus, the developed parallel algorithms are useful on shared-memory parallel computers with sufficient memory bandwidth.

  12. The design and implementation of MPI master-slave parallel genetic algorithm

    NASA Astrophysics Data System (ADS)

    Liu, Shuping; Cheng, Yanliu

    2013-03-01

    In this paper, the MPI master-slave parallel genetic algorithm is implemented by analyzing the basic genetic algorithm and parallel MPI program, and building a Linux cluster. This algorithm is used for the test of maximum value problems (Rosen brocks function) .And we acquire the factors influencing the master-slave parallel genetic algorithm by deriving from the analysis of test data. The experimental data shows that the balanced hardware configuration and software design optimization can improve the performance of system in the complexity of the computing environment using the master-slave parallel genetic algorithms.

  13. Parallel optimization algorithm for drone inspection in the building industry

    NASA Astrophysics Data System (ADS)

    Walczyński, Maciej; BoŻejko, Wojciech; Skorupka, Dariusz

    2017-07-01

    In this paper we present an approach for Vehicle Routing Problem with Drones (VRPD) in case of building inspection from the air. In autonomic inspection process there is a need to determine of the optimal route for inspection drone. This is especially important issue because of the very limited flight time of modern multicopters. The method of determining solutions for Traveling Salesman Problem(TSP), described in this paper bases on Parallel Evolutionary Algorithm (ParEA)with cooperative and independent approach for communication between threads. This method described first by Bożejko and Wodecki [1] bases on the observation that if exists some number of elements on certain positions in a number of permutations which are local minima, then those elements will be in the same position in the optimal solution for TSP problem. Numerical experiments were made on BEM computational cluster with using MPI library.

  14. Adaptive link selection algorithms for distributed estimation

    NASA Astrophysics Data System (ADS)

    Xu, Songcen; de Lamare, Rodrigo C.; Poor, H. Vincent

    2015-12-01

    This paper presents adaptive link selection algorithms for distributed estimation and considers their application to wireless sensor networks and smart grids. In particular, exhaustive search-based least mean squares (LMS) / recursive least squares (RLS) link selection algorithms and sparsity-inspired LMS / RLS link selection algorithms that can exploit the topology of networks with poor-quality links are considered. The proposed link selection algorithms are then analyzed in terms of their stability, steady-state, and tracking performance and computational complexity. In comparison with the existing centralized or distributed estimation strategies, the key features of the proposed algorithms are as follows: (1) more accurate estimates and faster convergence speed can be obtained and (2) the network is equipped with the ability of link selection that can circumvent link failures and improve the estimation performance. The performance of the proposed algorithms for distributed estimation is illustrated via simulations in applications of wireless sensor networks and smart grids.

  15. Performance of a parallel algorithm for standard cell placement on the Intel Hypercube

    NASA Technical Reports Server (NTRS)

    Jones, Mark; Banerjee, Prithviraj

    1987-01-01

    A parallel simulated annealing algorithm for standard cell placement on the Intel Hypercube is presented. A novel tree broadcasting strategy is used extensively for updating cell locations in the parallel environment. Studies on the performance of the algorithm on example industrial circuits show that it is faster and gives better final placement results than uniprocessor simulated annealing algorithms.

  16. Parallel multiphysics algorithms and software for computational nuclear engineering

    NASA Astrophysics Data System (ADS)

    Gaston, D.; Hansen, G.; Kadioglu, S.; Knoll, D. A.; Newman, C.; Park, H.; Permann, C.; Taitano, W.

    2009-07-01

    There is a growing trend in nuclear reactor simulation to consider multiphysics problems. This can be seen in reactor analysis where analysts are interested in coupled flow, heat transfer and neutronics, and in fuel performance simulation where analysts are interested in thermomechanics with contact coupled to species transport and chemistry. These more ambitious simulations usually motivate some level of parallel computing. Many of the coupling efforts to date utilize simple code coupling or first-order operator splitting, often referred to as loose coupling. While these approaches can produce answers, they usually leave questions of accuracy and stability unanswered. Additionally, the different physics often reside on separate grids which are coupled via simple interpolation, again leaving open questions of stability and accuracy. Utilizing state of the art mathematics and software development techniques we are deploying next generation tools for nuclear engineering applications. The Jacobian-free Newton-Krylov (JFNK) method combined with physics-based preconditioning provide the underlying mathematical structure for our tools. JFNK is understood to be a modern multiphysics algorithm, but we are also utilizing its unique properties as a scale bridging algorithm. To facilitate rapid development of multiphysics applications we have developed the Multiphysics Object-Oriented Simulation Environment (MOOSE). Examples from two MOOSE-based applications: PRONGHORN, our multiphysics gas cooled reactor simulation tool and BISON, our multiphysics, multiscale fuel performance simulation tool will be presented.

  17. Partitioning problems in parallel, pipelined and distributed computing

    NASA Technical Reports Server (NTRS)

    Bokhari, S.

    1985-01-01

    The problem of optimally assigning the modules of a parallel program over the processors of a multiple computer system is addressed. A Sum-Bottleneck path algorithm is developed that permits the efficient solution of many variants of this problem under some constraints on the structure of the partitions. In particular, the following problems are solved optimally for a single-host, multiple satellite system: partitioning multiple chain structured parallel programs, multiple arbitrarily structured serial programs and single tree structured parallel programs. In addition, the problems of partitioning chain structured parallel programs across chain connected systems and across shared memory (or shared bus) systems are also solved under certain constraints. All solutions for parallel programs are equally applicable to pipelined programs. These results extend prior research in this area by explicitly taking concurrency into account and permit the efficient utilization of multiple computer architectures for a wide range of problems of practical interest.

  18. Partitioning problems in parallel, pipelined, and distributed computing

    NASA Technical Reports Server (NTRS)

    Bokhari, Shahid H.

    1988-01-01

    The problem of optimally assigning the modules of a parallel program over the processors of a multiple-computer system is addressed. A sum-bottleneck path algorithm is developed that permits the efficient solution of many variants of this problem under some constraints on the structure of the partitions. In particular, the following problems are solved optimally for a single-host, multiple-satellite system: partitioning multiple chain-structured parallel programs, multiple arbitrarily structured serial programs, and single-tree structured parallel programs. In addition, the problem of partitioning chain-structured parallel programs across chain-connected systems is solved under certain constraints. All solutions for parallel programs are equally applicable to pipelined programs. These results extend prior research in this area by explicitly taking concurrency into account and permit the efficient utilization of multiple-computer architectures for a wide range of problems of practical interest.

  19. Parallel algorithms for placement and routing in VLSI design. Ph.D. Thesis

    NASA Technical Reports Server (NTRS)

    Brouwer, Randall Jay

    1991-01-01

    The computational requirements for high quality synthesis, analysis, and verification of very large scale integration (VLSI) designs have rapidly increased with the fast growing complexity of these designs. Research in the past has focused on the development of heuristic algorithms, special purpose hardware accelerators, or parallel algorithms for the numerous design tasks to decrease the time required for solution. Two new parallel algorithms are proposed for two VLSI synthesis tasks, standard cell placement and global routing. The first algorithm, a parallel algorithm for global routing, uses hierarchical techniques to decompose the routing problem into independent routing subproblems that are solved in parallel. Results are then presented which compare the routing quality to the results of other published global routers and which evaluate the speedups attained. The second algorithm, a parallel algorithm for cell placement and global routing, hierarchically integrates a quadrisection placement algorithm, a bisection placement algorithm, and the previous global routing algorithm. Unique partitioning techniques are used to decompose the various stages of the algorithm into independent tasks which can be evaluated in parallel. Finally, results are presented which evaluate the various algorithm alternatives and compare the algorithm performance to other placement programs. Measurements are presented on the parallel speedups available.

  20. Parallel Molecular Distributed Detection With Brownian Motion.

    PubMed

    Rogers, Uri; Koh, Min-Sung

    2016-12-01

    This paper explores the in vivo distributed detection of an undesired biological agent's (BAs) biomarkers by a group of biological sized nanomachines in an aqueous medium under drift. The term distributed, indicates that the system information relative to the BAs presence is dispersed across the collection of nanomachines, where each nanomachine possesses limited communication, computation, and movement capabilities. Using Brownian motion with drift, a probabilistic detection and optimal data fusion framework, coined molecular distributed detection, will be introduced that combines theory from both molecular communication and distributed detection. Using the optimal data fusion framework as a guide, simulation indicates that a sub-optimal fusion method exists, allowing for a significant reduction in implementation complexity while retaining BA detection accuracy.

  1. Parallel Molecular Distributed Detection with Brownian Motion.

    PubMed

    Rogers, Uri; Koh, Min-Sung

    2016-12-05

    This paper explores the in vivo distributed detection of an undesired biological agent's (BAs) biomarkers by a group of biological sized nanomachines in an aqueous medium under drift. The term distributed, indicates that the system information relative to the BAs presence is dispersed across the collection of nanomachines, where each nanomachine possesses limited communication, computation, and movement capabilities. Using Brownian motion with drift, a probabilistic detection and optimal data fusion framework, coined molecular distributed detection, will be introduced that combines theory from both molecular communication and distributed detection. Using the optimal data fusion framework as a guide, simulation indicates that a suboptimal fusion method exists, allowing for a significant reduction in implementation complexity while retaining BA detection accuracy.

  2. VLSI Design, Parallel Computation and Distributed Computing

    DTIC Science & Technology

    1991-09-30

    Operations Research and Manage - ment Scienc,. \\, I IV Product Planning and Inventory , North-Holland, 19T9. to api- ir 109. F ’. L,.t ’A 2,1 - I l.uwr...7- theory. ignifcan prgrs ha bee mad n th deeomndo fi n sorting circuiits, network management protocols for high speed nertworks, distributed...Significant progress has been made on the development of efficient sorting circuits, network management protocols for high speed networks, distributed graph

  3. Matrix distributed processing: a set of C++ tools for implementing generic lattice computations on parallel systems

    NASA Astrophysics Data System (ADS)

    Di Pierro, Massimo

    2001-11-01

    We present a set of programming tools (classes and functions written in C++ and based on Message Passing Interface) for fast development of generic parallel (and non-parallel) lattice simulations. They are collectively called MDP 1.2. These programming tools include classes and algorithms for matrices, random number generators, distributed lattices (with arbitrary topology), fields and parallel iterations. No previous knowledge of MPI is required in order to use them. Some applications in electromagnetism, electronics, condensed matter and lattice QCD are presented.

  4. Some parallel algorithms on the four processor Cray X-MP4 supercomputer

    SciTech Connect

    Kincaid, D.R.; Oppe, T.C.

    1988-05-01

    Three numerical studies of parallel algorithms on a four processor Cray X-MP4 supercomputer are presented. These numerical experiments involve the following: a parallel version of ITPACKV 2C, a package for solving large sparse linear systems, a parallel version of the conjugate gradient method with line Jacobi preconditioning, and several parallel algorithms for computing the LU-factorization of dense matrices. 27 refs., 4 tabs.

  5. Structure preserving parallel algorithms for solving the Bethe–Salpeter eigenvalue problem

    SciTech Connect

    Shao, Meiyue; da Jornada, Felipe H.; Yang, Chao; Deslippe, Jack; Louie, Steven G.

    2015-10-02

    The Bethe–Salpeter eigenvalue problem is a dense structured eigenvalue problem arising from discretized Bethe–Salpeter equation in the context of computing exciton energies and states. A computational challenge is that at least half of the eigenvalues and the associated eigenvectors are desired in practice. In this paper, we establish the equivalence between Bethe–Salpeter eigenvalue problems and real Hamiltonian eigenvalue problems. Based on theoretical analysis, structure preserving algorithms for a class of Bethe–Salpeter eigenvalue problems are proposed. We also show that for this class of problems all eigenvalues obtained from the Tamm–Dancoff approximation are overestimated. In order to solve large scale problems of practical interest, we discuss parallel implementations of our algorithms targeting distributed memory systems. Finally, several numerical examples are presented to demonstrate the efficiency and accuracy of our algorithms.

  6. Structure preserving parallel algorithms for solving the Bethe–Salpeter eigenvalue problem

    DOE PAGES

    Shao, Meiyue; da Jornada, Felipe H.; Yang, Chao; ...

    2015-10-02

    The Bethe–Salpeter eigenvalue problem is a dense structured eigenvalue problem arising from discretized Bethe–Salpeter equation in the context of computing exciton energies and states. A computational challenge is that at least half of the eigenvalues and the associated eigenvectors are desired in practice. In this paper, we establish the equivalence between Bethe–Salpeter eigenvalue problems and real Hamiltonian eigenvalue problems. Based on theoretical analysis, structure preserving algorithms for a class of Bethe–Salpeter eigenvalue problems are proposed. We also show that for this class of problems all eigenvalues obtained from the Tamm–Dancoff approximation are overestimated. In order to solve large scale problemsmore » of practical interest, we discuss parallel implementations of our algorithms targeting distributed memory systems. Finally, several numerical examples are presented to demonstrate the efficiency and accuracy of our algorithms.« less

  7. A conflict-free, path-level parallelization approach for sequential simulation algorithms

    NASA Astrophysics Data System (ADS)

    Rasera, Luiz Gustavo; Machado, Péricles Lopes; Costa, João Felipe C. L.

    2015-07-01

    Pixel-based simulation algorithms are the most widely used geostatistical technique for characterizing the spatial distribution of natural resources. However, sequential simulation does not scale well for stochastic simulation on very large grids, which are now commonly found in many petroleum, mining, and environmental studies. With the availability of multiple-processor computers, there is an opportunity to develop parallelization schemes for these algorithms to increase their performance and efficiency. Here we present a conflict-free, path-level parallelization strategy for sequential simulation. The method consists of partitioning the simulation grid into a set of groups of nodes and delegating all available processors for simulation of multiple groups of nodes concurrently. An automated classification procedure determines which groups are simulated in parallel according to their spatial arrangement in the simulation grid. The major advantage of this approach is that it does not require conflict resolution operations, and thus allows exact reproduction of results. Besides offering a large performance gain when compared to the traditional serial implementation, the method provides efficient use of computational resources and is generic enough to be adapted to several sequential algorithms.

  8. Implementation of a fully-balanced periodic tridiagonal solver on a parallel distributed memory architecture

    NASA Technical Reports Server (NTRS)

    Eidson, T. M.; Erlebacher, G.

    1994-01-01

    While parallel computers offer significant computational performance, it is generally necessary to evaluate several programming strategies. Two programming strategies for a fairly common problem - a periodic tridiagonal solver - are developed and evaluated. Simple model calculations as well as timing results are presented to evaluate the various strategies. The particular tridiagonal solver evaluated is used in many computational fluid dynamic simulation codes. The feature that makes this algorithm unique is that these simulation codes usually require simultaneous solutions for multiple right-hand-sides (RHS) of the system of equations. Each RHS solutions is independent and thus can be computed in parallel. Thus a Gaussian elimination type algorithm can be used in a parallel computation and the more complicated approaches such as cyclic reduction are not required. The two strategies are a transpose strategy and a distributed solver strategy. For the transpose strategy, the data is moved so that a subset of all the RHS problems is solved on each of the several processors. This usually requires significant data movement between processor memories across a network. The second strategy attempts to have the algorithm allow the data across processor boundaries in a chained manner. This usually requires significantly less data movement. An approach to accomplish this second strategy in a near-perfect load-balanced manner is developed. In addition, an algorithm will be shown to directly transform a sequential Gaussian elimination type algorithm into the parallel chained, load-balanced algorithm.

  9. Mesh-free data transfer algorithms for partitioned multiphysics problems: Conservation, accuracy, and parallelism

    NASA Astrophysics Data System (ADS)

    Slattery, Stuart R.

    2016-02-01

    In this paper we analyze and extend mesh-free algorithms for three-dimensional data transfer problems in partitioned multiphysics simulations. We first provide a direct comparison between a mesh-based weighted residual method using the common-refinement scheme and two mesh-free algorithms leveraging compactly supported radial basis functions: one using a spline interpolation and one using a moving least square reconstruction. Through the comparison we assess both the conservation and accuracy of the data transfer obtained from each of the methods. We do so for a varying set of geometries with and without curvature and sharp features and for functions with and without smoothness and with varying gradients. Our results show that the mesh-based and mesh-free algorithms are complementary with cases where each was demonstrated to perform better than the other. We then focus on the mesh-free methods by developing a set of algorithms to parallelize them based on sparse linear algebra techniques. This includes a discussion of fast parallel radius searching in point clouds and restructuring the interpolation algorithms to leverage data structures and linear algebra services designed for large distributed computing environments. The scalability of our new algorithms is demonstrated on a leadership class computing facility using a set of basic scaling studies. These scaling studies show that for problems with reasonable load balance, our new algorithms for both spline interpolation and moving least square reconstruction demonstrate both strong and weak scalability using more than 100,000 MPI processes with billions of degrees of freedom in the data transfer operation.

  10. Mesh-free data transfer algorithms for partitioned multiphysics problems: Conservation, accuracy, and parallelism

    SciTech Connect

    Slattery, Stuart R.

    2015-12-02

    In this study we analyze and extend mesh-free algorithms for three-dimensional data transfer problems in partitioned multiphysics simulations. We first provide a direct comparison between a mesh-based weighted residual method using the common-refinement scheme and two mesh-free algorithms leveraging compactly supported radial basis functions: one using a spline interpolation and one using a moving least square reconstruction. Through the comparison we assess both the conservation and accuracy of the data transfer obtained from each of the methods. We do so for a varying set of geometries with and without curvature and sharp features and for functions with and without smoothness and with varying gradients. Our results show that the mesh-based and mesh-free algorithms are complementary with cases where each was demonstrated to perform better than the other. We then focus on the mesh-free methods by developing a set of algorithms to parallelize them based on sparse linear algebra techniques. This includes a discussion of fast parallel radius searching in point clouds and restructuring the interpolation algorithms to leverage data structures and linear algebra services designed for large distributed computing environments. The scalability of our new algorithms is demonstrated on a leadership class computing facility using a set of basic scaling studies. Finally, these scaling studies show that for problems with reasonable load balance, our new algorithms for both spline interpolation and moving least square reconstruction demonstrate both strong and weak scalability using more than 100,000 MPI processes with billions of degrees of freedom in the data transfer operation.

  11. Mesh-free data transfer algorithms for partitioned multiphysics problems: Conservation, accuracy, and parallelism

    DOE PAGES

    Slattery, Stuart R.

    2015-12-02

    In this study we analyze and extend mesh-free algorithms for three-dimensional data transfer problems in partitioned multiphysics simulations. We first provide a direct comparison between a mesh-based weighted residual method using the common-refinement scheme and two mesh-free algorithms leveraging compactly supported radial basis functions: one using a spline interpolation and one using a moving least square reconstruction. Through the comparison we assess both the conservation and accuracy of the data transfer obtained from each of the methods. We do so for a varying set of geometries with and without curvature and sharp features and for functions with and without smoothnessmore » and with varying gradients. Our results show that the mesh-based and mesh-free algorithms are complementary with cases where each was demonstrated to perform better than the other. We then focus on the mesh-free methods by developing a set of algorithms to parallelize them based on sparse linear algebra techniques. This includes a discussion of fast parallel radius searching in point clouds and restructuring the interpolation algorithms to leverage data structures and linear algebra services designed for large distributed computing environments. The scalability of our new algorithms is demonstrated on a leadership class computing facility using a set of basic scaling studies. Finally, these scaling studies show that for problems with reasonable load balance, our new algorithms for both spline interpolation and moving least square reconstruction demonstrate both strong and weak scalability using more than 100,000 MPI processes with billions of degrees of freedom in the data transfer operation.« less

  12. A scalable parallel black oil simulator on distributed memory parallel computers

    NASA Astrophysics Data System (ADS)

    Wang, Kun; Liu, Hui; Chen, Zhangxin

    2015-11-01

    This paper presents our work on developing a parallel black oil simulator for distributed memory computers based on our in-house parallel platform. The parallel simulator is designed to overcome the performance issues of common simulators that are implemented for personal computers and workstations. The finite difference method is applied to discretize the black oil model. In addition, some advanced techniques are employed to strengthen the robustness and parallel scalability of the simulator, including an inexact Newton method, matrix decoupling methods, and algebraic multigrid methods. A new multi-stage preconditioner is proposed to accelerate the solution of linear systems from the Newton methods. Numerical experiments show that our simulator is scalable and efficient, and is capable of simulating extremely large-scale black oil problems with tens of millions of grid blocks using thousands of MPI processes on parallel computers.

  13. Para-GMRF: parallel algorithm for anomaly detection of hyperspectral image

    NASA Astrophysics Data System (ADS)

    Dong, Chao; Zhao, Huijie; Li, Na; Wang, Wei

    2007-12-01

    The hyperspectral imager is capable of collecting hundreds of images corresponding to different wavelength channels for the observed area simultaneously, which make it possible to discriminate man-made objects from natural background. However, the price paid for the wealthy information is the enormous amounts of data, usually hundreds of Gigabytes per day. Turning the huge volume data into useful information and knowledge in real time is critical for geoscientists. In this paper, the proposed parallel Gaussian-Markov random field (Para-GMRF) anomaly detection algorithm is an attempt of applying parallel computing technology to solve the problem. Based on the locality of GMRF algorithm, we partition the 3-D hyperspectral image cube in spatial domain and distribute data blocks to multiple computers for concurrent detection. Meanwhile, to achieve load balance, a work pool scheduler is designed for task assignment. The Para-GMRF algorithm is organized in master-slave architecture, coded in C programming language using message passing interface (MPI) library and tested on a Beowulf cluster. Experimental results show that Para-GMRF algorithm successfully conquers the challenge and can be used in time sensitive areas, such as environmental monitoring and battlefield reconnaissance.

  14. Optimal Design of Passive Power Filters Based on Pseudo-parallel Genetic Algorithm

    NASA Astrophysics Data System (ADS)

    Li, Pei; Li, Hongbo; Gao, Nannan; Niu, Lin; Guo, Liangfeng; Pei, Ying; Zhang, Yanyan; Xu, Minmin; Chen, Kerui

    2017-05-01

    The economic costs together with filter efficiency are taken as targets to optimize the parameter of passive filter. Furthermore, the method of combining pseudo-parallel genetic algorithm with adaptive genetic algorithm is adopted in this paper. In the early stages pseudo-parallel genetic algorithm is introduced to increase the population diversity, and adaptive genetic algorithm is used in the late stages to reduce the workload. At the same time, the migration rate of pseudo-parallel genetic algorithm is improved to change with population diversity adaptively. Simulation results show that the filter designed by the proposed method has better filtering effect with lower economic cost, and can be used in engineering.

  15. Performance of a parallel algorithm for standard cell placement on the Intel Hypercube

    NASA Technical Reports Server (NTRS)

    Jones, Mark; Banerjee, Prithviraj

    1987-01-01

    A parallel simulated annealing algorithm for standard cell placement that is targeted to run on the Intel Hypercube is presented. A tree broadcasting strategy that is used extensively in our algorithm for updating cell locations in the parallel environment is presented. Studies on the performance of our algorithm on example industrial circuits show that it is faster and gives better final placement results than the uniprocessor simulated annealing algorithms.

  16. Models and Measurements of Parallelism for a Distributed Computer System.

    DTIC Science & Technology

    1982-01-01

    that parallel execution of the processes comprising an application program will defray U the overhead costs of distributed computing . This...of Different Approaches to Distributed Computing ", Proceedings of the Ist International Conference on Distributed Comput er Systems, Huntsville, AL...Oct. 1-5, 1979), pp. 222-232. [20] Liskov, B., "Primitives for Distributed Computing ", Froceedings of the 7--th Symposium on Operating System

  17. Parallel Implementation of the Box Counting Algorithm in Opencl

    NASA Astrophysics Data System (ADS)

    Mukundan, Ramakrishnan

    2015-06-01

    The box counting algorithm is a well-known method for the computation of the fractal dimension of an image. It is often implemented using a recursive subdivision of the image into a set of regular tiles or boxes. Parallel implementations often try to map the boxes to different compute units, and combine the results to get the total number of boxes intersecting a shape. This paper presents a novel and highly efficient method using Open Computing Language (OpenCL) kernels to perform the computation on a per-pixel basis. The mapping and reduction stages are performed in a single pass, and therefore require the enqueuing of only a single kernel. Each instance of the kernel updates the information pertaining to all the boxes containing the pixel, and simultaneously increments the box counters at multiple levels, thereby eliminating the need for another pass to perform the summation. The complete implementation and coding details of the proposed method are outlined. The performance of the method on different processors are analyzed with respect to varying image sizes.

  18. Parallelization of the Wolff single-cluster algorithm

    NASA Astrophysics Data System (ADS)

    Kaupužs, J.; Rimšāns, J.; Melnik, R. V. N.

    2010-02-01

    A parallel [open multiprocessing (OpenMP)] implementation of the Wolff single-cluster algorithm has been developed and tested for the three-dimensional (3D) Ising model. The developed procedure is generalizable to other lattice spin models and its effectiveness depends on the specific application at hand. The applicability of the developed methodology is discussed in the context of the applications, where a sophisticated shuffling scheme is used to generate pseudorandom numbers of high quality, and an iterative method is applied to find the critical temperature of the 3D Ising model with a great accuracy. For the lattice with linear size L=1024 , we have reached the speedup about 1.79 times on two processors and about 2.67 times on four processors, as compared to the serial code. According to our estimation, the speedup about three times on four processors is reachable for the O(n) models with n≥2 . Furthermore, the application of the developed OpenMP code allows us to simulate larger lattices due to greater operative (shared) memory available.

  19. Parallelization of the Wolff single-cluster algorithm.

    PubMed

    Kaupuzs, J; Rimsāns, J; Melnik, R V N

    2010-02-01

    A parallel [open multiprocessing (OpenMP)] implementation of the Wolff single-cluster algorithm has been developed and tested for the three-dimensional (3D) Ising model. The developed procedure is generalizable to other lattice spin models and its effectiveness depends on the specific application at hand. The applicability of the developed methodology is discussed in the context of the applications, where a sophisticated shuffling scheme is used to generate pseudorandom numbers of high quality, and an iterative method is applied to find the critical temperature of the 3D Ising model with a great accuracy. For the lattice with linear size L=1024, we have reached the speedup about 1.79 times on two processors and about 2.67 times on four processors, as compared to the serial code. According to our estimation, the speedup about three times on four processors is reachable for the O(n) models with n> or =2. Furthermore, the application of the developed OpenMP code allows us to simulate larger lattices due to greater operative (shared) memory available.

  20. Learning theory of distributed spectral algorithms

    NASA Astrophysics Data System (ADS)

    Guo, Zheng-Chu; Lin, Shao-Bo; Zhou, Ding-Xuan

    2017-07-01

    Spectral algorithms have been widely used and studied in learning theory and inverse problems. This paper is concerned with distributed spectral algorithms, for handling big data, based on a divide-and-conquer approach. We present a learning theory for these distributed kernel-based learning algorithms in a regression framework including nice error bounds and optimal minimax learning rates achieved by means of a novel integral operator approach and a second order decomposition of inverse operators. Our quantitative estimates are given in terms of regularity of the regression function, effective dimension of the reproducing kernel Hilbert space, and qualification of the filter function of the spectral algorithm. They do not need any eigenfunction or noise conditions and are better than the existing results even for the classical family of spectral algorithms.

  1. Parallel and Distributed Computational Fluid Dynamics: Experimental Results and Challenges

    NASA Technical Reports Server (NTRS)

    Djomehri, Mohammad Jahed; Biswas, R.; VanderWijngaart, R.; Yarrow, M.

    2000-01-01

    This paper describes several results of parallel and distributed computing using a large scale production flow solver program. A coarse grained parallelization based on clustering of discretization grids combined with partitioning of large grids for load balancing is presented. An assessment is given of its performance on distributed and distributed-shared memory platforms using large scale scientific problems. An experiment with this solver, adapted to a Wide Area Network execution environment is presented. We also give a comparative performance assessment of computation and communication times on both the tightly and loosely-coupled machines.

  2. A Fast parallel tridiagonal algorithm for a class of CFD applications

    NASA Technical Reports Server (NTRS)

    Moitra, Stuti; Sun, Xian-He

    1996-01-01

    The parallel diagonal dominant (PDD) algorithm is an efficient tridiagonal solver. This paper presents for study a variation of the PDD algorithm, the reduced PDD algorithm. The new algorithm maintains the minimum communication provided by the PDD algorithm, but has a reduced operation count. The PDD algorithm also has a smaller operation count than the conventional sequential algorithm for many applications. Accuracy analysis is provided for the reduced PDD algorithm for symmetric Toeplitz tridiagonal (STT) systems. Implementation results on Langley's Intel Paragon and IBM SP2 show that both the PDD and reduced PDD algorithms are efficient and scalable.

  3. Mesh Algorithms for PDE with Sieve I: Mesh Distribution

    DOE PAGES

    Knepley, Matthew G.; Karpeev, Dmitry A.

    2009-01-01

    We have developed a new programming framework, called Sieve, to support parallel numerical partial differential equation(s) (PDE) algorithms operating over distributed meshes. We have also developed a reference implementation of Sieve in C++ as a library of generic algorithms operating on distributed containers conforming to the Sieve interface. Sieve makes instances of the incidence relation, or arrows, the conceptual first-class objects represented in the containers. Further, generic algorithms acting on this arrow container are systematically used to provide natural geometric operations on the topology and also, through duality, on the data. Finally, coverings and duality are used to encode notmore » only individual meshes, but all types of hierarchies underlying PDE data structures, including multigrid and mesh partitions. In order to demonstrate the usefulness of the framework, we show how the mesh partition data can be represented and manipulated using the same fundamental mechanisms used to represent meshes. We present the complete description of an algorithm to encode a mesh partition and then distribute a mesh, which is independent of the mesh dimension, element shape, or embedding. Moreover, data associated with the mesh can be similarly distributed with exactly the same algorithm. The use of a high level of abstraction within the Sieve leads to several benefits in terms of code reuse, simplicity, and extensibility. We discuss these benefits and compare our approach to other existing mesh libraries.« less

  4. DecGPU: distributed error correction on massively parallel graphics processing units using CUDA and MPI.

    PubMed

    Liu, Yongchao; Schmidt, Bertil; Maskell, Douglas L

    2011-03-29

    Next-generation sequencing technologies have led to the high-throughput production of sequence data (reads) at low cost. However, these reads are significantly shorter and more error-prone than conventional Sanger shotgun reads. This poses a challenge for the de novo assembly in terms of assembly quality and scalability for large-scale short read datasets. We present DecGPU, the first parallel and distributed error correction algorithm for high-throughput short reads (HTSRs) using a hybrid combination of CUDA and MPI parallel programming models. DecGPU provides CPU-based and GPU-based versions, where the CPU-based version employs coarse-grained and fine-grained parallelism using the MPI and OpenMP parallel programming models, and the GPU-based version takes advantage of the CUDA and MPI parallel programming models and employs a hybrid CPU+GPU computing model to maximize the performance by overlapping the CPU and GPU computation. The distributed feature of our algorithm makes it feasible and flexible for the error correction of large-scale HTSR datasets. Using simulated and real datasets, our algorithm demonstrates superior performance, in terms of error correction quality and execution speed, to the existing error correction algorithms. Furthermore, when combined with Velvet and ABySS, the resulting DecGPU-Velvet and DecGPU-ABySS assemblers demonstrate the potential of our algorithm to improve de novo assembly quality for de-Bruijn-graph-based assemblers. DecGPU is publicly available open-source software, written in CUDA C++ and MPI. The experimental results suggest that DecGPU is an effective and feasible error correction algorithm to tackle the flood of short reads produced by next-generation sequencing technologies.

  5. The openGL visualization of the 2D parallel FDTD algorithm

    NASA Astrophysics Data System (ADS)

    Walendziuk, Wojciech

    2005-02-01

    This paper presents a way of visualization of a two-dimensional version of a parallel algorithm of the FDTD method. The visualization module was created on the basis of the OpenGL graphic standard with the use of the GLUT interface. In addition, the work includes the results of the efficiency of the parallel algorithm in the form of speedup charts.

  6. A parallel row-based algorithm for standard cell placement with integrated error control

    NASA Technical Reports Server (NTRS)

    Sargent, Jeff S.; Banerjee, Prith

    1989-01-01

    A new row-based parallel algorithm for standard-cell placement targeted for execution on a hypercube multiprocessor is presented. Key features of this implementation include a dynamic simulated-annealing schedule, row-partitioning of the VLSI chip image, and two novel approaches to control error in parallel cell-placement algorithms: (1) Heuristic Cell-Coloring; (2) Adaptive Sequence Length Control.

  7. Advanced algorithms for distributed fusion

    NASA Astrophysics Data System (ADS)

    Gelfand, A.; Smith, C.; Colony, M.; Bowman, C.; Pei, R.; Huynh, T.; Brown, C.

    2008-03-01

    The US Military has been undergoing a radical transition from a traditional "platform-centric" force to one capable of performing in a "Network-Centric" environment. This transformation will place all of the data needed to efficiently meet tactical and strategic goals at the warfighter's fingertips. With access to this information, the challenge of fusing data from across the batttlespace into an operational picture for real-time Situational Awareness emerges. In such an environment, centralized fusion approaches will have limited application due to the constraints of real-time communications networks and computational resources. To overcome these limitations, we are developing a formalized architecture for fusion and track adjudication that allows the distribution of fusion processes over a dynamically created and managed information network. This network will support the incorporation and utilization of low level tracking information within the Army Distributed Common Ground System (DCGS-A) or Future Combat System (FCS). The framework is based on Bowman's Dual Node Network (DNN) architecture that utilizes a distributed network of interlaced fusion and track adjudication nodes to build and maintain a globally consistent picture across all assets.

  8. Parallel volume ray-casting for unstructured-grid data on distributed-memory architectures

    NASA Technical Reports Server (NTRS)

    Ma, Kwan-Liu

    1995-01-01

    As computing technology continues to advance, computational modeling of scientific and engineering problems produces data of increasing complexity: large in size and unstructured in shape. Volume visualization of such data is a challenging problem. This paper proposes a distributed parallel solution that makes ray-casting volume rendering of unstructured-grid data practical. Both the data and the rendering process are distributed among processors. At each processor, ray-casting of local data is performed independent of the other processors. The global image composing processes, which require inter-processor communication, are overlapped with the local ray-casting processes to achieve maximum parallel efficiency. This algorithm differs from previous ones in four ways: it is completely distributed, less view-dependent, reasonably scalable, and flexible. Without using dynamic load balancing, test results on the Intel Paragon using from two to 128 processors show, on average, about 60% parallel efficiency.

  9. Parallel vision algorithms. Annual technical report No. 1, 1 October 1986-30 September 1987

    SciTech Connect

    Ibrahim, H.A.; Kender, J.R.; Brown, L.G.

    1987-10-01

    The objective of this project is to develop and implement, on highly parallel computers, vision algorithms that combine stereo, texture, and multi-resolution techniques for determining local surface orientation and depth. Such algorithms will immediately serve as front-ends for autonomous land vehicle navigation systems. During the first year of the project, efforts have concentrated on two fronts. First, developing and testing the parallel programming environment that will be used to develop, implement and test the parallel vision algorithms. Second, developing and testing multi-resolution stereo, and texture algorithms. This report describes the status and progress on these two fronts. The authors describe first the programming environment developed, and mapping scheme that allows efficient use of the connection machine for pyramid (multi-resolution) algorithms. Second, they present algorithms and test results for multi-resolution stereo, and texture algorithms. Also the initial results of the starting efforts of integrating stereo and texture algorithms are presented.

  10. A matrix-algebraic formulation of distributed-memory maximal cardinality matching algorithms in bipartite graphs

    DOE PAGES

    Azad, Ariful; Buluç, Aydın

    2016-05-16

    We describe parallel algorithms for computing maximal cardinality matching in a bipartite graph on distributed-memory systems. Unlike traditional algorithms that match one vertex at a time, our algorithms process many unmatched vertices simultaneously using a matrix-algebraic formulation of maximal matching. This generic matrix-algebraic framework is used to develop three efficient maximal matching algorithms with minimal changes. The newly developed algorithms have two benefits over existing graph-based algorithms. First, unlike existing parallel algorithms, cardinality of matching obtained by the new algorithms stays constant with increasing processor counts, which is important for predictable and reproducible performance. Second, relying on bulk-synchronous matrix operations,more » these algorithms expose a higher degree of parallelism on distributed-memory platforms than existing graph-based algorithms. We report high-performance implementations of three maximal matching algorithms using hybrid OpenMP-MPI and evaluate the performance of these algorithm using more than 35 real and randomly generated graphs. On real instances, our algorithms achieve up to 200 × speedup on 2048 cores of a Cray XC30 supercomputer. Even higher speedups are obtained on larger synthetically generated graphs where our algorithms show good scaling on up to 16,384 cores.« less

  11. A matrix-algebraic formulation of distributed-memory maximal cardinality matching algorithms in bipartite graphs

    SciTech Connect

    Azad, Ariful; Buluç, Aydın

    2016-05-16

    We describe parallel algorithms for computing maximal cardinality matching in a bipartite graph on distributed-memory systems. Unlike traditional algorithms that match one vertex at a time, our algorithms process many unmatched vertices simultaneously using a matrix-algebraic formulation of maximal matching. This generic matrix-algebraic framework is used to develop three efficient maximal matching algorithms with minimal changes. The newly developed algorithms have two benefits over existing graph-based algorithms. First, unlike existing parallel algorithms, cardinality of matching obtained by the new algorithms stays constant with increasing processor counts, which is important for predictable and reproducible performance. Second, relying on bulk-synchronous matrix operations, these algorithms expose a higher degree of parallelism on distributed-memory platforms than existing graph-based algorithms. We report high-performance implementations of three maximal matching algorithms using hybrid OpenMP-MPI and evaluate the performance of these algorithm using more than 35 real and randomly generated graphs. On real instances, our algorithms achieve up to 200 × speedup on 2048 cores of a Cray XC30 supercomputer. Even higher speedups are obtained on larger synthetically generated graphs where our algorithms show good scaling on up to 16,384 cores.

  12. Scalable data parallel algorithms for texture synthesis using Gibbs random fields.

    PubMed

    Bader, D A; Jaja, J; Chellappa, R

    1995-01-01

    This article introduces scalable data parallel algorithms for image processing. Focusing on Gibbs and Markov random field model representation for textures, we present parallel algorithms for texture synthesis, compression, and maximum likelihood parameter estimation, currently implemented on Thinking Machines CM-2 and CM-5. The use of fine-grained, data parallel processing techniques yields real-time algorithms for texture synthesis and compression that are substantially faster than the previously known sequential implementations. Although current implementations are on Connection Machines, the methodology presented enables machine-independent scalable algorithms for a number of problems in image processing and analysis.

  13. Flood predictions using the parallel version of distributed numerical physical rainfall-runoff model TOPKAPI

    NASA Astrophysics Data System (ADS)

    Boyko, Oleksiy; Zheleznyak, Mark

    2015-04-01

    The original numerical code TOPKAPI-IMMS of the distributed rainfall-runoff model TOPKAPI ( Todini et al, 1996-2014) is developed and implemented in Ukraine. The parallel version of the code has been developed recently to be used on multiprocessors systems - multicore/processors PC and clusters. Algorithm is based on binary-tree decomposition of the watershed for the balancing of the amount of computation for all processors/cores. Message passing interface (MPI) protocol is used as a parallel computing framework. The numerical efficiency of the parallelization algorithms is demonstrated for the case studies for the flood predictions of the mountain watersheds of the Ukrainian Carpathian regions. The modeling results is compared with the predictions based on the lumped parameters models.

  14. The development of a scalable parallel 3-D CFD algorithm for turbomachinery. M.S. Thesis Final Report

    NASA Technical Reports Server (NTRS)

    Luke, Edward Allen

    1993-01-01

    Two algorithms capable of computing a transonic 3-D inviscid flow field about rotating machines are considered for parallel implementation. During the study of these algorithms, a significant new method of measuring the performance of parallel algorithms is developed. The theory that supports this new method creates an empirical definition of scalable parallel algorithms that is used to produce quantifiable evidence that a scalable parallel application was developed. The implementation of the parallel application and an automated domain decomposition tool are also discussed.

  15. High-Performance Computation of Distributed-Memory Parallel 3D Voronoi and Delaunay Tessellation

    SciTech Connect

    Peterka, Tom; Morozov, Dmitriy; Phillips, Carolyn

    2014-11-14

    Computing a Voronoi or Delaunay tessellation from a set of points is a core part of the analysis of many simulated and measured datasets: N-body simulations, molecular dynamics codes, and LIDAR point clouds are just a few examples. Such computational geometry methods are common in data analysis and visualization; but as the scale of simulations and observations surpasses billions of particles, the existing serial and shared-memory algorithms no longer suffice. A distributed-memory scalable parallel algorithm is the only feasible approach. The primary contribution of this paper is a new parallel Delaunay and Voronoi tessellation algorithm that automatically determines which neighbor points need to be exchanged among the subdomains of a spatial decomposition. Other contributions include periodic and wall boundary conditions, comparison of our method using two popular serial libraries, and application to numerous science datasets.

  16. Implementation of Parallel Dynamic Simulation on Shared-Memory vs. Distributed-Memory Environments

    SciTech Connect

    Jin, Shuangshuang; Chen, Yousu; Wu, Di; Diao, Ruisheng; Huang, Zhenyu

    2015-12-09

    Power system dynamic simulation computes the system response to a sequence of large disturbance, such as sudden changes in generation or load, or a network short circuit followed by protective branch switching operation. It consists of a large set of differential and algebraic equations, which is computational intensive and challenging to solve using single-processor based dynamic simulation solution. High-performance computing (HPC) based parallel computing is a very promising technology to speed up the computation and facilitate the simulation process. This paper presents two different parallel implementations of power grid dynamic simulation using Open Multi-processing (OpenMP) on shared-memory platform, and Message Passing Interface (MPI) on distributed-memory clusters, respectively. The difference of the parallel simulation algorithms and architectures of the two HPC technologies are illustrated, and their performances for running parallel dynamic simulation are compared and demonstrated.

  17. A Simple Physical Optics Algorithm Perfect for Parallel Computing Architecture

    NASA Technical Reports Server (NTRS)

    Imbriale, W. A.; Cwik, T.

    1994-01-01

    A reflector antenna computer program based upon a simple discreet approximation of the radiation integral has proven to be extremely easy to adapt to the parallel computing architecture of the modest number of large-gain computing elements such as are used in the Intel iPSC and Touchstone Delta parallel machines.

  18. A Simple Physical Optics Algorithm Perfect for Parallel Computing Architecture

    NASA Technical Reports Server (NTRS)

    Imbriale, W. A.; Cwik, T.

    1994-01-01

    A reflector antenna computer program based upon a simple discreet approximation of the radiation integral has proven to be extremely easy to adapt to the parallel computing architecture of the modest number of large-gain computing elements such as are used in the Intel iPSC and Touchstone Delta parallel machines.

  19. Speedup properties of phases in the execution profile of distributed parallel programs

    SciTech Connect

    Carlson, B.M. . Computer Systems Research Institute); Wagner, T.D.; Dowdy, L.W. . Dept. of Computer Science); Worley, P.H. )

    1992-08-01

    The execution profile of a distributed-memory parallel program specifies the number of busy processors as a function of time. Periods of homogeneous processor utilization are manifested in many execution profiles. These periods can usually be correlated with the algorithms implemented in the underlying parallel code. Three families of methods for smoothing execution profile data are presented. These approaches simplify the problem of detecting end points of periods of homogeneous utilization. These periods, called phases, are then examined in isolation, and their speedup characteristics are explored. A specific workload executed on an Intel iPSC/860 is used for validation of the techniques described.

  20. A simple parallel prefix algorithm for compact finite-difference schemes

    NASA Technical Reports Server (NTRS)

    Sun, Xian-He; Joslin, Ronald D.

    1993-01-01

    A compact scheme is a discretization scheme that is advantageous in obtaining highly accurate solutions. However, the resulting systems from compact schemes are tridiagonal systems that are difficult to solve efficiently on parallel computers. Considering the almost symmetric Toeplitz structure, a parallel algorithm, simple parallel prefix (SPP), is proposed. The SPP algorithm requires less memory than the conventional LU decomposition and is highly efficient on parallel machines. It consists of a prefix communication pattern and AXPY operations. Both the computation and the communication can be truncated without degrading the accuracy when the system is diagonally dominant. A formal accuracy study was conducted to provide a simple truncation formula. Experimental results were measured on a MasPar MP-1 SIMD machine and on a Cray 2 vector machine. Experimental results show that the simple parallel prefix algorithm is a good algorithm for the compact scheme on high-performance computers.

  1. Multi-Core Parallel Implementation of Data Filtering Algorithm for Multi-Beam Bathymetry Data

    NASA Astrophysics Data System (ADS)

    Liu, Tianyang; Xu, Weiming; Yin, Xiaodong; Zhao, Xiliang

    In order to improve the multi-beam bathymetry data processing speed, we propose a parallel filtering algorithm based on multi thread technology. The algorithm consists of two parts. The first is the parallel data re-order step, in which the surveying area is divided into a regular grid, and the discrete bathymetry data is arranged into each grid by parallel method. The second part is the parallel filtering step, which involves dividing the grid into blocks and parallel executing filtering process in each block. In the experiment, the speedup of the proposed algorithm reaches to about 3.67 with an 8 core computer. The result shows the method can improve computing efficiency significantly comparing to the traditional algorithm.

  2. Dynamic Load-Balancing for Distributed Heterogeneous Computing of Parallel CFD Problems

    NASA Technical Reports Server (NTRS)

    Ecer, A.; Chien, Y. P.; Boenisch, T.; Akay, H. U.

    2000-01-01

    The developed methodology is aimed at improving the efficiency of executing block-structured algorithms on parallel, distributed, heterogeneous computers. The basic approach of these algorithms is to divide the flow domain into many sub- domains called blocks, and solve the governing equations over these blocks. Dynamic load balancing problem is defined as the efficient distribution of the blocks among the available processors over a period of several hours of computations. In environments with computers of different architecture, operating systems, CPU speed, memory size, load, and network speed, balancing the loads and managing the communication between processors becomes crucial. Load balancing software tools for mutually dependent parallel processes have been created to efficiently utilize an advanced computation environment and algorithms. These tools are dynamic in nature because of the chances in the computer environment during execution time. More recently, these tools were extended to a second operating system: NT. In this paper, the problems associated with this application will be discussed. Also, the developed algorithms were combined with the load sharing capability of LSF to efficiently utilize workstation clusters for parallel computing. Finally, results will be presented on running a NASA based code ADPAC to demonstrate the developed tools for dynamic load balancing.

  3. Postscript: Parallel Distributed Processing in Localist Models without Thresholds

    ERIC Educational Resources Information Center

    Plaut, David C.; McClelland, James L.

    2010-01-01

    The current authors reply to a response by Bowers on a comment by the current authors on the original article. Bowers (2010) mischaracterizes the goals of parallel distributed processing (PDP research)--explaining performance on cognitive tasks is the primary motivation. More important, his claim that localist models, such as the interactive…

  4. Postscript: Parallel Distributed Processing in Localist Models without Thresholds

    ERIC Educational Resources Information Center

    Plaut, David C.; McClelland, James L.

    2010-01-01

    The current authors reply to a response by Bowers on a comment by the current authors on the original article. Bowers (2010) mischaracterizes the goals of parallel distributed processing (PDP research)--explaining performance on cognitive tasks is the primary motivation. More important, his claim that localist models, such as the interactive…

  5. Overview of a distributed parallel architecture for speech understanding

    SciTech Connect

    Bronson, E.C.; Siegel, L.J.

    1982-01-01

    The complexity of the speech understanding task requires extensive computation. To improve the processing speed, methods are explored by which tasks involved in speech understanding can be structured for execution on a parallel processing system. An architecture is described in which a speech understanding system is decomposed into a series of distributed processing computation stations. 24 references.

  6. NavP: Structured and Multithreaded Distributed Parallel Programming

    NASA Technical Reports Server (NTRS)

    Pan, Lei; Xu, Jingling

    2006-01-01

    This slide presentation reviews some of the issues around distributed parallel programming. It compares and contrast two methods of programming: Single Program Multiple Data (SPMD) with the Navigational Programming (NAVP). It then reviews the distributed sequential computing (DSC) method and the methodology of NavP. Case studies are presented. It also reviews the work that is being done to enable the NavP system.

  7. GPU based cloud system for high-performance arrhythmia detection with parallel k-NN algorithm.

    PubMed

    Tae Joon Jun; Hyun Ji Park; Hyuk Yoo; Young-Hak Kim; Daeyoung Kim

    2016-08-01

    In this paper, we propose an GPU based Cloud system for high-performance arrhythmia detection. Pan-Tompkins algorithm is used for QRS detection and we optimized beat classification algorithm with K-Nearest Neighbor (K-NN). To support high performance beat classification on the system, we parallelized beat classification algorithm with CUDA to execute the algorithm on virtualized GPU devices on the Cloud system. MIT-BIH Arrhythmia database is used for validation of the algorithm. The system achieved about 93.5% of detection rate which is comparable to previous researches while our algorithm shows 2.5 times faster execution time compared to CPU only detection algorithm.

  8. Programming environment for parallel-vision algorithms. Final technical report, February 1988-December 1989

    SciTech Connect

    Brown, C.

    1990-04-11

    This contract developed and disseminated papers, ideas, algorithms, analysis, software, applications, and implementations for parallel programming environments for computer vision and for vision applications. The work has been widely reported and highly influential. The most significant work centered on the Butterfly Parallel Processor, the MaxVideo pipelined parallel image processor, and the development of the real-time computer vision laboratory. For the Butterfly, the Psyche multi-model operating system was developed and the CONSUL autoparallelizing compiler was designed. Much basic and influential performance monitoring and debugging work was completed, resulting in working systems and novel algorithms. There was also significant research in systems and applications using other parallel architectures in the laboratory, such as the MaxVideo parallel pipelined image processor. The contract developed a heterogeneous parallel architecture involving pipelined and MIMD parallelism and integrated it with a robot head.

  9. A parallel algorithm for switch-level timing simulation on a hypercube multiprocessor

    NASA Technical Reports Server (NTRS)

    Rao, Hariprasad Nannapaneni

    1989-01-01

    The parallel approach to speeding up simulation is studied, specifically the simulation of digital LSI MOS circuitry on the Intel iPSC/2 hypercube. The simulation algorithm is based on RSIM, an event driven switch-level simulator that incorporates a linear transistor model for simulating digital MOS circuits. Parallel processing techniques based on the concepts of Virtual Time and rollback are utilized so that portions of the circuit may be simulated on separate processors, in parallel for as large an increase in speed as possible. A partitioning algorithm is also developed in order to subdivide the circuit for parallel processing.

  10. A sweep algorithm for massively parallel simulation of circuit-switched networks

    NASA Technical Reports Server (NTRS)

    Gaujal, Bruno; Greenberg, Albert G.; Nicol, David M.

    1992-01-01

    A new massively parallel algorithm is presented for simulating large asymmetric circuit-switched networks, controlled by a randomized-routing policy that includes trunk-reservation. A single instruction multiple data (SIMD) implementation is described, and corresponding experiments on a 16384 processor MasPar parallel computer are reported. A multiple instruction multiple data (MIMD) implementation is also described, and corresponding experiments on an Intel IPSC/860 parallel computer, using 16 processors, are reported. By exploiting parallelism, our algorithm increases the possible execution rate of such complex simulations by as much as an order of magnitude.

  11. A parallel encryption algorithm for dual-core processor based on chaotic map

    NASA Astrophysics Data System (ADS)

    Liu, Jiahui; Song, Dahua; Xu, Yiqiu

    2011-12-01

    In this paper, we propose a parallel chaos-based encryption scheme in order to take advantage of the dual-core processor. The chaos-based cryptosystem is combinatorially generated by the logistic map and Fibonacci sequence. Fibonacci sequence is employed to convert the value of the logistic map to integer data. The parallel algorithm is designed with a master/slave communication model with the Message Passing Interface (MPI). The experimental results show that chaotic cryptosystem possesses good statistical properties, and the parallel algorithm provides more enhanced performance against the serial version of the algorithm. It is suitable for encryption/decryption large sensitive data or multimedia.

  12. Parallel low-memory quasi-Newton optimization algorithm for molecular structure

    NASA Astrophysics Data System (ADS)

    Klemsa, Jakub; Řezáč, Jan

    2013-10-01

    We present a novel parallel gradient optimization algorithm designed for the optimization of molecular geometry - the parallel preconditioned LBFGS (PP-LBFGS) method. In each step, several additional gradient calculations (performed in parallel with the calculation of the potential) are used to improve the most important elements of the Hessian. The sparsity of the connectivity matrix and the graph theory are used to estimate multiple Hessian elements from each additional gradient calculation. The simplest variant of the algorithm, which requires 4 gradient evaluations per cycle, converges 2×-4× faster than the LBFGS algorithm, depending on the size of the system.

  13. Parallel algorithms for semi-Lagrangian transport in global atmospheric circulation models

    SciTech Connect

    Drake, J.B.; Worley, P.H.; Michalakes, J.; Foster, I.T.

    1995-02-01

    Global atmospheric circulation models (GCM) typically have three primary algorithmic components: columnar physics, spectral transform, and semi-Lagrangian transport. In developing parallel implementations, these three components are equally important and can be examined somewhat independently. A two-dimensional horizontal data decomposition of the three-dimensional computational grid leaves all physics computations on processor, and the only efficiency issues arise in load balancing. A recently completed study by the authors of different approaches to parallelizing the spectral transform showed several viable algorithms. Preliminary results of an analogous study of algorithmic alternatives for parallel semi-Lagrangian transport are described here.

  14. Object-oriented parallel algorithms for computing three-dimensional isopycnal flow

    SciTech Connect

    Concus, Paul; Golub, Gene H.; Sun, Yong

    2000-12-01

    In this paper, we derive an object-oriented parallel algorithm for three-dimensional isopycnal flow simulations. The matrix formulation is central to the algorithm. It enables us to apply an efficient preconditioned conjugate gradient linear solver for the global system of equations, and leads naturally to an object-oriented data structure design and parallel implementation. We discuss as well, in less detail, a similar algorithm based on the reduced system, suitable also for parallel computation. Favorable performances are observed on test problems.

  15. New SIMD Algorithms for Cluster Labeling on Parallel Computers

    NASA Astrophysics Data System (ADS)

    Apostolakis, John; Coddington, Paul; Marinari, Enzo

    Cluster algorithms are non-local Monte Carlo update schemes which can greatly increase the efficiency of computer simulations of spin models of magnets. The major computational task in these algorithms is connected component labeling, to identify clusters of connected sites on a lattice. We have devised some new SIMD component labeling algorithms, and implemented them on the Connection Machine. We investigate their performance when applied to the cluster update of the two-dimensional Ising spin model. These algorithms could also be applied to other problems which use connected component labeling, such as percolation and image analysis.

  16. Parallelization of exoplanets detection algorithms based on field rotation; example of the MOODS algorithm for SPHERE

    NASA Astrophysics Data System (ADS)

    Mattei, D.; Smith, I.; Ferrari, A.; Carbillet, M.

    2010-10-01

    Post-processing for exoplanet detection using direct imaging requires large data cubes and/or sophisticated signal processing technics. For alt-azimuthal mounts, a projection effect called field rotation makes the potential planet rotate in a known manner on the set of images. For ground based telescopes that use extreme adaptive optics and advanced coronagraphy, technics based on field rotation are already broadly used and still under progress. In most such technics, for a given initial position of the planet the planet intensity estimate is a linear function of the set of images. However, due to field rotation the modified instrumental response applied is not shift invariant like usual linear filters. Testing all possible initial positions is therefore very time-consuming. To reduce the time process, we propose to deal with each subset of initial positions computed on a different machine using parallelization programming. In particular, the MOODS algorithm dedicated to the VLT-SPHERE instrument, that estimates jointly the light contributions of the star and the potential exoplanet, is parallelized on the Observatoire de la Cote d'Azur cluster. Different parallelization methods (OpenMP, MPI, Jobs Array) have been elaborated for the initial MOODS code and compared to each other. The one finally chosen splits the initial positions on the processors available by accounting at best for the different constraints of the cluster structure: memory, job submission queues, number of available CPUs, cluster average load. At the end, a standard set of images is satisfactorily processed in a few hours instead of a few days.

  17. Measurements of parallel electron velocity distributions using whistler wave absorption

    SciTech Connect

    Thuecks, D. J.; Skiff, F.; Kletzing, C. A.

    2012-08-15

    We describe a diagnostic to measure the parallel electron velocity distribution in a magnetized plasma that is overdense ({omega}{sub pe} > {omega}{sub ce}). This technique utilizes resonant absorption of whistler waves by electrons with velocities parallel to a background magnetic field. The whistler waves were launched and received by a pair of dipole antennas immersed in a cylindrical discharge plasma at two positions along an axial background magnetic field. The whistler wave frequency was swept from somewhat below and up to the electron cyclotron frequency {omega}{sub ce}. As the frequency was swept, the wave was resonantly absorbed by the part of the electron phase space density which was Doppler shifted into resonance according to the relation {omega}-k{sub ||v||} = {omega}{sub ce}. The measured absorption is directly related to the reduced parallel electron distribution function integrated along the wave trajectory. The background theory and initial results from this diagnostic are presented here. Though this diagnostic is best suited to detect tail populations of the parallel electron distribution function, these first results show that this diagnostic is also rather successful in measuring the bulk plasma density and temperature both during the plasma discharge and into the afterglow.

  18. Strong Scalability Study of Distributed Memory Parallel Markov Random Fields Using Graph Partitioning

    NASA Astrophysics Data System (ADS)

    Heinemann, Colleen

    Research in material science is increasingly reliant on image-based data from experiments, demanding construction of new analysis tools that help scientists discover information from digital images. Because there is such a wide variety of materials and image modalities, detecting different compounds from imaged materials continues to be a challenging task. A vast collection of algorithms for filtering, image segmentation, and texture description have facilitated and improved accuracy for sample measurements (see Chapter 1 Introduction and Literature Review). Despite this, the community still lacks scalable, general purpose, easily configurable image analysis frameworks that allow pattern detection on different imaging modalities across multiple scales. The need for such a framework was the motivation behind the development of a distributed-memory parallel Markov Random Field based framework. Markov Random Field (MRF) algorithms provide the ability to explore contextual information about a given dataset. Given the complexity of such algorithms, however, they are limited by performance when running serial. Thus, running in some sort of parallel fashion is necessary. The effects are twofold. Not only does running the MRF algorithm in parallel provide the ability to run current datasets faster and more efficiently, it also provides the ability for datasets to continue to grow in size and still be able to be run with such frameworks. The variation of the Markov Random Field algorithm utilized in this study first oversegments the given input image and constructs a graph model based on photometric and geometric distances. Next, the resulting graph model is refactored specifically into the MRF model to target image segmentation. Finally, a distributed approach is used for the optimization process to obtain the best labeling for the graph, which is essentially the goal of using a MRF algorithm. Given the concept of using a distributed memory parallel framework, specifically

  19. Rapid optimization of tension distribution for cable-driven parallel manipulators with redundant cables

    NASA Astrophysics Data System (ADS)

    Ouyang, Bo; Shang, Weiwei

    2016-03-01

    The solution of tension distributions is infinite for cable-driven parallel manipulators(CDPMs) with redundant cables. A rapid optimization method for determining the optimal tension distribution is presented. The new optimization method is primarily based on the geometry properties of a polyhedron and convex analysis. The computational efficiency of the optimization method is improved by the designed projection algorithm, and a fast algorithm is proposed to determine which two of the lines are intersected at the optimal point. Moreover, a method for avoiding the operating point on the lower tension limit is developed. Simulation experiments are implemented on a six degree-of-freedom(6-DOF) CDPM with eight cables, and the results indicate that the new method is one order of magnitude faster than the standard simplex method. The optimal distribution of tension distribution is thus rapidly established on real-time by the proposed method.

  20. Estimation of distribution algorithms with Kikuchi approximations.

    PubMed

    Santana, Roberto

    2005-01-01

    The question of finding feasible ways for estimating probability distributions is one of the main challenges for Estimation of Distribution Algorithms (EDAs). To estimate the distribution of the selected solutions, EDAs use factorizations constructed according to graphical models. The class of factorizations that can be obtained from these probability models is highly constrained. Expanding the class of factorizations that could be employed for probability approximation is a necessary step for the conception of more robust EDAs. In this paper we introduce a method for learning a more general class of probability factorizations. The method combines a reformulation of a probability approximation procedure known in statistical physics as the Kikuchi approximation of energy, with a novel approach for finding graph decompositions. We present the Markov Network Estimation of Distribution Algorithm (MN-EDA), an EDA that uses Kikuchi approximations to estimate the distribution, and Gibbs Sampling (GS) to generate new points. A systematic empirical evaluation of MN-EDA is done in comparison with different Bayesian network based EDAs. From our experiments we conclude that the algorithm can outperform other EDAs that use traditional methods of probability approximation in the optimization of functions with strong interactions among their variables.

  1. Globalized Newton-Krylov-Schwarz algorithms and software for parallel implicit CFD.

    SciTech Connect

    Gropp, W. D.; Keyes, D. E.; McInnes, L. C.; Tidriri, M. D.; Mathematics and Computer Science; Old Dominion Univ.; Iowa State Univ.

    2000-01-01

    Implicit solution methods are important in applications modeled by PDEs with disparate temporal and spatial scales. Because such applications require high resolution with reasonable turnaround, parallelization is essential. The pseudo-transient matrix-free Newton-Krylov-Schwarz ({psi}NKS) algorithmic framework is presented as a widely applicable answer. This article shows that for the classical problem of three-dimensional transonic Euler flow about an M6 wing, {psi}NKS can simultaneously deliver globalized, asymptotically rapid convergence through adaptive pseudo-transient continuation and Newton's method; reasonable parallelizability for an implicit method through deferred synchronization and favorable communication-to-computation scaling in the Krylov linear solver; and high per processor performance through attention to distributed memory and cache locality, especially through the Schwarz preconditioner. Two discouraging features of {psi}NKS methods are their sensitivity to the coding of the underlying PDE discretization and the large number of parameters that must be selected to govern convergence. The authors therefore distill several recommendations from their experience and reading of the literature on various algorithmic components of {psi}NKS, and they describe a freely available MPI-based portable parallel software implementation of the solver employed here.

  2. Globalized Newton-Krylov-Schwarz Algorithms and Software for Parallel Implicit CFD

    NASA Technical Reports Server (NTRS)

    Gropp, W. D.; Keyes, D. E.; McInnes, L. C.; Tidriri, M. D.

    1998-01-01

    Implicit solution methods are important in applications modeled by PDEs with disparate temporal and spatial scales. Because such applications require high resolution with reasonable turnaround, "routine" parallelization is essential. The pseudo-transient matrix-free Newton-Krylov-Schwarz (Psi-NKS) algorithmic framework is presented as an answer. We show that, for the classical problem of three-dimensional transonic Euler flow about an M6 wing, Psi-NKS can simultaneously deliver: globalized, asymptotically rapid convergence through adaptive pseudo- transient continuation and Newton's method-, reasonable parallelizability for an implicit method through deferred synchronization and favorable communication-to-computation scaling in the Krylov linear solver; and high per- processor performance through attention to distributed memory and cache locality, especially through the Schwarz preconditioner. Two discouraging features of Psi-NKS methods are their sensitivity to the coding of the underlying PDE discretization and the large number of parameters that must be selected to govern convergence. We therefore distill several recommendations from our experience and from our reading of the literature on various algorithmic components of Psi-NKS, and we describe a freely available, MPI-based portable parallel software implementation of the solver employed here.

  3. Efficient parallel and out of core algorithms for constructing large bi-directed de Bruijn graphs.

    PubMed

    Kundeti, Vamsi K; Rajasekaran, Sanguthevar; Dinh, Hieu; Vaughn, Matthew; Thapar, Vishal

    2010-11-15

    Assembling genomic sequences from a set of overlapping reads is one of the most fundamental problems in computational biology. Algorithms addressing the assembly problem fall into two broad categories - based on the data structures which they employ. The first class uses an overlap/string graph and the second type uses a de Bruijn graph. However with the recent advances in short read sequencing technology, de Bruijn graph based algorithms seem to play a vital role in practice. Efficient algorithms for building these massive de Bruijn graphs are very essential in large sequencing projects based on short reads. In an earlier work, an O(n/p) time parallel algorithm has been given for this problem. Here n is the size of the input and p is the number of processors. This algorithm enumerates all possible bi-directed edges which can overlap with a node and ends up generating Θ(nΣ) messages (Σ being the size of the alphabet). In this paper we present a Θ(n/p) time parallel algorithm with a communication complexity that is equal to that of parallel sorting and is not sensitive to Σ. The generality of our algorithm makes it very easy to extend it even to the out-of-core model and in this case it has an optimal I/O complexity of Θ(nlog(n/B)Blog(M/B)) (M being the main memory size and B being the size of the disk block). We demonstrate the scalability of our parallel algorithm on a SGI/Altix computer. A comparison of our algorithm with the previous approaches reveals that our algorithm is faster--both asymptotically and practically. We demonstrate the scalability of our sequential out-of-core algorithm by comparing it with the algorithm used by VELVET to build the bi-directed de Bruijn graph. Our experiments reveal that our algorithm can build the graph with a constant amount of memory, which clearly outperforms VELVET. We also provide efficient algorithms for the bi-directed chain compaction problem. The bi-directed de Bruijn graph is a fundamental data structure for

  4. Distributed and parallel approach for handle and perform huge datasets

    NASA Astrophysics Data System (ADS)

    Konopko, Joanna

    2015-12-01

    Big Data refers to the dynamic, large and disparate volumes of data comes from many different sources (tools, machines, sensors, mobile devices) uncorrelated with each others. It requires new, innovative and scalable technology to collect, host and analytically process the vast amount of data. Proper architecture of the system that perform huge data sets is needed. In this paper, the comparison of distributed and parallel system architecture is presented on the example of MapReduce (MR) Hadoop platform and parallel database platform (DBMS). This paper also analyzes the problem of performing and handling valuable information from petabytes of data. The both paradigms: MapReduce and parallel DBMS are described and compared. The hybrid architecture approach is also proposed and could be used to solve the analyzed problem of storing and processing Big Data.

  5. Privacy-Preserving Location-Based Query Using Location Indexes and Parallel Searching in Distributed Networks

    PubMed Central

    Liu, Lei; Zhao, Jing

    2014-01-01

    An efficient location-based query algorithm of protecting the privacy of the user in the distributed networks is given. This algorithm utilizes the location indexes of the users and multiple parallel threads to search and select quickly all the candidate anonymous sets with more users and their location information with more uniform distribution to accelerate the execution of the temporal-spatial anonymous operations, and it allows the users to configure their custom-made privacy-preserving location query requests. The simulated experiment results show that the proposed algorithm can offer simultaneously the location query services for more users and improve the performance of the anonymous server and satisfy the anonymous location requests of the users. PMID:24790579

  6. Privacy-preserving location-based query using location indexes and parallel searching in distributed networks.

    PubMed

    Zhong, Cheng; Liu, Lei; Zhao, Jing

    2014-01-01

    An efficient location-based query algorithm of protecting the privacy of the user in the distributed networks is given. This algorithm utilizes the location indexes of the users and multiple parallel threads to search and select quickly all the candidate anonymous sets with more users and their location information with more uniform distribution to accelerate the execution of the temporal-spatial anonymous operations, and it allows the users to configure their custom-made privacy-preserving location query requests. The simulated experiment results show that the proposed algorithm can offer simultaneously the location query services for more users and improve the performance of the anonymous server and satisfy the anonymous location requests of the users.

  7. More Effective Distributed ML via a Stale Synchronous Parallel Parameter Server

    PubMed Central

    Ho, Qirong; Cipar, James; Cui, Henggang; Kim, Jin Kyu; Lee, Seunghak; Gibbons, Phillip B.; Gibson, Garth A.; Ganger, Gregory R.; Xing, Eric P.

    2014-01-01

    We propose a parameter server system for distributed ML, which follows a Stale Synchronous Parallel (SSP) model of computation that maximizes the time computational workers spend doing useful work on ML algorithms, while still providing correctness guarantees. The parameter server provides an easy-to-use shared interface for read/write access to an ML model’s values (parameters and variables), and the SSP model allows distributed workers to read older, stale versions of these values from a local cache, instead of waiting to get them from a central storage. This significantly increases the proportion of time workers spend computing, as opposed to waiting. Furthermore, the SSP model ensures ML algorithm correctness by limiting the maximum age of the stale values. We provide a proof of correctness under SSP, as well as empirical results demonstrating that the SSP model achieves faster algorithm convergence on several different ML problems, compared to fully-synchronous and asynchronous schemes. PMID:25400488

  8. Application of integration algorithms in a parallel processing environment for the simulation of jet engines

    SciTech Connect

    Krosel, S.M.; Milner, E.J.

    1982-01-01

    Illustrates the application of predictor-corrector integration algorithms developed for the digital parallel processing environment. The algorithms are implemented and evaluated through the use of a software simulator which provides an approximate representation of the parallel processing hardware. Test cases which focus on the use of the algorithms are presented and a specific application using a linear model of a turbofan engine is considered. Results are presented showing the effects of integration step size and the number of processors on simulation accuracy. Real-time performance, inter-processor communication and algorithm startup are also discussed. 10 references.

  9. PDoublePop: An implementation of parallel genetic algorithm for function optimization

    NASA Astrophysics Data System (ADS)

    Tsoulos, Ioannis G.; Tzallas, Alexandros; Tsalikakis, Dimitris

    2016-12-01

    A software for the implementation of parallel genetic algorithms is presented in this article. The underlying genetic algorithm is aimed to locate the global minimum of a multidimensional function inside a rectangular hyperbox. The proposed software named PDoublePop implements a client-server model for parallel genetic algorithms with advanced features for the local genetic algorithms such as: an enhanced stopping rule, an advanced mutation scheme and periodical application of a local search procedure. The user may code the objective function either in C++ or in Fortran77. The method is tested on a series of well-known test functions and the results are reported.

  10. Application of integration algorithms in a parallel processing environment for the simulation of jet engines

    NASA Technical Reports Server (NTRS)

    Krosel, S. M.; Milner, E. J.

    1982-01-01

    The application of Predictor corrector integration algorithms developed for the digital parallel processing environment are investigated. The algorithms are implemented and evaluated through the use of a software simulator which provides an approximate representation of the parallel processing hardware. Test cases which focus on the use of the algorithms are presented and a specific application using a linear model of a turbofan engine is considered. Results are presented showing the effects of integration step size and the number of processors on simulation accuracy. Real time performance, interprocessor communication, and algorithm startup are also discussed.

  11. Compact Graph Representations and Parallel Connectivity Algorithms for Massive Dynamic Network Analysis

    SciTech Connect

    Madduri, Kamesh; Bader, David A.

    2009-02-15

    Graph-theoretic abstractions are extensively used to analyze massive data sets. Temporal data streams from socioeconomic interactions, social networking web sites, communication traffic, and scientific computing can be intuitively modeled as graphs. We present the first study of novel high-performance combinatorial techniques for analyzing large-scale information networks, encapsulating dynamic interaction data in the order of billions of entities. We present new data structures to represent dynamic interaction networks, and discuss algorithms for processing parallel insertions and deletions of edges in small-world networks. With these new approaches, we achieve an average performance rate of 25 million structural updates per second and a parallel speedup of nearly28 on a 64-way Sun UltraSPARC T2 multicore processor, for insertions and deletions to a small-world network of 33.5 million vertices and 268 million edges. We also design parallel implementations of fundamental dynamic graph kernels related to connectivity and centrality queries. Our implementations are freely distributed as part of the open-source SNAP (Small-world Network Analysis and Partitioning) complex network analysis framework.

  12. The lower bound on complexity of parallel branch-and-bound algorithm for subset sum problem

    NASA Astrophysics Data System (ADS)

    Kolpakov, Roman; Posypkin, Mikhail

    2016-10-01

    The subset sum problem is a particular case of the Boolean knapsack problem where each item has the price equal to its weight. This problem can be informally stated as searching for most dense packing of a set of items into a box with limited capacity. Recently, coarse-grain parallelization approaches to Branch-and-Bound (B&B) method attracted some attention due to the growing popularity of weakly-connected distributed computing platforms. In this paper we consider one of such approaches for solving the subset sum problem. One of the processors (manager) performs some number of B&B steps on the first stage with generating some subproblems. On the second stage, the generated subproblems are sent to other processors, one subproblem per processor. The processors solve completely the received subproblems, the manager collects all the obtained solutions and chooses the optimal one. For this algorithm we formally define the parallel execution model (frontal scheme of parallelization) and the notion of the frontal scheme complexity. We study the frontal scheme complexity for a series of subset sum problems.

  13. Semirigorous synchronous sublattice algorithm for parallel kinetic Monte Carlo simulations of thin film growth

    NASA Astrophysics Data System (ADS)

    Shim, Yunsic; Amar, Jacques G.

    2005-03-01

    The standard kinetic Monte Carlo algorithm is an extremely efficient method to carry out serial simulations of dynamical processes such as thin film growth. However, in some cases it is necessary to study systems over extended time and length scales, and therefore a parallel algorithm is desired. Here we describe an efficient, semirigorous synchronous sublattice algorithm for parallel kinetic Monte Carlo simulations. The accuracy and parallel efficiency are studied as a function of diffusion rate, processor size, and number of processors for a variety of simple models of epitaxial growth. The effects of fluctuations on the parallel efficiency are also studied. Since only local communications are required, linear scaling behavior is observed, e.g., the parallel efficiency is independent of the number of processors for fixed processor size.

  14. Parallel OSEM Reconstruction Algorithm for Fully 3-D SPECT on a Beowulf Cluster.

    PubMed

    Rong, Zhou; Tianyu, Ma; Yongjie, Jin

    2005-01-01

    In order to improve the computation speed of ordered subset expectation maximization (OSEM) algorithm for fully 3-D single photon emission computed tomography (SPECT) reconstruction, an experimental beowulf-type cluster was built and several parallel reconstruction schemes were described. We implemented a single-program-multiple-data (SPMD) parallel 3-D OSEM reconstruction algorithm based on message passing interface (MPI) and tested it with combinations of different number of calculating processors and different size of voxel grid in reconstruction (64×64×64 and 128×128×128). Performance of parallelization was evaluated in terms of the speedup factor and parallel efficiency. This parallel implementation methodology is expected to be helpful to make fully 3-D OSEM algorithms more feasible in clinical SPECT studies.

  15. Parallel and serial variational inequality decomposition algorithms for multicommodity market equilibrium problems

    SciTech Connect

    Nagurney, A.; Kim, D.S.

    1989-01-01

    The authors have applied parallel and serial variational inequality (VI) diagonal decomposition algorithms to large-scale multicommodity market equilibrium problems. These decomposition algorithms resolve the VI problems into single commodity problems, which are then solved as quadratic programming problems. The algorithms are implemented on an IBM 3090-600E, and randomly generated linear and nonlinear problems with as many as 100 markets and 12 commodities are solved. The computational results demonstrate that the parallel diagonal decomposition scheme is amenable to parallelization. This is the first time that multicommodity equilibrium problems of this scale and level of generality have been solved. Furthermore, this is the first study to compare the efficiencies of parallel and serial VI decomposition algorithms. Although the authors have selected as a prototype an equilibrium problem in economics, virtually any equilibrium problem can be formulated and studied as a variational inequality problem. Hence, their results are not limited to applications in economics and operations research.

  16. Parallelized event chain algorithm for dense hard sphere and polymer systems

    SciTech Connect

    Kampmann, Tobias A. Boltz, Horst-Holger; Kierfeld, Jan

    2015-01-15

    We combine parallelization and cluster Monte Carlo for hard sphere systems and present a parallelized event chain algorithm for the hard disk system in two dimensions. For parallelization we use a spatial partitioning approach into simulation cells. We find that it is crucial for correctness to ensure detailed balance on the level of Monte Carlo sweeps by drawing the starting sphere of event chains within each simulation cell with replacement. We analyze the performance gains for the parallelized event chain and find a criterion for an optimal degree of parallelization. Because of the cluster nature of event chain moves massive parallelization will not be optimal. Finally, we discuss first applications of the event chain algorithm to dense polymer systems, i.e., bundle-forming solutions of attractive semiflexible polymers.

  17. LYDIAN: An Extensible Educational Animation Environment for Distributed Algorithms

    ERIC Educational Resources Information Center

    Koldehofe, Boris; Papatriantafilou, Marina; Tsigas, Philippas

    2006-01-01

    LYDIAN is an environment to support the teaching and learning of distributed algorithms. It provides a collection of distributed algorithms as well as continuous animations. Users can combine algorithms and animations with arbitrary network structures defining the interconnection and behavior of the distributed algorithm. Further, it facilitates…

  18. A computational fluid dynamics algorithm on a massively parallel computer

    NASA Technical Reports Server (NTRS)

    Jespersen, Dennis C.; Levit, Creon

    1989-01-01

    The implementation and performance of a finite-difference algorithm for the compressible Navier-Stokes equations in two or three dimensions on the Connection Machine are described. This machine is a single-instruction multiple-data machine with up to 65536 physical processors. The implicit portion of the algorithm is of particular interest. Running times and megadrop rates are given for two- and three-dimensional problems. Included are comparisons with the standard codes on a Cray X-MP/48.

  19. Two-dimensional frequency-domain visco-elastic full waveform inversion: Parallel algorithms, optimization and performance

    NASA Astrophysics Data System (ADS)

    Brossier, R.

    2011-04-01

    Full waveform inversion (FWI) is an appealing seismic data-fitting procedure for the derivation of high-resolution quantitative models of the subsurface at various scales. Full modelling and inversion of visco-elastic waves from multiple seismic sources allow for the recovering of different physical parameters, although they remain computationally challenging tasks. An efficient massively parallel, frequency-domain FWI algorithm is implemented here on large-scale distributed-memory platforms for imaging two-dimensional visco-elastic media. The resolution of the elastodynamic equations, as the forward problem of the inversion, is performed in the frequency domain on unstructured triangular meshes, using a low-order finite element discontinuous Galerkin method. The linear system resulting from discretization of the forward problem is solved with a parallel direct solver. The inverse problem, which is presented as a non-linear local optimization problem, is solved in parallel with a quasi-Newton method, and this allows for reliable estimation of multiple classes of visco-elastic parameters. Two levels of parallelism are implemented in the algorithm, based on message passing interfaces and multi-threading, for optimal use of computational time and the core-memory resources available on modern distributed-memory multi-core computational platforms. The algorithm allows for imaging of realistic targets at various scales, ranging from near-surface geotechnic applications to crustal-scale exploration.

  20. Parallel vision algorithms. Annual technical report No. 2, 1 October 1987-28 December 1988

    SciTech Connect

    Ibrahim, H.A.; Kender, J.R.; Brown, L.G.

    1989-01-01

    This Second Annual Technical Report covers the project activities during the period from October 1, 1987 through December 31, 1988. The objective of this project is to develop and implement, on highly parallel computers, vision algorithms that combine stereo, texture, and multi-resolution techniques for determining local surface orientation and depth. Such algorithms can serve as front-end components of autonomous land-vehicle vision systems. During the second year of the project, efforts concentrated on the following: first, implementing and testing on the Connection Machine the parallel programming environment that will be used to develop, implement and test our parallel vision algorithms; second, implementing and testing primitives for the multi-resolution stereo and texture algorithms, in this environment. Also, efforts were continued to refine techniques used in the texture algorithms, and to develop a system that integrates information from several shape-from-texture methods. This report describes the status and progress of these efforts. The authors describe first the programming environment implementation, and how to use it. They summarize the results for multi-resolution based depth-interpolation algorithms on parallel architectures. Then, they present algorithms and test results for the texture algorithms. Finally, the results of the efforts of integrating information from various shape-from-texture algorithms are presented.

  1. Implementation and Performance of a Binary Lattice Gas Algorithm on Parallel Processor Systems

    NASA Astrophysics Data System (ADS)

    Hayot, F.; Mandal, M.; Sadayappan, P.

    1989-02-01

    We study the performance of a lattice gas binary algorithm on a "real arithmetic" machine, a 32 processor INTEL iPSC hypercube. The implementation is based on so-called multi-spin coding techniques. From the measured performance we extrapolate to larger and more powerful parallel systems. Comparisons are made with "bit" machines, such as the parallel Connection Machine.

  2. Towards a HPC-oriented parallel implementation of a learning algorithm for bioinformatics applications

    PubMed Central

    2014-01-01

    Background The huge quantity of data produced in Biomedical research needs sophisticated algorithmic methodologies for its storage, analysis, and processing. High Performance Computing (HPC) appears as a magic bullet in this challenge. However, several hard to solve parallelization and load balancing problems arise in this context. Here we discuss the HPC-oriented implementation of a general purpose learning algorithm, originally conceived for DNA analysis and recently extended to treat uncertainty on data (U-BRAIN). The U-BRAIN algorithm is a learning algorithm that finds a Boolean formula in disjunctive normal form (DNF), of approximately minimum complexity, that is consistent with a set of data (instances) which may have missing bits. The conjunctive terms of the formula are computed in an iterative way by identifying, from the given data, a family of sets of conditions that must be satisfied by all the positive instances and violated by all the negative ones; such conditions allow the computation of a set of coefficients (relevances) for each attribute (literal), that form a probability distribution, allowing the selection of the term literals. The great versatility that characterizes it, makes U-BRAIN applicable in many of the fields in which there are data to be analyzed. However the memory and the execution time required by the running are of O(n3) and of O(n5) order, respectively, and so, the algorithm is unaffordable for huge data sets. Results We find mathematical and programming solutions able to lead us towards the implementation of the algorithm U-BRAIN on parallel computers. First we give a Dynamic Programming model of the U-BRAIN algorithm, then we minimize the representation of the relevances. When the data are of great size we are forced to use the mass memory, and depending on where the data are actually stored, the access times can be quite different. According to the evaluation of algorithmic efficiency based on the Disk Model, in order to

  3. Towards a HPC-oriented parallel implementation of a learning algorithm for bioinformatics applications.

    PubMed

    D'Angelo, Gianni; Rampone, Salvatore

    2014-01-01

    The huge quantity of data produced in Biomedical research needs sophisticated algorithmic methodologies for its storage, analysis, and processing. High Performance Computing (HPC) appears as a magic bullet in this challenge. However, several hard to solve parallelization and load balancing problems arise in this context. Here we discuss the HPC-oriented implementation of a general purpose learning algorithm, originally conceived for DNA analysis and recently extended to treat uncertainty on data (U-BRAIN). The U-BRAIN algorithm is a learning algorithm that finds a Boolean formula in disjunctive normal form (DNF), of approximately minimum complexity, that is consistent with a set of data (instances) which may have missing bits. The conjunctive terms of the formula are computed in an iterative way by identifying, from the given data, a family of sets of conditions that must be satisfied by all the positive instances and violated by all the negative ones; such conditions allow the computation of a set of coefficients (relevances) for each attribute (literal), that form a probability distribution, allowing the selection of the term literals. The great versatility that characterizes it, makes U-BRAIN applicable in many of the fields in which there are data to be analyzed. However the memory and the execution time required by the running are of O(n(3)) and of O(n(5)) order, respectively, and so, the algorithm is unaffordable for huge data sets. We find mathematical and programming solutions able to lead us towards the implementation of the algorithm U-BRAIN on parallel computers. First we give a Dynamic Programming model of the U-BRAIN algorithm, then we minimize the representation of the relevances. When the data are of great size we are forced to use the mass memory, and depending on where the data are actually stored, the access times can be quite different. According to the evaluation of algorithmic efficiency based on the Disk Model, in order to reduce the costs of

  4. A portable implementation of ARPACK for distributed memory parallel architectures

    SciTech Connect

    Maschhoff, K.J.; Sorensen, D.C.

    1996-12-31

    ARPACK is a package of Fortran 77 subroutines which implement the Implicitly Restarted Arnoldi Method used for solving large sparse eigenvalue problems. A parallel implementation of ARPACK is presented which is portable across a wide range of distributed memory platforms and requires minimal changes to the serial code. The communication layers used for message passing are the Basic Linear Algebra Communication Subprograms (BLACS) developed for the ScaLAPACK project and Message Passing Interface(MPI).

  5. WAMR: An adaptive wavelet method for the simulation of compressible reacting flow. Part II. The parallel algorithm

    NASA Astrophysics Data System (ADS)

    Paolucci, Samuel; Zikoski, Zachary J.; Grenga, Temistocle

    2014-09-01

    The Wavelet Adaptive Multiresolution Representation (WAMR) algorithm is parallelized using a domain decomposition approach suitable to a wide range of distributed-memory parallel architectures. The method is applied to the solution of two unsteady, compressible, reactive flow problems and includes detailed diffusive transport and chemical kinetics models. The first problem is a cellular detonation in a hydrogen-oxygen-argon mixture. The second problem corresponds to the ignition and combustion of a hydrogen bubble by a shock wave in air. In both cases, results agree favorably with previous computational results.

  6. Pruning Neural Networks with Distribution Estimation Algorithms

    SciTech Connect

    Cantu-Paz, E

    2003-01-15

    This paper describes the application of four evolutionary algorithms to the pruning of neural networks used in classification problems. Besides of a simple genetic algorithm (GA), the paper considers three distribution estimation algorithms (DEAs): a compact GA, an extended compact GA, and the Bayesian Optimization Algorithm. The objective is to determine if the DEAs present advantages over the simple GA in terms of accuracy or speed in this problem. The experiments used a feed forward neural network trained with standard back propagation and public-domain and artificial data sets. The pruned networks seemed to have better or equal accuracy than the original fully-connected networks. Only in a few cases, pruning resulted in less accurate networks. We found few differences in the accuracy of the networks pruned by the four EAs, but found important differences in the execution time. The results suggest that a simple GA with a small population might be the best algorithm for pruning networks on the data sets we tested.

  7. Current distribution within parallel-connected battery cells

    NASA Astrophysics Data System (ADS)

    Brand, Martin J.; Hofmann, Markus H.; Steinhardt, Marco; Schuster, Simon F.; Jossen, Andreas

    2016-12-01

    Parallel connections can be found in many battery applications. Therefore, it is of high interest to understand how the current distributes within parallel battery cells. However, the number of publications on this topic is comparably low. Furthermore, the measurement set-ups are often not clearly defined in existing publications and it is likely that additional impedances distorted the measured current distributions. In this work, the principles of current distributions within parallel-connected battery cells are investigated theoretically, with an equivalent electric circuit model, and by measurements. A measurement set-up is developed that does not significantly influence the measurements, as proven by impedance spectroscopy. On this basis, two parameter scenarios are analyzed: the ΔR scenario stands for battery cells with differing impedances but similar capacities and the ΔC scenario for differing capacities and similar impedances. Out of 172 brand-new lithium-ion battery cells, pairs are built to practically represent the ΔR and ΔC scenarios. If a charging pulse is applied to the ΔR scenario, currents initially divide according to the current divider but equalize in constant current phases. The current divider has no effect on ΔC pairs but, as a rule of thumb for long-term loads, currents divide according to the battery cell capacities.

  8. Distributed parallel computing in stochastic modeling of groundwater systems.

    PubMed

    Dong, Yanhui; Li, Guomin; Xu, Haizhen

    2013-03-01

    Stochastic modeling is a rapidly evolving, popular approach to the study of the uncertainty and heterogeneity of groundwater systems. However, the use of Monte Carlo-type simulations to solve practical groundwater problems often encounters computational bottlenecks that hinder the acquisition of meaningful results. To improve the computational efficiency, a system that combines stochastic model generation with MODFLOW-related programs and distributed parallel processing is investigated. The distributed computing framework, called the Java Parallel Processing Framework, is integrated into the system to allow the batch processing of stochastic models in distributed and parallel systems. As an example, the system is applied to the stochastic delineation of well capture zones in the Pinggu Basin in Beijing. Through the use of 50 processing threads on a cluster with 10 multicore nodes, the execution times of 500 realizations are reduced to 3% compared with those of a serial execution. Through this application, the system demonstrates its potential in solving difficult computational problems in practical stochastic modeling. © 2012, The Author(s). Groundwater © 2012, National Ground Water Association.

  9. Perm Web: remote parallel and distributed volume visualization

    SciTech Connect

    Wittenbrink, C.M.; Kim, K.; Story, J.; Pang, A.; Hollerbach, K.; Max, N.

    1997-01-01

    In this paper we present a system for visualizing volume data from remote supercomputers (PermWeb). We have developed both parallel volume rendering algorithms, and the World Wide Web software for accessing the data at the remote sites. The implementation uses Hypertext Markup Language (HTML), Java, and Common Gateway Interface (CGI) scripts to connect World Wide Web (WWW) servers/clients to our volume renderers. The front ends are interactive Java classes for specification of view, shading, and classification inputs. We present performance results, and implementation details for connections to our computing resources at the University of California Santa Cruz including a MasPar MP-2, SGI Reality Engine-RE2, and SGI Challenge machines. We apply the system to the task of visualizing trabecular bone from finite element simulations. Fast volume rendering on remote compute servers through a web interface allows us to increase the accessibility of the results to more users. User interface issues, overviews of parallel algorithm developments, and overall system interfaces and protocols are presented. Access is available through Uniform Resource Locator (URL) http://www.cse.ucsc.edu/research/slvg/. 26 refs., 7 figs.

  10. Parallel genetic algorithm with population-based sampling approach to discrete optimization under uncertainty

    NASA Astrophysics Data System (ADS)

    Subramanian, Nithya

    Optimization under uncertainty accounts for design variables and external parameters or factors with probabilistic distributions instead of fixed deterministic values; it enables problem formulations that might maximize or minimize an expected value while satisfying constraints using probabilities. For discrete optimization under uncertainty, a Monte Carlo Sampling (MCS) approach enables high-accuracy estimation of expectations but it also results in high computational expense. The Genetic Algorithm (GA) with a Population-Based Sampling (PBS) technique enables optimization under uncertainty with discrete variables at a lower computational expense than using Monte Carlo sampling for every fitness evaluation. Population-Based Sampling uses fewer samples in the exploratory phase of the GA and a larger number of samples when `good designs' start emerging over the generations. This sampling technique therefore reduces the computational effort spent on `poor designs' found in the initial phase of the algorithm. Parallel computation evaluates the expected value of the objective and constraints in parallel to facilitate reduced wall-clock time. A customized stopping criterion is also developed for the GA with Population-Based Sampling. The stopping criterion requires that the design with the minimum expected fitness value to have at least 99% constraint satisfaction and to have accumulated at least 10,000 samples. The average change in expected fitness values in the last ten consecutive generations is also monitored. The optimization of composite laminates using ply orientation angle as a discrete variable provides an example to demonstrate further developments of the GA with Population-Based Sampling for discrete optimization under uncertainty. The focus problem aims to reduce the expected weight of the composite laminate while treating the laminate's fiber volume fraction and externally applied loads as uncertain quantities following normal distributions. Construction of

  11. Reducing communication costs in the conjugate gradient algorithm on distributed memory multiprocessors

    SciTech Connect

    D'Azevedo, E.F.; Romine, C.H.

    1992-09-01

    The standard formulation of the conjugate gradient algorithm involves two inner product computations. The results of these two inner products are needed to update the search direction and the computed solution. In a distributed memory parallel environment, the computation and subsequent distribution of these two values requires two separate communication and synchronization phases. In this paper, we present a mathematically equivalent rearrangement of the standard algorithm that reduces the number of communication phases. We give a second derivation of the modified conjugate gradient algorithm in terms of the natural relationship with the underlying Lanczos process. We also present empirical evidence of the stability of this modified algorithm.

  12. Reducing communication costs in the conjugate gradient algorithm on distributed memory multiprocessors

    SciTech Connect

    D`Azevedo, E.F.; Romine, C.H.

    1992-09-01

    The standard formulation of the conjugate gradient algorithm involves two inner product computations. The results of these two inner products are needed to update the search direction and the computed solution. In a distributed memory parallel environment, the computation and subsequent distribution of these two values requires two separate communication and synchronization phases. In this paper, we present a mathematically equivalent rearrangement of the standard algorithm that reduces the number of communication phases. We give a second derivation of the modified conjugate gradient algorithm in terms of the natural relationship with the underlying Lanczos process. We also present empirical evidence of the stability of this modified algorithm.

  13. Event parallelism: Distributed memory parallel computing for high energy physics experiments

    SciTech Connect

    Nash, T.

    1989-05-01

    This paper describes the present and expected future development of distributed memory parallel computers for high energy physics experiments. It covers the use of event parallel microprocessor farms, particularly at Fermilab, including both ACP multiprocessors and farms of MicroVAXES. These systems have proven very cost effective in the past. A case is made for moving to the more open environment of UNIX and RISC processors. The 2nd Generation ACP Multiprocessor System, which is based on powerful RISC systems, is described. Given the promise of still more extraordinary increases in processor performance, a new emphasis on point to point, rather than bussed, communication will be required. Developments in this direction are described. 6 figs.

  14. A Parallel Processing Algorithm for Remote Sensing Classification

    NASA Technical Reports Server (NTRS)

    Gualtieri, J. Anthony

    2005-01-01

    A current thread in parallel computation is the use of cluster computers created by networking a few to thousands of commodity general-purpose workstation-level commuters using the Linux operating system. For example on the Medusa cluster at NASA/GSFC, this provides for super computing performance, 130 G(sub flops) (Linpack Benchmark) at moderate cost, $370K. However, to be useful for scientific computing in the area of Earth science, issues of ease of programming, access to existing scientific libraries, and portability of existing code need to be considered. In this paper, I address these issues in the context of tools for rendering earth science remote sensing data into useful products. In particular, I focus on a problem that can be decomposed into a set of independent tasks, which on a serial computer would be performed sequentially, but with a cluster computer can be performed in parallel, giving an obvious speedup. To make the ideas concrete, I consider the problem of classifying hyperspectral imagery where some ground truth is available to train the classifier. In particular I will use the Support Vector Machine (SVM) approach as applied to hyperspectral imagery. The approach will be to introduce notions about parallel computation and then to restrict the development to the SVM problem. Pseudocode (an outline of the computation) will be described and then details specific to the implementation will be given. Then timing results will be reported to show what speedups are possible using parallel computation. The paper will close with a discussion of the results.

  15. Multiscale Architectures and Parallel Algorithms for Video Object Tracking

    DTIC Science & Technology

    2011-10-01

    than Government procurement does not in any way obligate the U.S. Government. The fact that the Government formulated or supplied the drawings...SUPPLEMENTARY NOTES 14. ABSTRACT Implementation and performance of an extended set of parallel multicore video processing chain of modules were investigated...Processing Elements (SPEs) without any cache but 256 KB of local store memory. . . . . . . . . . . . . . . . . . . 6 3 N-CET video processing chain

  16. Parallel algorithms and archtectures for computational structural mechanics

    NASA Technical Reports Server (NTRS)

    Patrick, Merrell; Ma, Shing; Mahajan, Umesh

    1989-01-01

    The determination of the fundamental (lowest) natural vibration frequencies and associated mode shapes is a key step used to uncover and correct potential failures or problem areas in most complex structures. However, the computation time taken by finite element codes to evaluate these natural frequencies is significant, often the most computationally intensive part of structural analysis calculations. There is continuing need to reduce this computation time. This study addresses this need by developing methods for parallel computation.

  17. Parallel algorithms for simulating continuous time Markov chains

    NASA Technical Reports Server (NTRS)

    Nicol, David M.; Heidelberger, Philip

    1992-01-01

    We have previously shown that the mathematical technique of uniformization can serve as the basis of synchronization for the parallel simulation of continuous-time Markov chains. This paper reviews the basic method and compares five different methods based on uniformization, evaluating their strengths and weaknesses as a function of problem characteristics. The methods vary in their use of optimism, logical aggregation, communication management, and adaptivity. Performance evaluation is conducted on the Intel Touchstone Delta multiprocessor, using up to 256 processors.

  18. Advanced Algorithms and Automation Tools for Discrete Ordinates Methods in Parallel Environments

    SciTech Connect

    Alireza Haghighat

    2003-05-07

    This final report discusses major accomplishments of a 3-year project under the DOE's NEER Program. The project has developed innovative and automated algorithms, codes, and tools for solving the discrete ordinates particle transport method efficiently in parallel environments. Using a number of benchmark and real-life problems, the performance and accuracy of the new algorithms have been measured and analyzed.

  19. Parallel Directionally Split Solver Based on Reformulation of Pipelined Thomas Algorithm

    NASA Technical Reports Server (NTRS)

    Povitsky, A.

    1998-01-01

    In this research an efficient parallel algorithm for 3-D directionally split problems is developed. The proposed algorithm is based on a reformulated version of the pipelined Thomas algorithm that starts the backward step computations immediately after the completion of the forward step computations for the first portion of lines This algorithm has data available for other computational tasks while processors are idle from the Thomas algorithm. The proposed 3-D directionally split solver is based on the static scheduling of processors where local and non-local, data-dependent and data-independent computations are scheduled while processors are idle. A theoretical model of parallelization efficiency is used to define optimal parameters of the algorithm, to show an asymptotic parallelization penalty and to obtain an optimal cover of a global domain with subdomains. It is shown by computational experiments and by the theoretical model that the proposed algorithm reduces the parallelization penalty about two times over the basic algorithm for the range of the number of processors (subdomains) considered and the number of grid nodes per subdomain.

  20. Comparison of several stochastic parallel optimization algorithms for adaptive optics system without a wavefront sensor

    NASA Astrophysics Data System (ADS)

    Yang, Huizhen; Li, Xinyang

    2011-04-01

    Optimizing the system performance metric directly is an important method for correcting wavefront aberrations in an adaptive optics (AO) system where wavefront sensing methods are unavailable or ineffective. An appropriate "Deformable Mirror" control algorithm is the key to successful wavefront correction. Based on several stochastic parallel optimization control algorithms, an adaptive optics system with a 61-element Deformable Mirror (DM) is simulated. Genetic Algorithm (GA), Stochastic Parallel Gradient Descent (SPGD), Simulated Annealing (SA) and Algorithm Of Pattern Extraction (Alopex) are compared in convergence speed and correction capability. The results show that all these algorithms have the ability to correct for atmospheric turbulence. Compared with least squares fitting, they almost obtain the best correction achievable for the 61-element DM. SA is the fastest and GA is the slowest in these algorithms. The number of perturbation by GA is almost 20 times larger than that of SA, 15 times larger than SPGD and 9 times larger than Alopex.

  1. Constant-time parallel sorting algorithm and its optical implementation using smart pixels.

    PubMed

    Louri, A; Hatch, J A; Na, J

    1995-06-10

    Sorting is a fundamental operation that has important implications in a vast number of areas. For instance, sorting is heavily utilized in applications such as database machines, in which hashing techniques are used to accelerate data-processing algorithms. It is also the basis for interprocessor message routing and has strong implications in video telecommunications. However, high-speed electronic sorting networks are difficult to implement with VLSI technology because of the dense, global connectivity required. Optics eliminates this bottleneck by offering global interconnects, massive parallelism, and noninterfering communications. We present a parallel sorting algorithm and its efficient optical implementation. The algorithm sorts n data elements in few steps, independent of the number of elements to be sorted. Thus it is a constant-time sorting algorithm [i.e., O(1) time]. We also estimate the system's performance to show that the proposed sorting algorithm can provide at least 2 orders of magnitude improvement in execution time over conventional electronic algorithms.

  2. Communication-Avoiding Parallel Recursive Algorithms for Matrix Multiplication

    DTIC Science & Technology

    2013-05-17

    given subproblem share the same m-digit suffix . After the above communication is performed, the layout of Si and Ti has parameters (n/2, P/7, s − 1...MULTIPLICATION 11 Algorithm 2 CAPS, in detail Input: A, B, are n× n matrices P = number of processors rank = processor number base-7 as an array M = local

  3. Image coding using parallel implementations of the embedded zerotree wavelet algorithm

    NASA Astrophysics Data System (ADS)

    Creusere, Charles D.

    1996-03-01

    We explore here the implementation of Shapiro's embedded zerotree wavelet (EZW) image coding algorithms on an array of parallel processors. To this end, we first consider the problem of parallelizing the basic wavelet transform, discussing past work in this area and the compatibility of that work with the zerotree coding process. From this discussion, we present a parallel partitioning of the transform which is computationally efficient and which allows the wavelet coefficients to be coded with little or no additional inter-processor communication. The key to achieving low data dependence between the processors is to ensure that each processor contains only entire zerotrees of wavelet coefficients after the decomposition is complete. We next quantify the rate-distortion tradeoffs associated with different levels of parallelization for a few variations of the basic coding algorithm. Studying these results, we conclude that the quality of the coder decreases as the number of parallel processors used to implement it increases. Noting that the performance of the parallel algorithm might be unacceptably poor for large processor arrays, we also develop an alternate algorithm which always achieves the same rate-distortion performance as the original sequential EZW algorithm at the cost of higher complexity and reduced scalability.

  4. Concurrent extensions to the FORTRAN language for parallel programming of computational fluid dynamics algorithms

    NASA Technical Reports Server (NTRS)

    Weeks, Cindy Lou

    1986-01-01

    Experiments were conducted at NASA Ames Research Center to define multi-tasking software requirements for multiple-instruction, multiple-data stream (MIMD) computer architectures. The focus was on specifying solutions for algorithms in the field of computational fluid dynamics (CFD). The program objectives were to allow researchers to produce usable parallel application software as soon as possible after acquiring MIMD computer equipment, to provide researchers with an easy-to-learn and easy-to-use parallel software language which could be implemented on several different MIMD machines, and to enable researchers to list preferred design specifications for future MIMD computer architectures. Analysis of CFD algorithms indicated that extensions of an existing programming language, adaptable to new computer architectures, provided the best solution to meeting program objectives. The CoFORTRAN Language was written in response to these objectives and to provide researchers a means to experiment with parallel software solutions to CFD algorithms on machines with parallel architectures.

  5. Estimation of theoretical maximum speedup ratio for parallel computing of grid-based distributed hydrological models

    NASA Astrophysics Data System (ADS)

    Liu, Junzhi; Zhu, A.-Xing; Qin, Cheng-Zhi

    2013-10-01

    Theoretical maximum speedup ratio (TMSR) can be used as a goal for improving parallel computing methods for distributed hydrological models. Different types of distributed hydrological models need different TMSR estimation methods because of the different computing characteristics of models. Existing TMSR estimation methods, such as those for sub-basin based distributed hydrological models, are inappropriate for grid-based distributed hydrological models. In this paper, we proposed a TMSR estimation method suitable for grid-based distributed hydrological models. With this method, TMSRs for hillslope processes and channel routing processes are calculated separately and then combined to obtain the overall TMSR. A branch-and-bound algorithm and a critical path heuristic algorithm are used to estimate TMSRs for parallel computing of hillslope processes and channel routing processes, respectively. The overall TMSR is calculated according to the proportions of computing these two types of processes. A preliminary application showed that the more the number of sub-basins, the larger the TMSRs and that the compact watersheds had larger TMSRs than the long narrow watersheds.

  6. An efficient parallel algorithm for the solution of a tridiagonal linear system of equations

    NASA Technical Reports Server (NTRS)

    Stone, H. S.

    1971-01-01

    Tridiagonal linear systems of equations are solved on conventional serial machines in a time proportional to N, where N is the number of equations. The conventional algorithms do not lend themselves directly to parallel computations on computers of the ILLIAC IV class, in the sense that they appear to be inherently serial. An efficient parallel algorithm is presented in which computation time grows as log sub 2 N. The algorithm is based on recursive doubling solutions of linear recurrence relations, and can be used to solve recurrence relations of all orders.

  7. On the impact of communication complexity in the design of parallel numerical algorithms

    NASA Technical Reports Server (NTRS)

    Gannon, D.; Vanrosendale, J.

    1984-01-01

    This paper describes two models of the cost of data movement in parallel numerical algorithms. One model is a generalization of an approach due to Hockney, and is suitable for shared memory multiprocessors where each processor has vector capabilities. The other model is applicable to highly parallel nonshared memory MIMD systems. In the second model, algorithm performance is characterized in terms of the communication network design. Techniques used in VLSI complexity theory are also brought in, and algorithm independent upper bounds on system performance are derived for several problems that are important to scientific computation.

  8. GPU-based parallel algorithm for blind image restoration using midfrequency-based methods

    NASA Astrophysics Data System (ADS)

    Xie, Lang; Luo, Yi-han; Bao, Qi-liang

    2013-08-01

    GPU-based general-purpose computing is a new branch of modern parallel computing, so the study of parallel algorithms specially designed for GPU hardware architecture is of great significance. In order to solve the problem of high computational complexity and poor real-time performance in blind image restoration, the midfrequency-based algorithm for blind image restoration was analyzed and improved in this paper. Furthermore, a midfrequency-based filtering method is also used to restore the image hardly with any recursion or iteration. Combining the algorithm with data intensiveness, data parallel computing and GPU execution model of single instruction and multiple threads, a new parallel midfrequency-based algorithm for blind image restoration is proposed in this paper, which is suitable for stream computing of GPU. In this algorithm, the GPU is utilized to accelerate the estimation of class-G point spread functions and midfrequency-based filtering. Aiming at better management of the GPU threads, the threads in a grid are scheduled according to the decomposition of the filtering data in frequency domain after the optimization of data access and the communication between the host and the device. The kernel parallelism structure is determined by the decomposition of the filtering data to ensure the transmission rate to get around the memory bandwidth limitation. The results show that, with the new algorithm, the operational speed is significantly increased and the real-time performance of image restoration is effectively improved, especially for high-resolution images.

  9. Commodity cluster and hardware-based massively parallel implementations of hyperspectral imaging algorithms

    NASA Astrophysics Data System (ADS)

    Plaza, Antonio; Chang, Chein-I.; Plaza, Javier; Valencia, David

    2006-05-01

    The incorporation of hyperspectral sensors aboard airborne/satellite platforms is currently producing a nearly continual stream of multidimensional image data, and this high data volume has soon introduced new processing challenges. The price paid for the wealth spatial and spectral information available from hyperspectral sensors is the enormous amounts of data that they generate. Several applications exist, however, where having the desired information calculated quickly enough for practical use is highly desirable. High computing performance of algorithm analysis is particularly important in homeland defense and security applications, in which swift decisions often involve detection of (sub-pixel) military targets (including hostile weaponry, camouflage, concealment, and decoys) or chemical/biological agents. In order to speed-up computational performance of hyperspectral imaging algorithms, this paper develops several fast parallel data processing techniques. Techniques include four classes of algorithms: (1) unsupervised classification, (2) spectral unmixing, and (3) automatic target recognition, and (4) onboard data compression. A massively parallel Beowulf cluster (Thunderhead) at NASA's Goddard Space Flight Center in Maryland is used to measure parallel performance of the proposed algorithms. In order to explore the viability of developing onboard, real-time hyperspectral data compression algorithms, a Xilinx Virtex-II field programmable gate array (FPGA) is also used in experiments. Our quantitative and comparative assessment of parallel techniques and strategies may help image analysts in selection of parallel hyperspectral algorithms for specific applications.

  10. Parallel Implementation of the Wideband DOA Algorithm on the IBM Cell BE Processor

    DTIC Science & Technology

    2010-05-01

    Abstract—The Multiple Signal Classification ( MUSIC ) algorithm is a powerful technique for determining the Direction of Arrival (DOA) of signals...Broadband Engine Processor (Cell BE). The process of adapting the serial based MUSIC algorithm to the Cell BE will be analyzed in terms of parallelism and...using Multiple Signal Classification MUSIC algorithm [4] • Computation of Focus matrix • Computation of number of sources • Separation of Signal

  11. OpenMP Parallelization and Optimization of Graph-based Machine Learning Algorithms

    DTIC Science & Technology

    2016-05-01

    OpenMP Parallelization and Optimization of Graph-based Machine Learning Algorithms Zhaoyi Meng, Alice Koniges, Yun (Helen) He, Samuel Williams...within a class is stronger than that between different classes. This is a standard problem in machine learning. Recently, novel algorithms have been pro... Machine Learning Algorithm 3 In the vanishing limit we recover the graph TV functional [7]. Different fidelity items are added to GL functional for

  12. Parallel field line and stream line tracing algorithms for space physics applications

    NASA Astrophysics Data System (ADS)

    Toth, G.; de Zeeuw, D.; Monostori, G.

    2004-05-01

    Field line and stream line tracing is required in various space physics applications, such as the coupling of the global magnetosphere and inner magnetosphere models, the coupling of the solar energetic particle and heliosphere models, or the modeling of comets, where the multispecies chemical equations are solved along stream lines of a steady state solution obtained with single fluid MHD model. Tracing a vector field is an inherently serial process, which is difficult to parallelize. This is especially true when the data corresponding to the vector field is distributed over a large number of processors. We designed algorithms for the various applications, which scale well to a large number of processors. In the first algorithm the computational domain is divided into blocks. Each block is on a single processor. The algorithm folows the vector field inside the blocks, and calculates a mapping of the block surfaces. The blocks communicate the values at the coinciding surfaces, and the results are interpolated. Finally all block surfaces are defined and values inside the blocks are obtained. In the second algorithm all processors start integrating along the vector field inside the accessible volume. When the field line leaves the local subdomain, the position and other information is stored in a buffer. Periodically the processors exchange the buffers, and continue integration of the field lines until they reach a boundary. At that point the results are sent back to the originating processor. Efficiency is achieved by a careful phasing of computation and communication. In the third algorithm the results of a steady state simulation are stored on a hard drive. The vector field is contained in blocks. All processors read in all the grid and vector field data and the stream lines are integrated in parallel. If a stream line enters a block, which has already been integrated, the results can be interpolated. By a clever ordering of the blocks the execution speed can be

  13. Parallelization of Finite Element Analysis Codes Using Heterogeneous Distributed Computing

    NASA Technical Reports Server (NTRS)

    Ozguner, Fusun

    1996-01-01

    Performance gains in computer design are quickly consumed as users seek to analyze larger problems to a higher degree of accuracy. Innovative computational methods, such as parallel and distributed computing, seek to multiply the power of existing hardware technology to satisfy the computational demands of large applications. In the early stages of this project, experiments were performed using two large, coarse-grained applications, CSTEM and METCAN. These applications were parallelized on an Intel iPSC/860 hypercube. It was found that the overall speedup was very low, due to large, inherently sequential code segments present in the applications. The overall execution time T(sub par), of the application is dependent on these sequential segments. If these segments make up a significant fraction of the overall code, the application will have a poor speedup measure.

  14. Execution models for mapping programs onto distributed memory parallel computers

    NASA Technical Reports Server (NTRS)

    Sussman, Alan

    1992-01-01

    The problem of exploiting the parallelism available in a program to efficiently employ the resources of the target machine is addressed. The problem is discussed in the context of building a mapping compiler for a distributed memory parallel machine. The paper describes using execution models to drive the process of mapping a program in the most efficient way onto a particular machine. Through analysis of the execution models for several mapping techniques for one class of programs, we show that the selection of the best technique for a particular program instance can make a significant difference in performance. On the other hand, the results of benchmarks from an implementation of a mapping compiler show that our execution models are accurate enough to select the best mapping technique for a given program.

  15. apGA: An adaptive parallel genetic algorithm

    SciTech Connect

    Liepins, G.E. ); Baluja, S. )

    1991-01-01

    We develop apGA, a parallel variant of the standard generational GA, that combines aggressive search with perpetual novelty, yet is able to preserve enough genetic structure to optimally solve variably scaled, non-uniform block deceptive and hierarchical deceptive problems. apGA combines elitism, adaptive mutation, adaptive exponential scaling, and temporal memory. We present empirical results for six classes of problems, including the DeJong test suite. Although we have not investigated hybrids, we note that apGA could be incorporated into other recent GA variants such as GENITOR, CHC, and the recombination stage of mGA. 12 refs., 2 figs., 2 tabs.

  16. A dataflow analysis tool for parallel processing of algorithms

    NASA Technical Reports Server (NTRS)

    Jones, Robert L., III

    1993-01-01

    A graph-theoretic design process and software tool is presented for selecting a multiprocessing scheduling solution for a class of computational problems. The problems of interest are those that can be described using a dataflow graph and are intended to be executed repetitively on a set of identical parallel processors. Typical applications include signal processing and control law problems. Graph analysis techniques are introduced and shown to effectively determine performance bounds, scheduling constraints, and resource requirements. The software tool is shown to facilitate the application of the design process to a given problem.

  17. A parallel and incremental algorithm for efficient unique signature discovery on DNA databases.

    PubMed

    Lee, Hsiao Ping; Sheu, Tzu-Fang; Tang, Chuan Yi

    2010-03-16

    DNA signatures are distinct short nucleotide sequences that provide valuable information that is used for various purposes, such as the design of Polymerase Chain Reaction primers and microarray experiments. Biologists usually use a discovery algorithm to find unique signatures from DNA databases, and then apply the signatures to microarray experiments. Such discovery algorithms require to set some input factors, such as signature length l and mismatch tolerance d, which affect the discovery results. However, suggestions about how to select proper factor values are rare, especially when an unfamiliar DNA database is used. In most cases, biologists typically select factor values based on experience, or even by guessing. If the discovered result is unsatisfactory, biologists change the input factors of the algorithm to obtain a new result. This process is repeated until a proper result is obtained. Implicit signatures under the discovery condition (l, d) are defined as the signatures of length < or = l with mismatch tolerance > or = d. A discovery algorithm that could discover all implicit signatures, such that those that meet the requirements concerning the results, would be more helpful than one that depends on trial and error. However, existing discovery algorithms do not address the need to discover all implicit signatures. This work proposes two discovery algorithms - the consecutive multiple discovery (CMD) algorithm and the parallel and incremental signature discovery (PISD) algorithm. The PISD algorithm is designed for efficiently discovering signatures under a certain discovery condition. The algorithm finds new results by using previously discovered results as candidates, rather than by using the whole database. The PISD algorithm further increases discovery efficiency by applying parallel computing. The CMD algorithm is designed to discover implicit signatures efficiently. It uses the PISD algorithm as a kernel routine to discover implicit signatures

  18. Constraint treatment techniques and parallel algorithms for multibody dynamic analysis. Ph.D. Thesis

    NASA Technical Reports Server (NTRS)

    Chiou, Jin-Chern

    1990-01-01

    Computational procedures for kinematic and dynamic analysis of three-dimensional multibody dynamic (MBD) systems are developed from the differential-algebraic equations (DAE's) viewpoint. Constraint violations during the time integration process are minimized and penalty constraint stabilization techniques and partitioning schemes are developed. The governing equations of motion, a two-stage staggered explicit-implicit numerical algorithm, are treated which takes advantage of a partitioned solution procedure. A robust and parallelizable integration algorithm is developed. This algorithm uses a two-stage staggered central difference algorithm to integrate the translational coordinates and the angular velocities. The angular orientations of bodies in MBD systems are then obtained by using an implicit algorithm via the kinematic relationship between Euler parameters and angular velocities. It is shown that the combination of the present solution procedures yields a computationally more accurate solution. To speed up the computational procedures, parallel implementation of the present constraint treatment techniques, the two-stage staggered explicit-implicit numerical algorithm was efficiently carried out. The DAE's and the constraint treatment techniques were transformed into arrowhead matrices to which Schur complement form was derived. By fully exploiting the sparse matrix structural analysis techniques, a parallel preconditioned conjugate gradient numerical algorithm is used to solve the systems equations written in Schur complement form. A software testbed was designed and implemented in both sequential and parallel computers. This testbed was used to demonstrate the robustness and efficiency of the constraint treatment techniques, the accuracy of the two-stage staggered explicit-implicit numerical algorithm, and the speed up of the Schur-complement-based parallel preconditioned conjugate gradient algorithm on a parallel computer.

  19. A Self Consistent Multiprocessor Space Charge Algorithm that is Almost Embarrassingly Parallel

    SciTech Connect

    Edward Nissen, B. Erdelyi, S.L. Manikonda

    2012-07-01

    We present a space charge code that is self consistent, massively parallelizeable, and requires very little communication between computer nodes; making the calculation almost embarrassingly parallel. This method is implemented in the code COSY Infinity where the differential algebras used in this code are important to the algorithm's proper functioning. The method works by calculating the self consistent space charge distribution using the statistical moments of the test particles, and converting them into polynomial series coefficients. These coefficients are combined with differential algebraic integrals to form the potential, and electric fields. The result is a map which contains the effects of space charge. This method allows for massive parallelization since its statistics based solver doesn't require any binning of particles, and only requires a vector containing the partial sums of the statistical moments for the different nodes to be passed. All other calculations are done independently. The resulting maps can be used to analyze the system using normal form analysis, as well as advance particles in numbers and at speeds that were previously impossible.

  20. Intracellular signalling proteins as smart' agents in parallel distributed processes.

    PubMed

    Fisher, M J; Paton, R C; Matsuno, K

    1999-06-01

    In eucaryotic organisms, responses to external signals are mediated by a repertoire of intracellular signalling pathways that ultimately bring about the activation/inactivation of protein kinases and/or protein phosphatases. Until relatively recently, little thought had been given to the intracellular distribution of the components of these signalling pathways. However, experimental evidence from a diverse range of organisms indicates that rather than being freely distributed, many of the protein components of signalling cascades show a significant degree of spatial organisation. Here, we briefly review the roles of 'anchor' 'scaffold' and 'adaptor' proteins in the organisation and functioning of intracellular signalling pathways. We then consider some of the parallel distributed processing capacities of these adaptive systems. We focus on signalling proteins-both as individual 'devices' (agents) and as 'networks' (ecologies) of parallel processes. Signalling proteins are described as 'smart thermodynamic machines' which satisfy 'gluing' (functorial) roles in the information economy of the cell. This combines two information-processing views of signalling proteins. Individually, they show 'cognitive' capacities and collectively they integrate (cohere) cellular processes. We exploit these views by drawing comparisons between signalling proteins and verbs. This text/dialogical metaphor also helps refine our view of signalling proteins as context-sensitive information processing agents.

  1. New sampling distributions for evolution algorithms

    NASA Astrophysics Data System (ADS)

    Sweeney, Francis Dermot

    Evolution algorithms are stochastic optimization methods based on evolutionary principles. They have long been used in optimization, and are gaining in popularity. They are particularly useful in high dimensional problems, or in problems where gradient methods fails. Evolution strategies, a class of evolutionary algorithms, are stochastic searches which evolve by mutation. This work proposes a new mutation distribution for use in single objective optimization. Up to now, cost function information obtained by mutations that do not improve fitness has been discarded. In many problems, particularly when cost function calls are expensive, it is desirable to use all available information to guide the search. The new method in this work patches Gaussians of different variances together to create a sampling distribution which delivers mutations designed to direct the search away from regions where low values of fitness have been observed. Analytic results for this new method are derived on idealized problems. The method is compared with existing methods on a range of test problems, and its overall performance attributes are assessed. A new method for multiobjective optimization is also developed. Genetic Algorithms introduce innovation into their populations by a process of bit mutation. This small scale mutation is often insufficient to successfully direct the search, unless the initial population is of sufficient quality. The new method proposed here, termed Rank Biased Sampling, uses the population to create new members, which are resampled across the entire search space from a distribution designed to favor regions which are inadequately represented by the current population. Again, this method is compared to existing methods on some standard test problems. These new optimization methods are then applied to some real-world problems of engineering interest. The optimization routines developed in this work performed well on these applications, and provide good

  2. Algorithms for distributed and mobile sensing

    NASA Astrophysics Data System (ADS)

    Isler, Ibrahim Volkan

    Sensing remote, complex and large environments is an important task that arises in diverse applications including planetary exploration, monitoring forest fires and the surveillance of large factories. Currently, automation of such sensing tasks in complex environments is achieved either by deploying many stationary sensors to the environment, or by mounting a sensor on a mobile device and using the device to sense the environment. The Eighties and Nineties witnessed tremendous advances in both distributed and mobile sensing technologies. To take advantage of these technologies, it is crucial to design algorithms to perform sensing tasks in an autonomous fashion. In this dissertation, we study four fundamental sensing problems that arise in sensing complex environments with distributed and mobile systems. For mobile sensing systems we study exploration and pursuit-evasion problems. In the exploration problem, the goal is to design a strategy for a mobile robot so that the robot sees every point in an unknown environment as quickly as possible. In the pursuit-evasion problem, the goal is to design a strategy for a pursuer to capture an adversarial evader. For distributed sensing systems we study placement and assignment problems. In the placement problem, the goal is to place sensors to an environment so that every point in the environment is in the range of at least one sensor. The assignment problem deals with the issue of assigning targets to sensors in a network, so that overall error in estimating the position of the targets is minimized. We present algorithms to perform these sensing tasks in an efficient fashion. Performance guarantees of the algorithms are mathematically proven and evaluated by simulations.

  3. The Expected Time Complexity of Parallel Graph and Digraph Algorithms.

    DTIC Science & Technology

    1982-04-01

    2n) processors [Hirschberg, Chandra, Sarwate, 79] and O(log n) time in SP-RAM with O(n+m) processors [Shiloah, Vishkin, 80 ]. [ JaJa , 78J has an O(log...n log d) time and O(n 3/log n) processors algorithm for the P-RAM where d is the depth of the graph. For the biconnected components, [ Savage, JaJa ...log n) processors where k is the number of components and m =edges of the graph. For the minimum spanning tree [-Savace, Jaja , 81] given an O(log 2n

  4. A block-wise approximate parallel implementation for ART algorithm on CUDA-enabled GPU.

    PubMed

    Fan, Zhongyin; Xie, Yaoqin

    2015-01-01

    Computed tomography (CT) has been widely used to acquire volumetric anatomical information in the diagnosis and treatment of illnesses in many clinics. However, the ART algorithm for reconstruction from under-sampled and noisy projection is still time-consuming. It is the goal of our work to improve a block-wise approximate parallel implementation for the ART algorithm on CUDA-enabled GPU to make the ART algorithm applicable to the clinical environment. The resulting method has several compelling features: (1) the rays are allotted into blocks, making the rays in the same block parallel; (2) GPU implementation caters to the actual industrial and medical application demand. We test the algorithm on a digital shepp-logan phantom, and the results indicate that our method is more efficient than the existing CPU implementation. The high computation efficiency achieved in our algorithm makes it possible for clinicians to obtain real-time 3D images.

  5. Field programmable gate array based parallel strapdown algorithm design for strapdown inertial navigation systems.

    PubMed

    Li, Zong-Tao; Wu, Tie-Jun; Lin, Can-Long; Ma, Long-Hua

    2011-01-01

    A new generalized optimum strapdown algorithm with coning and sculling compensation is presented, in which the position, velocity and attitude updating operations are carried out based on the single-speed structure in which all computations are executed at a single updating rate that is sufficiently high to accurately account for high frequency angular rate and acceleration rectification effects. Different from existing algorithms, the updating rates of the coning and sculling compensations are unrelated with the number of the gyro incremental angle samples and the number of the accelerometer incremental velocity samples. When the output sampling rate of inertial sensors remains constant, this algorithm allows increasing the updating rate of the coning and sculling compensation, yet with more numbers of gyro incremental angle and accelerometer incremental velocity in order to improve the accuracy of system. Then, in order to implement the new strapdown algorithm in a single FPGA chip, the parallelization of the algorithm is designed and its computational complexity is analyzed. The performance of the proposed parallel strapdown algorithm is tested on the Xilinx ISE 12.3 software platform and the FPGA device XC6VLX550T hardware platform on the basis of some fighter data. It is shown that this parallel strapdown algorithm on the FPGA platform can greatly decrease the execution time of algorithm to meet the real-time and high precision requirements of system on the high dynamic environment, relative to the existing implemented on the DSP platform.

  6. Field Programmable Gate Array Based Parallel Strapdown Algorithm Design for Strapdown Inertial Navigation Systems

    PubMed Central

    Li, Zong-Tao; Wu, Tie-Jun; Lin, Can-Long; Ma, Long-Hua

    2011-01-01

    A new generalized optimum strapdown algorithm with coning and sculling compensation is presented, in which the position, velocity and attitude updating operations are carried out based on the single-speed structure in which all computations are executed at a single updating rate that is sufficiently high to accurately account for high frequency angular rate and acceleration rectification effects. Different from existing algorithms, the updating rates of the coning and sculling compensations are unrelated with the number of the gyro incremental angle samples and the number of the accelerometer incremental velocity samples. When the output sampling rate of inertial sensors remains constant, this algorithm allows increasing the updating rate of the coning and sculling compensation, yet with more numbers of gyro incremental angle and accelerometer incremental velocity in order to improve the accuracy of system. Then, in order to implement the new strapdown algorithm in a single FPGA chip, the parallelization of the algorithm is designed and its computational complexity is analyzed. The performance of the proposed parallel strapdown algorithm is tested on the Xilinx ISE 12.3 software platform and the FPGA device XC6VLX550T hardware platform on the basis of some fighter data. It is shown that this parallel strapdown algorithm on the FPGA platform can greatly decrease the execution time of algorithm to meet the real-time and high precision requirements of system on the high dynamic environment, relative to the existing implemented on the DSP platform. PMID:22164058

  7. Using a model of parallel distributed processing associated with data mining in the characterization of sexuality in a university population.

    PubMed

    de Azevedo Simões, Priscyla Waleska Targino; Martins, Paulo João; Casagrandre, Rogério Antônio; Madeira, Kristian; de Mattos, Merisandra Côrtes; Manenti, Sandra Aparecida; da Rosa, Maria Inês; Dal-Pizzol, Felipe; Venson, Ramon; Coral, Leandro Natal; de Souza, Gabriel Scheffer; Pandini, Jeison Cleiton; Cassettari Junior, José Márcio; Moretti, Gustavo Pasquali; Cesconetto, Samuel

    2013-01-01

    Using the framework for developing parallel applications Java Parallel Programming Framework were conducted performance analysis of an application for the clustering data by the method of fuzzy logic combined with Gustafson-Kessel algorithm. In addition to running in a distributed environment, for comparative purposes, were also conducted collections of processing time in environments with a single Personal Computer approach. With the results obtained by collecting time of application, there was a statistical analysis to validate the application and the algorithm as well as the use of computational clustering as a way to increase performance applications.

  8. A Parallel EM Algorithm for Model-Based Clustering Applied to the Exploration of Large Spatio-Temporal Data

    SciTech Connect

    Chen, Wei-Chen; Ostrouchov, George; Pugmire, Dave; Prabhat,; Wehner, Michael

    2013-01-01

    We develop a parallel EM algorithm for multivariate Gaussian mixture models and use it to perform model-based clustering of a large climate data set. Three variants of the EM algorithm are reformulated in parallel and a new variant that is faster is presented. All are implemented using the single program, multiple data (SPMD) programming model, which is able to take advantage of the combined collective memory of large distributed computer architectures to process larger data sets. Displays of the estimated mixture model rather than the data allow us to explore multivariate relationships in a way that scales to arbitrary size data. We study the performance of our methodology on simulated data and apply our methodology to a high resolution climate dataset produced by the community atmosphere model (CAM5). This article has supplementary material online.

  9. PMCR-Miner: parallel maximal confident association rules miner algorithm for microarray data set.

    PubMed

    Zakaria, Wael; Kotb, Yasser; Ghaleb, Fayed F M

    2015-01-01

    The MCR-Miner algorithm is aimed to mine all maximal high confident association rules form the microarray up/down-expressed genes data set. This paper introduces two new algorithms: IMCR-Miner and PMCR-Miner. The IMCR-Miner algorithm is an extension of the MCR-Miner algorithm with some improvements. These improvements implement a novel way to store the samples of each gene into a list of unsigned integers in order to benefit using the bitwise operations. In addition, the IMCR-Miner algorithm overcomes the drawbacks faced by the MCR-Miner algorithm by setting some restrictions to ignore repeated comparisons. The PMCR-Miner algorithm is a parallel version of the new proposed IMCR-Miner algorithm. The PMCR-Miner algorithm is based on shared-memory systems and task parallelism, where no time is needed in the process of sharing and combining data between processors. The experimental results on real microarray data sets show that the PMCR-Miner algorithm is more efficient and scalable than the counterparts.

  10. Two and Three-Dimensional Nonlocal DFT for Inhomogeneous Fluids I: Algorithms and Parallelization

    SciTech Connect

    Frink, Laura J. Douglas; Salinger, Andrew

    1999-08-09

    Fluids adsorbed near surfaces, macromolecules, and in porous materials are inhomogeneous, inhibiting spatially varying density distributions. This inhomogeneity in the fluid plays an important role in controlling a wide variety of complex physical phenomena including wetting, self-assembly, corrosion, and molecular recognition. One of the key methods for studying the properties of inhomogeneous fluids in simple geometries has been density functional theory (DFT). However, there has been a conspicuous lack of calculations in complex 2D and 3D geometries. The computational difficulty arises from the need to perform nested integrals that are due to nonlocal terms in the free energy functional These integral equations are expensive both in evaluation time and in memory requirements; however, the expense can be mitigated by intelligent algorithms and the use of parallel computers. This paper details our efforts to develop efficient numerical algorithms so that no local DFT calculations in complex geometries that require two or three dimensions can be performed. The success of this implementation will enable the study of solvation effects at heterogeneous surfaces, in zeolites, in solvated (bio)polymers, and in colloidal suspensions.

  11. Parallel algorithm to analyze the brain signals: application on epileptic spikes.

    PubMed

    Keshri, Anup Kumar; Das, Barda Nand; Mallick, Dheeresh Kumar; Sinha, Rakesh Kumar

    2011-02-01

    In the current work, we have proposed a parallel algorithm for the recognition of Epileptic Spikes (ES) in EEG. The automated systems are used in biomedical field to help the doctors and pathologist by producing the result of an inspection in real time. Generally, the biomedical signal data to be processed are very large in size. A uniprocessor computer is having its own limitation regarding its speed. So the fastest available computer with latest configuration also may not produce results in real time for the immense computation. Parallel computing can be proved as a useful tool for processing the huge data with higher speed. In the proposed algorithm 'Data Parallelism' has been applied where multiple processors perform the same operation on different part of the data to produce fast result. All the processors are interconnected with each other by an interconnection network. The complexity of the algorithm was analyzed as Θ((n + δn) / N) where, 'n' is the length of the input data, 'N' is the number of processor used in the algorithm and 'δn' is the amount of overlapped data between two consecutive intermediate processors (IPs). This algorithm is scalable as the level of parallelism increase linearly with the increase in number of processors. The algorithm has been implemented in Message Passing Interface (MPI). It was tested with 60 min recorded EEG signal data files. The recognition rate of ES on an average was 95.68%.

  12. Parallel Algorithms for Computer Vision on the Connection Machine.

    DTIC Science & Technology

    1986-11-01

    INTELLIGENCE LAB J J LITTLE UNCLASSIFIED NOV 86 AI-M-928 DRCA76-85-C-0818 F/G 12/7 NL EmlolEllllllEIIIIIIEIIEIIIE El ..... 9’-2 4 2. 0 ~~1.8 .22 -C% .1...connect ed cornpontoit label ii ig (; ii’, - Bl~~~ ello ( h explained the use of se 1’irig. osltdoiayo i o tii - and devise~d the NIST algorithm), Mike 1...tinliated """ Edge (hetec t ion . Convolution 3ms 2rus . Find Zero-Crossings 0.5ms (.57, I Propagate lal) el 36ms 3r)ins * La urricrate c u rves 350ps

  13. Distributed data organization and parallel data retrieval methods for huge laser scanner point clouds

    NASA Astrophysics Data System (ADS)

    Hongchao, Ma; Wang, Zongyue

    2011-02-01

    This paper proposes a novel method for distributed data organization and parallel data retrieval from huge volume point clouds generated by airborne Light Detection and Ranging (LiDAR) technology under a cluster computing environment, in order to allow fast analysis, processing, and visualization of the point clouds within a given area. The proposed method is suitable for both grid and quadtree data structures. As for distribution strategy, cross distribution of the dataset would be more efficient than serial distribution in terms of non-redundant datasets, since a dataset is more uniformly distributed in the former arrangement. However, redundant datasets are necessary in order to meet the frequent need of input and output operations in multi-client scenarios: the first copy would be distributed by a cross distribution strategy while the second (and later) would be distributed by an iterated exchanging distribution strategy. Such a distribution strategy would distribute datasets more uniformly to each data server. In data retrieval, a greedy algorithm is used to allocate the query task to a data server, where the computing load is lightest if the data block needing to be retrieved is stored among multiple data servers. Experiments show that the method proposed in this paper can satisfy the demands of frequent and fast data query.

  14. Parallel processors and nonlinear structural dynamics algorithms and software

    NASA Technical Reports Server (NTRS)

    Belytschko, Ted

    1990-01-01

    Techniques are discussed for the implementation and improvement of vectorization and concurrency in nonlinear explicit structural finite element codes. In explicit integration methods, the computation of the element internal force vector consumes the bulk of the computer time. The program can be efficiently vectorized by subdividing the elements into blocks and executing all computations in vector mode. The structuring of elements into blocks also provides a convenient way to implement concurrency by creating tasks which can be assigned to available processors for evaluation. The techniques were implemented in a 3-D nonlinear program with one-point quadrature shell elements. Concurrency and vectorization were first implemented in a single time step version of the program. Techniques were developed to minimize processor idle time and to select the optimal vector length. A comparison of run times between the program executed in scalar, serial mode and the fully vectorized code executed concurrently using eight processors shows speed-ups of over 25. Conjugate gradient methods for solving nonlinear algebraic equations are also readily adapted to a parallel environment. A new technique for improving convergence properties of conjugate gradients in nonlinear problems is developed in conjunction with other techniques such as diagonal scaling. A significant reduction in the number of iterations required for convergence is shown for a statically loaded rigid bar suspended by three equally spaced springs.

  15. A Parallel Numerical Algorithm To Solve Linear Systems Of Equations Emerging From 3D Radiative Transfer

    NASA Astrophysics Data System (ADS)

    Wichert, Viktoria; Arkenberg, Mario; Hauschildt, Peter H.

    2016-10-01

    Highly resolved state-of-the-art 3D atmosphere simulations will remain computationally extremely expensive for years to come. In addition to the need for more computing power, rethinking coding practices is necessary. We take a dual approach by introducing especially adapted, parallel numerical methods and correspondingly parallelizing critical code passages. In the following, we present our respective work on PHOENIX/3D. With new parallel numerical algorithms, there is a big opportunity for improvement when iteratively solving the system of equations emerging from the operator splitting of the radiative transfer equation J = ΛS. The narrow-banded approximate Λ-operator Λ* , which is used in PHOENIX/3D, occurs in each iteration step. By implementing a numerical algorithm which takes advantage of its characteristic traits, the parallel code's efficiency is further increased and a speed-up in computational time can be achieved.

  16. Evaluation of a new parallel numerical parameter optimization algorithm for a dynamical system

    NASA Astrophysics Data System (ADS)

    Duran, Ahmet; Tuncel, Mehmet

    2016-10-01

    It is important to have a scalable parallel numerical parameter optimization algorithm for a dynamical system used in financial applications where time limitation is crucial. We use Message Passing Interface parallel programming and present such a new parallel algorithm for parameter estimation. For example, we apply the algorithm to the asset flow differential equations that have been developed and analyzed since 1989 (see [3-6] and references contained therein). We achieved speed-up for some time series to run up to 512 cores (see [10]). Unlike [10], we consider more extensive financial market situations, for example, in presence of low volatility, high volatility and stock market price at a discount/premium to its net asset value with varying magnitude, in this work. Moreover, we evaluated the convergence of the model parameter vector, the nonlinear least squares error and maximum improvement factor to quantify the success of the optimization process depending on the number of initial parameter vectors.

  17. An Efficient Parallel Algorithm for Multiple Sequence Similarities Calculation Using a Low Complexity Method

    PubMed Central

    Marucci, Evandro A.; Neves, Leandro A.; Valêncio, Carlo R.; Pinto, Alex R.; Cansian, Adriano M.; de Souza, Rogeria C. G.; Shiyou, Yang; Machado, José M.

    2014-01-01

    With the advance of genomic researches, the number of sequences involved in comparative methods has grown immensely. Among them, there are methods for similarities calculation, which are used by many bioinformatics applications. Due the huge amount of data, the union of low complexity methods with the use of parallel computing is becoming desirable. The k-mers counting is a very efficient method with good biological results. In this work, the development of a parallel algorithm for multiple sequence similarities calculation using the k-mers counting method is proposed. Tests show that the algorithm presents a very good scalability and a nearly linear speedup. For 14 nodes was obtained 12x speedup. This algorithm can be used in the parallelization of some multiple sequence alignment tools, such as MAFFT and MUSCLE. PMID:25140318

  18. The remote sensing image segmentation mean shift algorithm parallel processing based on MapReduce

    NASA Astrophysics Data System (ADS)

    Chen, Xi; Zhou, Liqing

    2015-12-01

    With the development of satellite remote sensing technology and the remote sensing image data, traditional remote sensing image segmentation technology cannot meet the massive remote sensing image processing and storage requirements. This article put cloud computing and parallel computing technology in remote sensing image segmentation process, and build a cheap and efficient computer cluster system that uses parallel processing to achieve MeanShift algorithm of remote sensing image segmentation based on the MapReduce model, not only to ensure the quality of remote sensing image segmentation, improved split speed, and better meet the real-time requirements. The remote sensing image segmentation MeanShift algorithm parallel processing algorithm based on MapReduce shows certain significance and a realization of value.

  19. A Parallel Compact Multi-Dimensional Numerical Algorithm with Aeroacoustics Applications

    NASA Technical Reports Server (NTRS)

    Povitsky, Alex; Morris, Philip J.

    1999-01-01

    In this study we propose a novel method to parallelize high-order compact numerical algorithms for the solution of three-dimensional PDEs (Partial Differential Equations) in a space-time domain. For this numerical integration most of the computer time is spent in computation of spatial derivatives at each stage of the Runge-Kutta temporal update. The most efficient direct method to compute spatial derivatives on a serial computer is a version of Gaussian elimination for narrow linear banded systems known as the Thomas algorithm. In a straightforward pipelined implementation of the Thomas algorithm processors are idle due to the forward and backward recurrences of the Thomas algorithm. To utilize processors during this time, we propose to use them for either non-local data independent computations, solving lines in the next spatial direction, or local data-dependent computations by the Runge-Kutta method. To achieve this goal, control of processor communication and computations by a static schedule is adopted. Thus, our parallel code is driven by a communication and computation schedule instead of the usual "creative, programming" approach. The obtained parallelization speed-up of the novel algorithm is about twice as much as that for the standard pipelined algorithm and close to that for the explicit DRP algorithm.

  20. Genetic Algorithms in a Distributed Computing Environment Using PVM

    NASA Astrophysics Data System (ADS)

    Cronje, G. A.; Steeb, W.-H.

    The Parallel Virtual Machine (PVM) is a software system that enables a collection of heterogeneous computer systems to be used as a coherent and flexible concurrent computation resource. We show that genetic algorithms can be implemented using a Parallel Virtual Machine and C++. Problems with constraints are also discussed.

  1. Genetic algorithms in a distributed computing environment using PVM

    SciTech Connect

    Cronje, G.A.; Steeb, W.H.

    1997-04-01

    The Parallel Virtual Machine (PVM) is a software system that enables a collection of heterogeneous computer systems to be used as a coherent and flexible concurrent computation resource. We show that genetic algorithms can be implemented using a Parallel Virtual Machine and C++. Problems with constraints are also discussed.

  2. Aggressively Parallel Algorithms of Collision and Nearest Neighbor Detection for GPU Planetesimal Disk Simulation

    NASA Astrophysics Data System (ADS)

    Quillen, Alice C.; Moore, A.

    2008-09-01

    Planetesimal and dust dynamical simulations require collision and nearest neighbor detection. A brute force implementation for sorting interparticle distances requires O(N2) computations for N particles, limiting the numbers of particles that have been simulated. Parallel algorithms recently developed for the GPU (graphics processing unit), such as the radix sort, can run as fast as O(N) and sort distances between a million particles in a few hundred milliseconds. We introduce improvements in collision and nearest neighbor detection algorithms and how we have incorporated them into our efficient parallel 2nd order democratic heliocentric method symplectic integrator written in NVIDIA's CUDA for the GPU.

  3. A computationally efficient parallel Levenberg-Marquardt algorithm for highly parameterized inverse model analyses

    NASA Astrophysics Data System (ADS)

    Lin, Youzuo; O'Malley, Daniel; Vesselinov, Velimir V.

    2016-09-01

    Inverse modeling seeks model parameters given a set of observations. However, for practical problems because the number of measurements is often large and the model parameters are also numerous, conventional methods for inverse modeling can be computationally expensive. We have developed a new, computationally efficient parallel Levenberg-Marquardt method for solving inverse modeling problems with a highly parameterized model space. Levenberg-Marquardt methods require the solution of a linear system of equations which can be prohibitively expensive to compute for moderate to large-scale problems. Our novel method projects the original linear problem down to a Krylov subspace such that the dimensionality of the problem can be significantly reduced. Furthermore, we store the Krylov subspace computed when using the first damping parameter and recycle the subspace for the subsequent damping parameters. The efficiency of our new inverse modeling algorithm is significantly improved using these computational techniques. We apply this new inverse modeling method to invert for random transmissivity fields in 2-D and a random hydraulic conductivity field in 3-D. Our algorithm is fast enough to solve for the distributed model parameters (transmissivity) in the model domain. The algorithm is coded in Julia and implemented in the MADS computational framework (http://mads.lanl.gov). By comparing with Levenberg-Marquardt methods using standard linear inversion techniques such as QR or SVD methods, our Levenberg-Marquardt method yields a speed-up ratio on the order of ˜101 to ˜102 in a multicore computational environment. Therefore, our new inverse modeling method is a powerful tool for characterizing subsurface heterogeneity for moderate to large-scale problems.

  4. A computationally efficient parallel Levenberg-Marquardt algorithm for highly parameterized inverse model analyses

    SciTech Connect

    Lin, Youzuo; O'Malley, Daniel; Vesselinov, Velimir V.

    2016-09-01

    Inverse modeling seeks model parameters given a set of observations. However, for practical problems because the number of measurements is often large and the model parameters are also numerous, conventional methods for inverse modeling can be computationally expensive. We have developed a new, computationally-efficient parallel Levenberg-Marquardt method for solving inverse modeling problems with a highly parameterized model space. Levenberg-Marquardt methods require the solution of a linear system of equations which can be prohibitively expensive to compute for moderate to large-scale problems. Our novel method projects the original linear problem down to a Krylov subspace, such that the dimensionality of the problem can be significantly reduced. Furthermore, we store the Krylov subspace computed when using the first damping parameter and recycle the subspace for the subsequent damping parameters. The efficiency of our new inverse modeling algorithm is significantly improved using these computational techniques. We apply this new inverse modeling method to invert for random transmissivity fields in 2D and a random hydraulic conductivity field in 3D. Our algorithm is fast enough to solve for the distributed model parameters (transmissivity) in the model domain. The algorithm is coded in Julia and implemented in the MADS computational framework (http://mads.lanl.gov). By comparing with Levenberg-Marquardt methods using standard linear inversion techniques such as QR or SVD methods, our Levenberg-Marquardt method yields a speed-up ratio on the order of ~101 to ~102 in a multi-core computational environment. Furthermore, our new inverse modeling method is a powerful tool for characterizing subsurface heterogeneity for moderate- to large-scale problems.

  5. A computationally efficient parallel Levenberg-Marquardt algorithm for highly parameterized inverse model analyses

    DOE PAGES

    Lin, Youzuo; O'Malley, Daniel; Vesselinov, Velimir V.

    2016-09-01

    Inverse modeling seeks model parameters given a set of observations. However, for practical problems because the number of measurements is often large and the model parameters are also numerous, conventional methods for inverse modeling can be computationally expensive. We have developed a new, computationally-efficient parallel Levenberg-Marquardt method for solving inverse modeling problems with a highly parameterized model space. Levenberg-Marquardt methods require the solution of a linear system of equations which can be prohibitively expensive to compute for moderate to large-scale problems. Our novel method projects the original linear problem down to a Krylov subspace, such that the dimensionality of themore » problem can be significantly reduced. Furthermore, we store the Krylov subspace computed when using the first damping parameter and recycle the subspace for the subsequent damping parameters. The efficiency of our new inverse modeling algorithm is significantly improved using these computational techniques. We apply this new inverse modeling method to invert for random transmissivity fields in 2D and a random hydraulic conductivity field in 3D. Our algorithm is fast enough to solve for the distributed model parameters (transmissivity) in the model domain. The algorithm is coded in Julia and implemented in the MADS computational framework (http://mads.lanl.gov). By comparing with Levenberg-Marquardt methods using standard linear inversion techniques such as QR or SVD methods, our Levenberg-Marquardt method yields a speed-up ratio on the order of ~101 to ~102 in a multi-core computational environment. Furthermore, our new inverse modeling method is a powerful tool for characterizing subsurface heterogeneity for moderate- to large-scale problems.« less

  6. A computationally efficient parallel Levenberg-Marquardt algorithm for highly parameterized inverse model analyses

    SciTech Connect

    Lin, Youzuo; O'Malley, Daniel; Vesselinov, Velimir V.

    2016-09-01

    Inverse modeling seeks model parameters given a set of observations. However, for practical problems because the number of measurements is often large and the model parameters are also numerous, conventional methods for inverse modeling can be computationally expensive. We have developed a new, computationally-efficient parallel Levenberg-Marquardt method for solving inverse modeling problems with a highly parameterized model space. Levenberg-Marquardt methods require the solution of a linear system of equations which can be prohibitively expensive to compute for moderate to large-scale problems. Our novel method projects the original linear problem down to a Krylov subspace, such that the dimensionality of the problem can be significantly reduced. Furthermore, we store the Krylov subspace computed when using the first damping parameter and recycle the subspace for the subsequent damping parameters. The efficiency of our new inverse modeling algorithm is significantly improved using these computational techniques. We apply this new inverse modeling method to invert for random transmissivity fields in 2D and a random hydraulic conductivity field in 3D. Our algorithm is fast enough to solve for the distributed model parameters (transmissivity) in the model domain. The algorithm is coded in Julia and implemented in the MADS computational framework (http://mads.lanl.gov). By comparing with Levenberg-Marquardt methods using standard linear inversion techniques such as QR or SVD methods, our Levenberg-Marquardt method yields a speed-up ratio on the order of ~101 to ~102 in a multi-core computational environment. Furthermore, our new inverse modeling method is a powerful tool for characterizing subsurface heterogeneity for moderate- to large-scale problems.

  7. An Optimization Algorithm for Multipath Parallel Allocation for Service Resource in the Simulation Task Workflow

    PubMed Central

    Zhang, Hongjun; Zhang, Rui; Li, Yong; Zhang, Xuliang

    2014-01-01

    Service oriented modeling and simulation are hot issues in the field of modeling and simulation, and there is need to call service resources when simulation task workflow is running. How to optimize the service resource allocation to ensure that the task is complete effectively is an important issue in this area. In military modeling and simulation field, it is important to improve the probability of success and timeliness in simulation task workflow. Therefore, this paper proposes an optimization algorithm for multipath service resource parallel allocation, in which multipath service resource parallel allocation model is built and multiple chains coding scheme quantum optimization algorithm is used for optimization and solution. The multiple chains coding scheme quantum optimization algorithm is to extend parallel search space to improve search efficiency. Through the simulation experiment, this paper investigates the effect for the probability of success in simulation task workflow from different optimization algorithm, service allocation strategy, and path number, and the simulation result shows that the optimization algorithm for multipath service resource parallel allocation is an effective method to improve the probability of success and timeliness in simulation task workflow. PMID:24963506

  8. An optimization algorithm for multipath parallel allocation for service resource in the simulation task workflow.

    PubMed

    Wang, Zhiteng; Zhang, Hongjun; Zhang, Rui; Li, Yong; Zhang, Xuliang

    2014-01-01

    Service oriented modeling and simulation are hot issues in the field of modeling and simulation, and there is need to call service resources when simulation task workflow is running. How to optimize the service resource allocation to ensure that the task is complete effectively is an important issue in this area. In military modeling and simulation field, it is important to improve the probability of success and timeliness in simulation task workflow. Therefore, this paper proposes an optimization algorithm for multipath service resource parallel allocation, in which multipath service resource parallel allocation model is built and multiple chains coding scheme quantum optimization algorithm is used for optimization and solution. The multiple chains coding scheme quantum optimization algorithm is to extend parallel search space to improve search efficiency. Through the simulation experiment, this paper investigates the effect for the probability of success in simulation task workflow from different optimization algorithm, service allocation strategy, and path number, and the simulation result shows that the optimization algorithm for multipath service resource parallel allocation is an effective method to improve the probability of success and timeliness in simulation task workflow.

  9. Distributed Storage Algorithm for Geospatial Image Data Based on Data Access Patterns.

    PubMed

    Pan, Shaoming; Li, Yongkai; Xu, Zhengquan; Chong, Yanwen

    2015-01-01

    Declustering techniques are widely used in distributed environments to reduce query response time through parallel I/O by splitting large files into several small blocks and then distributing those blocks among multiple storage nodes. Unfortunately, however, many small geospatial image data files cannot be further split for distributed storage. In this paper, we propose a complete theoretical system for the distributed storage of small geospatial image data files based on mining the access patterns of geospatial image data using their historical access log information. First, an algorithm is developed to construct an access correlation matrix based on the analysis of the log information, which reveals the patterns of access to the geospatial image data. Then, a practical heuristic algorithm is developed to determine a reasonable solution based on the access correlation matrix. Finally, a number of comparative experiments are presented, demonstrating that our algorithm displays a higher total parallel access probability than those of other algorithms by approximately 10-15% and that the performance can be further improved by more than 20% by simultaneously applying a copy storage strategy. These experiments show that the algorithm can be applied in distributed environments to help realize parallel I/O and thereby improve system performance.

  10. Distributed Storage Algorithm for Geospatial Image Data Based on Data Access Patterns

    PubMed Central

    Pan, Shaoming; Li, Yongkai; Xu, Zhengquan; Chong, Yanwen

    2015-01-01

    Declustering techniques are widely used in distributed environments to reduce query response time through parallel I/O by splitting large files into several small blocks and then distributing those blocks among multiple storage nodes. Unfortunately, however, many small geospatial image data files cannot be further split for distributed storage. In this paper, we propose a complete theoretical system for the distributed storage of small geospatial image data files based on mining the access patterns of geospatial image data using their historical access log information. First, an algorithm is developed to construct an access correlation matrix based on the analysis of the log information, which reveals the patterns of access to the geospatial image data. Then, a practical heuristic algorithm is developed to determine a reasonable solution based on the access correlation matrix. Finally, a number of comparative experiments are presented, demonstrating that our algorithm displays a higher total parallel access probability than those of other algorithms by approximately 10–15% and that the performance can be further improved by more than 20% by simultaneously applying a copy storage strategy. These experiments show that the algorithm can be applied in distributed environments to help realize parallel I/O and thereby improve system performance. PMID:26181628

  11. Applications of New Surrogate Global Optimization Algorithms including Efficient Synchronous and Asynchronous Parallelism for Calibration of Expensive Nonlinear Geophysical Simulation Models.

    NASA Astrophysics Data System (ADS)

    Shoemaker, C. A.; Pang, M.; Akhtar, T.; Bindel, D.

    2016-12-01

    New parallel surrogate global optimization algorithms are developed and applied to objective functions that are expensive simulations (possibly with multiple local minima). The algorithms can be applied to most geophysical simulations, including those with nonlinear partial differential equations. The optimization does not require simulations be parallelized. Asynchronous (and synchronous) parallel execution is available in the optimization toolbox "pySOT". The parallel algorithms are modified from serial to eliminate fine grained parallelism. The optimization is computed with open source software pySOT, a Surrogate Global Optimization Toolbox that allows user to pick the type of surrogate (or ensembles), the search procedure on surrogate, and the type of parallelism (synchronous or asynchronous). pySOT also allows the user to develop new algorithms by modifying parts of the code. In the applications here, the objective function takes up to 30 minutes for one simulation, and serial optimization can take over 200 hours. Results from Yellowstone (NSF) and NCSS (Singapore) supercomputers are given for groundwater contaminant hydrology simulations with applications to model parameter estimation and decontamination management. All results are compared with alternatives. The first results are for optimization of pumping at many wells to reduce cost for decontamination of groundwater at a superfund site. The optimization runs with up to 128 processors. Superlinear speed up is obtained for up to 16 processors, and efficiency with 64 processors is over 80%. Each evaluation of the objective function requires the solution of nonlinear partial differential equations to describe the impact of spatially distributed pumping and model parameters on model predictions for the spatial and temporal distribution of groundwater contaminants. The second application uses an asynchronous parallel global optimization for groundwater quality model calibration. The time for a single objective

  12. Experiments with a Parallel Multi-Objective Evolutionary Algorithm for Scheduling

    NASA Technical Reports Server (NTRS)

    Brown, Matthew; Johnston, Mark D.

    2013-01-01

    Evolutionary multi-objective algorithms have great potential for scheduling in those situations where tradeoffs among competing objectives represent a key requirement. One challenge, however, is runtime performance, as a consequence of evolving not just a single schedule, but an entire population, while attempting to sample the Pareto frontier as accurately and uniformly as possible. The growing availability of multi-core processors in end user workstations, and even laptops, has raised the question of the extent to which such hardware can be used to speed up evolutionary algorithms. In this paper we report on early experiments in parallelizing a Generalized Differential Evolution (GDE) algorithm for scheduling long-range activities on NASA's Deep Space Network. Initial results show that significant speedups can be achieved, but that performance does not necessarily improve as more cores are utilized. We describe our preliminary results and some initial suggestions from parallelizing the GDE algorithm. Directions for future work are outlined.

  13. A New Parallel Algorithm Analogous to Elastic Net Method forBipartite Subgraph Problem

    NASA Astrophysics Data System (ADS)

    Tang, Zheng; Wang, Rong Long; Wang, Jia Hai; Cao, Qi Ping

    The goal of the bipartite subgraph problem, which is an NP-complete problem, is to remove the minimum number of edges in a given graph such that the remaining graph is a bipartite graph. Enlightened by the elastic net method that was introduced by Durbin and Willshaw for finding shortest route for the Traveling Salesman Problem (TSP), we proposed a new parallel algorithm for the bipartite subgraph problem. The approach jointly tends to satisfy the constraint condition and minimizes the number of removed edges. The collective computational properties of the proposed approach are also proved theoretically. A large number of instances have been simulated to verify the proposed algorithm. The simulation results show that our algorithm finds a solution superior to that of the best existing parallel algorithms.

  14. Variation in efficiency of parallel algorithms. [for study of stiffness matrices in planar trusses

    NASA Technical Reports Server (NTRS)

    Hayashi, A.; Melosh, R. J.; Utku, S.; Salama, M.

    1985-01-01

    The present study has the objective to investigate some iterative parallel-processor linear equation solving algorithms with respect to efficiency for analyses of typical linear engineering systems. Attention is given to a set of n linear equations, Ku = p, where K = an n x n positive definite, sparsely populated, symmetric matrix, u = an n x 1 vector of unknown responses, and p = an n x 1 vector of prescribed constants. This study is concerned with a hybrid method in which iteration is used to solve the problem, while a direct method is used on the local processor level. Variations in the efficiency of parallel algorithms are explored. Measures of the efficiency are based on computer experiments regarding the algorithms. For all the algorithms, the wall clock time is found to decrease as the number of processors increases.

  15. A GPU-paralleled implementation of an enhanced face recognition algorithm

    NASA Astrophysics Data System (ADS)

    Chen, Hao; Liu, Xiyang; Shao, Shuai; Zan, Jiguo

    2013-03-01

    Face recognition algorithm based on compressed sensing and sparse representation is hotly argued in these years. The scheme of this algorithm increases recognition rate as well as anti-noise capability. However, the computational cost is expensive and has become a main restricting factor for real world applications. In this paper, we introduce a GPU-accelerated hybrid variant of face recognition algorithm named parallel face recognition algorithm (pFRA). We describe here how to carry out parallel optimization design to take full advantage of many-core structure of a GPU. The pFRA is tested and compared with several other implementations under different data sample size. Finally, Our pFRA, implemented with NVIDIA GPU and Computer Unified Device Architecture (CUDA) programming model, achieves a significant speedup over the traditional CPU implementations.

  16. Algorithm comparison and benchmarking using a parallel spectra transform shallow water model

    SciTech Connect

    Worley, P.H.; Foster, I.T.; Toonen, B.

    1995-04-01

    In recent years, a number of computer vendors have produced supercomputers based on a massively parallel processing (MPP) architecture. These computers have been shown to be competitive in performance with conventional vector supercomputers for some applications. As spectral weather and climate models are heavy users of vector supercomputers, it is interesting to determine how these models perform on MPPS, and which MPPs are best suited to the execution of spectral models. The benchmarking of MPPs is complicated by the fact that different algorithms may be more efficient on different architectures. Hence, a comprehensive benchmarking effort must answer two related questions: which algorithm is most efficient on each computer and how do the most efficient algorithms compare on different computers. In general, these are difficult questions to answer because of the high cost associated with implementing and evaluating a range of different parallel algorithms on each MPP platform.

  17. The convergence analysis of parallel genetic algorithm based on allied strategy

    NASA Astrophysics Data System (ADS)

    Lin, Feng; Sun, Wei; Chang, K. C.

    2010-04-01

    Genetic algorithms (GAs) have been applied to many difficult optimization problems such as track assignment and hypothesis managements for multisensor integration and data fusion. However, premature convergence has been a main problem for GAs. In order to prevent premature convergence, we introduce an allied strategy based on biological evolution and present a parallel Genetic Algorithm with the allied strategy (PGAAS). The PGAAS can prevent premature convergence, increase the optimization speed, and has been successfully applied in a few applications. In this paper, we first present a Markov chain model in the PGAAS. Based on this model, we analyze the convergence property of PGAAS. We then present the proof of global convergence for the PGAAS algorithm. The experiments results show that PGAAS is an efficient and effective parallel Genetic algorithm. Finally, we discuss several potential applications of the proposed methodology.

  18. Experiments with a Parallel Multi-Objective Evolutionary Algorithm for Scheduling

    NASA Technical Reports Server (NTRS)

    Brown, Matthew; Johnston, Mark D.

    2013-01-01

    Evolutionary multi-objective algorithms have great potential for scheduling in those situations where tradeoffs among competing objectives represent a key requirement. One challenge, however, is runtime performance, as a consequence of evolving not just a single schedule, but an entire population, while attempting to sample the Pareto frontier as accurately and uniformly as possible. The growing availability of multi-core processors in end user workstations, and even laptops, has raised the question of the extent to which such hardware can be used to speed up evolutionary algorithms. In this paper we report on early experiments in parallelizing a Generalized Differential Evolution (GDE) algorithm for scheduling long-range activities on NASA's Deep Space Network. Initial results show that significant speedups can be achieved, but that performance does not necessarily improve as more cores are utilized. We describe our preliminary results and some initial suggestions from parallelizing the GDE algorithm. Directions for future work are outlined.

  19. Parallelizing flow-accumulation calculations on graphics processing units—From iterative DEM preprocessing algorithm to recursive multiple-flow-direction algorithm

    NASA Astrophysics Data System (ADS)

    Qin, Cheng-Zhi; Zhan, Lijun

    2012-06-01

    As one of the important tasks in digital terrain analysis, the calculation of flow accumulations from gridded digital elevation models (DEMs) usually involves two steps in a real application: (1) using an iterative DEM preprocessing algorithm to remove the depressions and flat areas commonly contained in real DEMs, and (2) using a recursive flow-direction algorithm to calculate the flow accumulation for every cell in the DEM. Because both algorithms are computationally intensive, quick calculation of the flow accumulations from a DEM (especially for a large area) presents a practical challenge to personal computer (PC) users. In recent years, rapid increases in hardware capacity of the graphics processing units (GPUs) provided in modern PCs have made it possible to meet this challenge in a PC environment. Parallel computing on GPUs using a compute-unified-device-architecture (CUDA) programming model has been explored to speed up the execution of the single-flow-direction algorithm (SFD). However, the parallel implementation on a GPU of the multiple-flow-direction (MFD) algorithm, which generally performs better than the SFD algorithm, has not been reported. Moreover, GPU-based parallelization of the DEM preprocessing step in the flow-accumulation calculations has not been addressed. This paper proposes a parallel approach to calculate flow accumulations (including both iterative DEM preprocessing and a recursive MFD algorithm) on a CUDA-compatible GPU. For the parallelization of an MFD algorithm (MFD-md), two different parallelization strategies using a GPU are explored. The first parallelization strategy, which has been used in the existing parallel SFD algorithm on GPU, has the problem of computing redundancy. Therefore, we designed a parallelization strategy based on graph theory. The application results show that the proposed parallel approach to calculate flow accumulations on a GPU performs much faster than either sequential algorithms or other parallel GPU

  20. A new chirp scaling algorithm of bistatic SAR with parallel flight paths

    NASA Astrophysics Data System (ADS)

    Li, Ning; Wang, Luping

    2011-10-01

    The precise point target reference spectrum of bistatic SAR has been a difficult problem for a long time. Many of the current available algorithms have approximation during deducing. This paper deduces the precise expression in Doppler- Frequency domain with the configuration of parallel flight paths and constant velocity of each platform. Then a new chirp scaling algorithm is put forward. At last, simulations are given to demonstrate the good focusing performance.

  1. Implementation of (omega)-k synthetic aperture radar imaging algorithm on a massively parallel supercomputer

    NASA Astrophysics Data System (ADS)

    Yerkes, Christopher R.; Webster, Eric D.

    1994-06-01

    Advanced algorithms for synthetic aperture radar (SAR) imaging have in the past required computing capabilities only available from high performance special purpose hardware. Such architectures have tended to have short life cycles with respect to development expense. Current generation Massively Parallel Processors (MPP) are offering high performance capabilities necessary for such applications with both a scalable architecture and a longer projected life cycle. In this paper we explore issues associated with implementation of a SAR imaging algorithm on a mesh configured MPP architecture.

  2. Algorithm for reconstructing wide space-bandwidth information in parallel two-step phase-shifting digital holography.

    PubMed

    Tahara, Tatsuki; Shimozato, Yuki; Xia, Peng; Ito, Yasunori; Awatsuji, Yasuhiro; Nishio, Kenzo; Ura, Shogo; Matoba, Osamu; Kubota, Toshihiro

    2012-08-27

    We propose an image-reconstruction algorithm of parallel phase-shifting digital holography (PPSDH) which is a technique of single-shot phase-shifting interferometry. In the conventional algorithms in PPSDH, the residual 0th-order diffraction wave and the conjugate images cannot be removed completely and a part of space-bandwidth information is discarded. The proposed algorithm can remove these residual images by modifying the calculation of phase-shifting interferometry and by using Fourier transform technique, respectively. Then, several types of complex amplitudes are derived from a recorded hologram according to the directions in which the neighboring pixels used for carrying out the spatial phase-shifting interferometry are aligned. Several distributions are Fourier-transformed and wide space-bandwidth information of the object wave is obtained by selecting the spectrum among the Fourier-transformed images in each region of the spatial frequency domain and synthesizing a Fourier-transformed image from the spectrum.

  3. Parallel algorithms for separation of two sets of points and recognition of digital convex polygons

    SciTech Connect

    Sarkar, D. ); Stojmenovic, I. )

    1992-04-01

    Given two finite sets of points in a plane, the polygon separation problem is to construct a separating convex k-gon with smallest k. In this paper, we present a parallel algorithm for the polygon separation problem. The algorithm runs in O(log n) time on a CREW PRAM with n processors, where n is the number of points in the two given sets. The algorithm is cost-optimal, since [Omega](n log n) is a lower-bound for the first time needed by any sequential algorithm. We apply this algorithm to the problem of finding a convex region is its digital image. The algorithm in this paper constructs one such polygon with possibly two more edges than the minimal one.

  4. Parallel algorithms of relative radiometric correction for images of TH-1 satellite

    NASA Astrophysics Data System (ADS)

    Wang, Xiang; Zhang, Tingtao; Cheng, Jiasheng; Yang, Tao

    2014-05-01

    The first generation of transitive stereo-metric satellites in China, TH-1 Satellite, is able to gain stereo images of three-line-array with resolution of 5 meters, multispectral images of 10 meters, and panchromatic high resolution images of 2 meters. The procedure between level 0 and level 1A of high resolution images is so called relative radiometric correction (RRC for short). The processing algorithm of high resolution images, with large volumes of data, is complicated and time consuming. In order to bring up the processing speed, people in industry commonly apply parallel processing techniques based on CPU or GPU. This article firstly introduces the whole process and each step of the algorithm - that is in application - of RRC for high resolution images in level 0; secondly, the theory and characteristics of MPI (Message Passing Interface) and OpenMP (Open Multi-Processing) parallel programming techniques is briefly described, as well as the superiority for parallel technique in image processing field; thirdly, aiming at each step of the algorithm in application and based on MPI+OpenMP hybrid paradigm, the parallelizability and the strategies of parallelism for three processing steps: Radiometric Correction, Splicing Pieces of TDICCD (Time Delay Integration Charge-Coupled Device) and Gray Level Adjustment among pieces of TDICCD are deeply discussed, and furthermore, deducts the theoretical acceleration rates of each step and the one of whole procedure, according to the processing styles and independence of calculation; for the step Splicing Pieces of TDICCD, two different strategies of parallelism are proposed, which are to be chosen with consideration of hardware capabilities; finally, series of experiments are carried out to verify the parallel algorithms by applying 2-meter panchromatic high resolution images of TH-1 Satellite, and the experimental results are analyzed. Strictly on the basis of former parallel algorithms, the programs in the experiments

  5. A Parallel Nonrigid Registration Algorithm Based on B-Spline for Medical Images.

    PubMed

    Du, Xiaogang; Dang, Jianwu; Wang, Yangping; Wang, Song; Lei, Tao

    2016-01-01

    The nonrigid registration algorithm based on B-spline Free-Form Deformation (FFD) plays a key role and is widely applied in medical image processing due to the good flexibility and robustness. However, it requires a tremendous amount of computing time to obtain more accurate registration results especially for a large amount of medical image data. To address the issue, a parallel nonrigid registration algorithm based on B-spline is proposed in this paper. First, the Logarithm Squared Difference (LSD) is considered as the similarity metric in the B-spline registration algorithm to improve registration precision. After that, we create a parallel computing strategy and lookup tables (LUTs) to reduce the complexity of the B-spline registration algorithm. As a result, the computing time of three time-consuming steps including B-splines interpolation, LSD computation, and the analytic gradient computation of LSD, is efficiently reduced, for the B-spline registration algorithm employs the Nonlinear Conjugate Gradient (NCG) optimization method. Experimental results of registration quality and execution efficiency on the large amount of medical images show that our algorithm achieves a better registration accuracy in terms of the differences between the best deformation fields and ground truth and a speedup of 17 times over the single-threaded CPU implementation due to the powerful parallel computing ability of Graphics Processing Unit (GPU).

  6. A Parallel Nonrigid Registration Algorithm Based on B-Spline for Medical Images

    PubMed Central

    Wang, Yangping; Wang, Song

    2016-01-01

    The nonrigid registration algorithm based on B-spline Free-Form Deformation (FFD) plays a key role and is widely applied in medical image processing due to the good flexibility and robustness. However, it requires a tremendous amount of computing time to obtain more accurate registration results especially for a large amount of medical image data. To address the issue, a parallel nonrigid registration algorithm based on B-spline is proposed in this paper. First, the Logarithm Squared Difference (LSD) is considered as the similarity metric in the B-spline registration algorithm to improve registration precision. After that, we create a parallel computing strategy and lookup tables (LUTs) to reduce the complexity of the B-spline registration algorithm. As a result, the computing time of three time-consuming steps including B-splines interpolation, LSD computation, and the analytic gradient computation of LSD, is efficiently reduced, for the B-spline registration algorithm employs the Nonlinear Conjugate Gradient (NCG) optimization method. Experimental results of registration quality and execution efficiency on the large amount of medical images show that our algorithm achieves a better registration accuracy in terms of the differences between the best deformation fields and ground truth and a speedup of 17 times over the single-threaded CPU implementation due to the powerful parallel computing ability of Graphics Processing Unit (GPU). PMID:28053653

  7. A Parallel Attractor Finding Algorithm Based on Boolean Satisfiability for Genetic Regulatory Networks

    PubMed Central

    Guo, Wensheng; Yang, Guowu; Wu, Wei; He, Lei; Sun, Mingyu

    2014-01-01

    In biological systems, the dynamic analysis method has gained increasing attention in the past decade. The Boolean network is the most common model of a genetic regulatory network. The interactions of activation and inhibition in the genetic regulatory network are modeled as a set of functions of the Boolean network, while the state transitions in the Boolean network reflect the dynamic property of a genetic regulatory network. A difficult problem for state transition analysis is the finding of attractors. In this paper, we modeled the genetic regulatory network as a Boolean network and proposed a solving algorithm to tackle the attractor finding problem. In the proposed algorithm, we partitioned the Boolean network into several blocks consisting of the strongly connected components according to their gradients, and defined the connection between blocks as decision node. Based on the solutions calculated on the decision nodes and using a satisfiability solving algorithm, we identified the attractors in the state transition graph of each block. The proposed algorithm is benchmarked on a variety of genetic regulatory networks. Compared with existing algorithms, it achieved similar performance on small test cases, and outperformed it on larger and more complex ones, which happens to be the trend of the modern genetic regulatory network. Furthermore, while the existing satisfiability-based algorithms cannot be parallelized due to their inherent algorithm design, the proposed algorithm exhibits a good scalability on parallel computing architectures. PMID:24718686

  8. On Parallel Push-Relabel based Algorithms for Bipartite Maximum Matching

    SciTech Connect

    Langguth, Johannes; Azad, Md Ariful; Halappanavar, Mahantesh; Manne, Fredrik

    2014-07-01

    We study multithreaded push-relabel based algorithms for computing maximum cardinality matching in bipartite graphs. Matching is a fundamental combinatorial (graph) problem with applications in a wide variety of problems in science and engineering. We are motivated by its use in the context of sparse linear solvers for computing maximum transversal of a matrix. We implement and test our algorithms on several multi-socket multicore systems and compare their performance to state-of-the-art augmenting path-based serial and parallel algorithms using a testset comprised of a wide range of real-world instances. Building on several heuristics for enhancing performance, we demonstrate good scaling for the parallel push-relabel algorithm. We show that it is comparable to the best augmenting path-based algorithms for bipartite matching. To the best of our knowledge, this is the first extensive study of multithreaded push-relabel based algorithms. In addition to a direct impact on the applications using matching, the proposed algorithmic techniques can be extended to preflow-push based algorithms for computing maximum flow in graphs.

  9. A parallel attractor-finding algorithm based on Boolean satisfiability for genetic regulatory networks.

    PubMed

    Guo, Wensheng; Yang, Guowu; Wu, Wei; He, Lei; Sun, Mingyu

    2014-01-01

    In biological systems, the dynamic analysis method has gained increasing attention in the past decade. The Boolean network is the most common model of a genetic regulatory network. The interactions of activation and inhibition in the genetic regulatory network are modeled as a set of functions of the Boolean network, while the state transitions in the Boolean network reflect the dynamic property of a genetic regulatory network. A difficult problem for state transition analysis is the finding of attractors. In this paper, we modeled the genetic regulatory network as a Boolean network and proposed a solving algorithm to tackle the attractor finding problem. In the proposed algorithm, we partitioned the Boolean network into several blocks consisting of the strongly connected components according to their gradients, and defined the connection between blocks as decision node. Based on the solutions calculated on the decision nodes and using a satisfiability solving algorithm, we identified the attractors in the state transition graph of each block. The proposed algorithm is benchmarked on a variety of genetic regulatory networks. Compared with existing algorithms, it achieved similar performance on small test cases, and outperformed it on larger and more complex ones, which happens to be the trend of the modern genetic regulatory network. Furthermore, while the existing satisfiability-based algorithms cannot be parallelized due to their inherent algorithm design, the proposed algorithm exhibits a good scalability on parallel computing architectures.

  10. Reusable Component Model Development Approach for Parallel and Distributed Simulation

    PubMed Central

    Zhu, Feng; Yao, Yiping; Chen, Huilong; Yao, Feng

    2014-01-01

    Model reuse is a key issue to be resolved in parallel and distributed simulation at present. However, component models built by different domain experts usually have diversiform interfaces, couple tightly, and bind with simulation platforms closely. As a result, they are difficult to be reused across different simulation platforms and applications. To address the problem, this paper first proposed a reusable component model framework. Based on this framework, then our reusable model development approach is elaborated, which contains two phases: (1) domain experts create simulation computational modules observing three principles to achieve their independence; (2) model developer encapsulates these simulation computational modules with six standard service interfaces to improve their reusability. The case study of a radar model indicates that the model developed using our approach has good reusability and it is easy to be used in different simulation platforms and applications. PMID:24729751

  11. Improved load distribution in parallel sparse Cholesky factorization

    NASA Technical Reports Server (NTRS)

    Rothberg, Edward; Schreiber, Robert

    1994-01-01

    Compared to the customary column-oriented approaches, block-oriented, distributed-memory sparse Cholesky factorization benefits from an asymptotic reduction in interprocessor communication volume and an asymptotic increase in the amount of concurrency that is exposed in the problem. Unfortunately, block-oriented approaches (specifically, the block fan-out method) have suffered from poor balance of the computational load. As a result, achieved performance can be quite low. This paper investigates the reasons for this load imbalance and proposes simple block mapping heuristics that dramatically improve it. The result is a roughly 20% increase in realized parallel factorization performance, as demonstrated by performance results from an Intel Paragon system. We have achieved performance of nearly 3.2 billion floating point operations per second with this technique on a 196-node Paragon system.

  12. Sentence comprehension: A parallel distributed processing approach. Technical report

    SciTech Connect

    McClelland, J.L.; St John, M.; Taraban, R.

    1989-07-14

    Basic aspects are reviewed of conventional approaches to sentence comprehension and point out are some of the difficulties faced by models that take these approaches. An alternative approach is described, based on the principles of parallel distributed processing, and shown how it offers different answers to basic questions about the nature of the language processing mechanism. An illustrative simulation model captures the key characteristics of the approach, and illustrates how it can cope with the difficulties faced by conventional models. Alternative ways of conceptualizing basic aspects of language processing within the framework of this approach will consider how it can address several arguments that might be brought to bear against it, and suggest avenues for future development.

  13. A parallel hybrid numerical algorithm for simulating gas flow and gas discharge of an atmospheric-pressure plasma jet

    NASA Astrophysics Data System (ADS)

    Lin, K.-M.; Hu, M.-H.; Hung, C.-T.; Wu, J.-S.; Hwang, F.-N.; Chen, Y.-S.; Cheng, G.

    2012-12-01

    Development of a hybrid numerical algorithm which couples weakly with the gas flow model (GFM) and the plasma fluid model (PFM) for simulating an atmospheric-pressure plasma jet (APPJ) and its acceleration by two approaches is presented. The weak coupling between gas flow and discharge is introduced by transferring between the results obtained from the steady-state solution of the GFM and cycle-averaged solution of the PFM respectively. Approaches of reducing the overall runtime include parallel computing of the GFM and the PFM solvers, and employing a temporal multi-scale method (TMSM) for PFM. Parallel computing of both solvers is realized using the domain decomposition method with the message passing interface (MPI) on distributed-memory machines. The TMSM considers only chemical reactions by ignoring the transport terms when integrating temporally the continuity equations of heavy species at each time step, and then the transport terms are restored only at an interval of time marching steps. The total reduction of runtime is 47% by applying the TMSM to the APPJ example presented in this study. Application of the proposed hybrid algorithm is demonstrated by simulating a parallel-plate helium APPJ impinging onto a substrate, which the cycle-averaged properties of the 200th cycle are presented. The distribution patterns of species densities are strongly correlated by the background gas flow pattern, which shows that consideration of gas flow in APPJ simulations is critical.

  14. Tools and Techniques for Adding Fault Tolerance to Distributed and Parallel Programs

    DTIC Science & Technology

    1991-12-07

    identify by block number) FIELD IGROUP SUB-GROUP parallel processing , reliability, transactions, checkpoint ing, -- recovery, replication, reliable...we ’survey some of the principal paradigms for fault-tolerant distributed camputing and discuss their relevance to parallel processing . One particular...parallel programnming environment. Keywords: Parallel processing , reliability, transactions, checkpointing, recovery, replication, reli- able broadcast

  15. A parallel domain decomposition algorithm for coastal ocean circulation models based on integer linear programming

    NASA Astrophysics Data System (ADS)

    Jordi, Antoni; Georgas, Nickitas; Blumberg, Alan

    2017-05-01

    This paper presents a new parallel domain decomposition algorithm based on integer linear programming (ILP), a mathematical optimization method. To minimize the computation time of coastal ocean circulation models, the ILP decomposition algorithm divides the global domain in local domains with balanced work load according to the number of processors and avoids computations over as many as land grid cells as possible. In addition, it maintains the use of logically rectangular local domains and achieves the exact same results as traditional domain decomposition algorithms (such as Cartesian decomposition). However, the ILP decomposition algorithm may not converge to an exact solution for relatively large domains. To overcome this problem, we developed two ILP decomposition formulations. The first one (complete formulation) has no additional restriction, although it is impractical for large global domains. The second one (feasible) imposes local domains with the same dimensions and looks for the feasibility of such decomposition, which allows much larger global domains. Parallel performance of both ILP formulations is compared to a base Cartesian decomposition by simulating two cases with the newly created parallel version of the Stevens Institute of Technology's Estuarine and Coastal Ocean Model (sECOM). Simulations with the ILP formulations run always faster than the ones with the base decomposition, and the complete formulation is better than the feasible one when it is applicable. In addition, parallel efficiency with the ILP decomposition may be greater than one.

  16. A Hybrid Shared-Memory Parallel Max-Tree Algorithm for Extreme Dynamic-Range Images.

    PubMed

    Moschini, Ugo; Meijster, Arnold; Wilkinson, Michael

    2017-03-30

    Max-trees, or component trees, are graph structures that represent the connected components of an image in a hierarchical way. Nowadays, many application fields rely on images with high-dynamic range or floating point values. Efficient sequential algorithms exist to build trees and compute attributes for images of any bit depth. However, we show that the current parallel algorithms perform poorly already with integers at bit depths higher than 16 bits per pixel. We propose a parallel method combining the two worlds of flooding and merging max-tree algorithms. First, a pilot max-tree of a quantized version of the image is built in parallel using a flooding method. Later, this structure is used in a parallel leaf-to-root approach to compute efficiently the final max-tree and to drive the merging of the sub-trees computed by the threads. We present an analysis of the performance both on simulated and actual 2D images and 3D volumes. Execution times are about 20 better than the fastest sequential algorithm and speed-up goes up to 30 40 on 64 threads.

  17. Creating IRT-Based Parallel Test Forms Using the Genetic Algorithm Method

    ERIC Educational Resources Information Center

    Sun, Koun-Tem; Chen, Yu-Jen; Tsai, Shu-Yen; Cheng, Chien-Fen

    2008-01-01

    In educational measurement, the construction of parallel test forms is often a combinatorial optimization problem that involves the time-consuming selection of items to construct tests having approximately the same test information functions (TIFs) and constraints. This article proposes a novel method, genetic algorithm (GA), to construct parallel…

  18. A 1 log N parallel algorithm for detecting convex hulls on image boards.

    PubMed

    Lin, J C; Lin, J Y

    1998-01-01

    By finding the maximum and minimum of {yi-mxi|1=orparallel algorithm to obtain the convex hull of N arbitrarily given points on an image board, The mathematical theory needed is included, and computation time is 1 log N.

  19. Parallel algorithms for computer vision. Final report, 31 August 1988-31 January 1990

    SciTech Connect

    Poggio, T.

    1990-04-01

    The main effort in this project has been directed towards the development of an integrated vision system, - the Vision Machine - based on a parallel supercomputer. The core of the Vision Machine is in fact a set of parallel algorithms for visual recognition and navigation in an unstructured environment. The present version of the Vision Machine has been demonstrated to process images in close to real time by (1) computing first several low-level cues, such as edges, stereo disparity, optical flow, color and texture, (2) integrating them to extract a cartoon-like description of the scene in terms of the physical discontinuities of surfaces, and (3) using this cartoon in a recognition stage, based on parallel model matching. In addition to the development of the parallel algorithms, their implementation and testing, we have also done substantial work in several areas that are very closely related. These include (1) design and fabrication of VLSI circuits to transfer to potentially cheap and fast hardware some of the software algorithms, (2) initial development of techniques to synthesize by learning vision algorithms, and (3) several projects involving autonomous navigation of small robots.

  20. Creating IRT-Based Parallel Test Forms Using the Genetic Algorithm Method

    ERIC Educational Resources Information Center

    Sun, Koun-Tem; Chen, Yu-Jen; Tsai, Shu-Yen; Cheng, Chien-Fen

    2008-01-01

    In educational measurement, the construction of parallel test forms is often a combinatorial optimization problem that involves the time-consuming selection of items to construct tests having approximately the same test information functions (TIFs) and constraints. This article proposes a novel method, genetic algorithm (GA), to construct parallel…

  1. Development of Variational Guiding Center Algorithms for Parallel Calculations in Experimental Magnetic Equilibria

    SciTech Connect

    Ellison, C. Leland; Finn, J. M.; Qin, H.; Tang, William M.

    2014-10-01

    Structure-preserving algorithms obtained via discrete variational principles exhibit strong promise for the calculation of guiding center test particle trajectories. The non-canonical Hamiltonian structure of the guiding center equations forms a novel and challenging context for geometric integration. To demonstrate the practical relevance of these methods, a prototypical variational midpoint algorithm is applied to an experimental magnetic equilibrium. The stability characteristics, conservation properties, and implementation requirements associated with the variational algorithms are addressed. Furthermore, computational run time is reduced for large numbers of particles by parallelizing the calculation on GPU hardware.

  2. A Parallel Domain Decomposition BEM Algorithm for Three Dimensional Exponentially Graded Elasticity

    SciTech Connect

    Ortiz Tavara, Jhonny E; Shelton Jr, William Allison; Mantic, Vladislav; Criado, Rafael; Paris, Federico; Gray, Leonard J

    2008-01-01

    A parallel domain decomposition boundary integral algorithm for three-dimensional exponentially graded elasticity has been developed. As this subdomain algorithm allows the grading direction to vary in the structure, geometries arising from practical FGM applications can be handled. Moreover, the boundary integral algorithm scales well with the number of processors, also helping to alleviate the high computational cost of evaluating the Green's function. Numerical results for cylindrical geometries show excellent agreement with the new analytical solution deduced for axisymmetric plane strain states in a radially graded material.

  3. Fast parallel molecular algorithms for DNA-based computation: factoring integers.

    PubMed

    Chang, Weng-Long; Guo, Minyi; Ho, Michael Shan-Hui

    2005-06-01

    The RSA public-key cryptosystem is an algorithm that converts input data to an unrecognizable encryption and converts the unrecognizable data back into its original decryption form. The security of the RSA public-key cryptosystem is based on the difficulty of factoring the product of two large prime numbers. This paper demonstrates to factor the product of two large prime numbers, and is a breakthrough in basic biological operations using a molecular computer. In order to achieve this, we propose three DNA-based algorithms for parallel subtractor, parallel comparator, and parallel modular arithmetic that formally verify our designed molecular solutions for factoring the product of two large prime numbers. Furthermore, this work indicates that the cryptosystems using public-key are perhaps insecure and also presents clear evidence of the ability of molecular computing to perform complicated mathematical operations.

  4. Parallel Fock matrix construction with distributed shared memory model for the FMO-MO method.

    PubMed

    Umeda, Hiroaki; Inadomi, Yuichi; Watanabe, Toshio; Yagi, Toru; Ishimoto, Takayoshi; Ikegami, Tsutomu; Tadano, Hiroto; Sakurai, Tetsuya; Nagashima, Umpei

    2010-10-01

    A parallel Fock matrix construction program for FMO-MO method has been developed with the distributed shared memory model. To construct a large-sized Fock matrix during FMO-MO calculations, a distributed parallel algorithm was designed to make full use of local memory to reduce communication, and was implemented on the Global Array toolkit. A benchmark calculation for a small system indicates that the parallelization efficiency of the matrix construction portion is as high as 93% at 1,024 processors. A large FMO-MO application on the epidermal growth factor receptor (EGFR) protein (17,246 atoms and 96,234 basis functions) was also carried out at the HF/6-31G level of theory, with the frontier orbitals being extracted by a Sakurai-Sugiura eigensolver. It takes 11.3 h for the FMO calculation, 49.1 h for the Fock matrix construction, and 10 min to extract 94 eigen-components on a PC cluster system using 256 processors.

  5. Image quality improvement of parallel four-step phase-shifting digital holography by using the algorithm of parallel two-step phase-shifting digital holography.

    PubMed

    Kakue, Takashi; Moritani, Yuri; Ito, Kenichi; Shimozato, Yuki; Awatsuji, Yasuhiro; Nishio, Kenzo; Ura, Shogo; Kubota, Toshihiro; Matoba, Osamu

    2010-04-26

    We propose an algorithm that can improve the quality of the reconstructed image from the single hologram recorded by the optical system of the parallel four-step phase-shifting digital holography. The proposed algorithm applies the image-reconstruction algorithm of parallel two-step phase-shifting digital holography to the hologram so as to reduce errors in the reconstructed image and eliminate ghosts. We numerically and experimentally confirmed that the proposed algorithm decreased 25% in terms of root mean square error in amplitude, and eliminated the ghosts, respectively.

  6. Multi-objective optimization of a parallel ankle rehabilitation robot using modified differential evolution algorithm

    NASA Astrophysics Data System (ADS)

    Wang, Congzhe; Fang, Yuefa; Guo, Sheng

    2015-07-01

    Dimensional synthesis is one of the most difficult issues in the field of parallel robots with actuation redundancy. To deal with the optimal design of a redundantly actuated parallel robot used for ankle rehabilitation, a methodology of dimensional synthesis based on multi-objective optimization is presented. First, the dimensional synthesis of the redundant parallel robot is formulated as a nonlinear constrained multi-objective optimization problem. Then four objective functions, separately reflecting occupied space, input/output transmission and torque performances, and multi-criteria constraints, such as dimension, interference and kinematics, are defined. In consideration of the passive exercise of plantar/dorsiflexion requiring large output moment, a torque index is proposed. To cope with the actuation redundancy of the parallel robot, a new output transmission index is defined as well. The multi-objective optimization problem is solved by using a modified Differential Evolution(DE) algorithm, which is characterized by new selection and mutation strategies. Meanwhile, a special penalty method is presented to tackle the multi-criteria constraints. Finally, numerical experiments for different optimization algorithms are implemented. The computation results show that the proposed indices of output transmission and torque, and constraint handling are effective for the redundant parallel robot; the modified DE algorithm is superior to the other tested algorithms, in terms of the ability of global search and the number of non-dominated solutions. The proposed methodology of multi-objective optimization can be also applied to the dimensional synthesis of other redundantly actuated parallel robots only with rotational movements.

  7. A Parallel Point Matching Algorithm for Landmark Based Image Registration Using Multicore Platform

    PubMed Central

    Yang, Lin; Gong, Leiguang; Zhang, Hong; Nosher, John L.; Foran, David J.

    2013-01-01

    Point matching is crucial for many computer vision applications. Establishing the correspondence between a large number of data points is a computationally intensive process. Some point matching related applications, such as medical image registration, require real time or near real time performance if applied to critical clinical applications like image assisted surgery. In this paper, we report a new multicore platform based parallel algorithm for fast point matching in the context of landmark based medical image registration. We introduced a non-regular data partition algorithm which utilizes the K-means clustering algorithm to group the landmarks based on the number of available processing cores, which optimize the memory usage and data transfer. We have tested our method using the IBM Cell Broadband Engine (Cell/B.E.) platform. The results demonstrated a significant speed up over its sequential implementation. The proposed data partition and parallelization algorithm, though tested only on one multicore platform, is generic by its design. Therefore the parallel algorithm can be extended to other computing platforms, as well as other point matching related applications. PMID:24308014

  8. Implementation and analysis of a Navier-Stokes algorithm on parallel computers

    NASA Technical Reports Server (NTRS)

    Fatoohi, Raad A.; Grosch, Chester E.

    1988-01-01

    The results of the implementation of a Navier-Stokes algorithm on three parallel/vector computers are presented. The object of this research is to determine how well, or poorly, a single numerical algorithm would map onto three different architectures. The algorithm is a compact difference scheme for the solution of the incompressible, two-dimensional, time-dependent Navier-Stokes equations. The computers were chosen so as to encompass a variety of architectures. They are the following: the MPP, an SIMD machine with 16K bit serial processors; Flex/32, an MIMD machine with 20 processors; and Cray/2. The implementation of the algorithm is discussed in relation to these architectures and measures of the performance on each machine are given. The basic comparison is among SIMD instruction parallelism on the MPP, MIMD process parallelism on the Flex/32, and vectorization of a serial code on the Cray/2. Simple performance models are used to describe the performance. These models highlight the bottlenecks and limiting factors for this algorithm on these architectures. Finally, conclusions are presented.

  9. A Parallel Point Matching Algorithm for Landmark Based Image Registration Using Multicore Platform

    NASA Astrophysics Data System (ADS)

    Yang, Lin; Gong, Leiguang; Zhang, Hong; Nosher, John L.; Foran, David J.

    Point matching is crucial for many computer vision applications. Establishing the correspondence between a large number of data points is a computationally intensive process. Some point matching related applications, such as medical image registration, require real time or near real time performance if applied to critical clinical applications like image assisted surgery. In this paper, we report a new multicore platform based parallel algorithm for fast point matching in the context of landmark based medical image registration. We introduced a non-regular data partition algorithm which utilizes the K-means clustering algorithm to group the landmarks based on the number of available processing cores, which optimize the memory usage and data transfer. We have tested our method using the IBM Cell Broadband Engine (Cell/B.E.) platform. The results demonstrated a significant speed up over its sequential implementation. The proposed data partition and parallelization algorithm, though tested only on one multicore platform, is generic by its design. Therefore the parallel algorithm can be extended to other computing platforms, as well as other point matching related applications.

  10. BitPAl: a bit-parallel, general integer-scoring sequence alignment algorithm

    PubMed Central

    Loving, Joshua; Hernandez, Yozen; Benson, Gary

    2014-01-01

    Motivation: Mapping of high-throughput sequencing data and other bulk sequence comparison applications have motivated a search for high-efficiency sequence alignment algorithms. The bit-parallel approach represents individual cells in an alignment scoring matrix as bits in computer words and emulates the calculation of scores by a series of logic operations composed of AND, OR, XOR, complement, shift and addition. Bit-parallelism has been successfully applied to the longest common subsequence (LCS) and edit-distance problems, producing fast algorithms in practice. Results: We have developed BitPAl, a bit-parallel algorithm for general, integer-scoring global alignment. Integer-scoring schemes assign integer weights for match, mismatch and insertion/deletion. The BitPAl method uses structural properties in the relationship between adjacent scores in the scoring matrix to construct classes of efficient algorithms, each designed for a particular set of weights. In timed tests, we show that BitPAl runs 7–25 times faster than a standard iterative algorithm. Availability and implementation: Source code is freely available for download at http://lobstah.bu.edu/BitPAl/BitPAl.html. BitPAl is implemented in C and runs on all major operating systems. Contact: jloving@bu.edu or yhernand@bu.edu or gbenson@bu.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25075119

  11. Parallel algorithm for determining motion vectors in ice floe images by matching edge features

    NASA Technical Reports Server (NTRS)

    Manohar, M.; Ramapriyan, H. K.; Strong, J. P.

    1988-01-01

    A parallel algorithm is described to determine motion vectors of ice floes using time sequences of images of the Arctic ocean obtained from the Synthetic Aperture Radar (SAR) instrument flown on-board the SEASAT spacecraft. Researchers describe a parallel algorithm which is implemented on the MPP for locating corresponding objects based on their translationally and rotationally invariant features. The algorithm first approximates the edges in the images by polygons or sets of connected straight-line segments. Each such edge structure is then reduced to a seed point. Associated with each seed point are the descriptions (lengths, orientations and sequence numbers) of the lines constituting the corresponding edge structure. A parallel matching algorithm is used to match packed arrays of such descriptions to identify corresponding seed points in the two images. The matching algorithm is designed such that fragmentation and merging of ice floes are taken into account by accepting partial matches. The technique has been demonstrated to work on synthetic test patterns and real image pairs from SEASAT in times ranging from .5 to 0.7 seconds for 128 x 128 images.

  12. Parallelism exploitation of a PCA algorithm for hyperspectral images using RVC-CAL

    NASA Astrophysics Data System (ADS)

    Lazcano, R.; Sidrach-Cardona, I.; Madroñal, D.; Desnos, K.; Pelcat, M.; Juárez, E.; Sanz, C.

    2016-10-01

    Hyperspectral imaging (HI) collects information from across the electromagnetic spectrum, covering a wide range of wavelengths. The tremendous development of this technology within the field of remote sensing has led to new research fields, such as cancer automatic detection or precision agriculture, but has also increased the performance requirements of the applications. For instance, strong time constraints need to be respected, since many applications imply real-time responses. Achieving real-time is a challenge, as hyperspectral sensors generate high volumes of data to process. Thus, so as to achieve this requisite, first the initial image data needs to be reduced by discarding redundancies and keeping only useful information. Then, the intrinsic parallelism in a system specification must be explicitly highlighted. In this paper, the PCA (Principal Component Analysis) algorithm is implemented using the RVC-CAL dataflow language, which specifies a system as a set of blocks or actors and allows its parallelization by scheduling the blocks over different processing units. Two implementations of PCA for hyperspectral images have been compared when aiming at obtaining the first few principal components: first, the algorithm has been implemented using the Jacobi approach for obtaining the eigenvectors; thereafter, the NIPALS-PCA algorithm, which approximates the principal components iteratively, has also been studied. Both implementations have been compared in terms of accuracy and computation time; then, the parallelization of both models has also been analyzed. These comparisons show promising results in terms of computation time and parallelization: the performance of the NIPALS-PCA algorithm is clearly better when only the first principal component is achieved, while the partitioning of the algorithm execution over several cores shows an important speedup for the PCA-Jacobi. Thus, experimental results show the potential of RVC-CAL to automatically generate

  13. In-line print defect inspection system based on parallelized algorithms

    NASA Astrophysics Data System (ADS)

    Lv, Chao; Zhou, Hongjun

    2015-03-01

    The core algorithm of an on-line print defects detection system is template matching. In this paper, we introduce a kind of edge-based template matching based on Canny's edge detection method to find the edge information and do the matching work. Of all the detection algorithms, the most difficult problem is execution time, in order to reduce the execution time and improve the efficiency of execution, we introduce four different ways to solve and compare. They are Pyramidal algorithm, Multicore and Multi-Threading algorithm based on OpenMP, a Parallel algorithm based on Intel AVX Instruction Set, GPU computing based on OpenCL model. Through the results, we can find different characters of different ways, and then choose the best for your own system.

  14. A divide-and-inner product parallel algorithm for polynomial evaluation

    SciTech Connect

    Hu, Jie; Li, Lei; Nakamura, Tadao

    1994-12-31

    In this paper, a divide-and-inner product parallel algorithm for evaluating a polynomial of degree N (N+1=KL) on a MIMD computer is presented. It needs 2K + log{sub 2}L steps to evaluate a polynomial of degree N in parallel on L+1 processors (L{<=}2K-2log{sub 2}K) which is a decrease of log{sub 2}L steps as compared with the L-order Homer`s method, and which is a decrease of (2log{sub 2}L){sup 1/2} steps as compared with the some MIMD algorithms. The new algorithm is simple in structure and easy to be realized.

  15. An Optimal Parallel Algorithm for Constructing a Spanning Tree on Circular Permutation Graphs

    NASA Astrophysics Data System (ADS)

    Honma, Hirotoshi; Honma, Saki; Masuyama, Shigeru

    The spanning tree problem is to find a tree that connects all the vertices of G. This problem has many applications, such as electric power systems, computer network design and circuit analysis. Klein and Stein demonstrated that a spanning tree can be found in O(log n) time with O(n + m) processors on the CRCW PRAM. In general, it is known that more efficient parallel algorithms can be developed by restricting classes of graphs. Circular permutation graphs properly contain the set of permutation graphs as a subclass and are first introduced by Rotem and Urrutia. They provided O(n2.376) time recognition algorithm. Circular permutation graphs and their models find several applications in VLSI layout. In this paper, we propose an optimal parallel algorithm for constructing a spanning tree on circular permutation graphs. It runs in O(log n) time with O(n/ log n) processors on the EREW PRAM.

  16. A Moldable Online Scheduling Algorithm and Its Application to Parallel Short Sequence Mapping

    NASA Astrophysics Data System (ADS)

    Saule, Erik; Bozdağ, Doruk; Catalyurek, Umit V.

    A crucial step in DNA sequence analysis is mapping short sequences generated by next-generation instruments to a reference genome. In this paper, we focus on efficient online scheduling of multi-user parallel short sequence mapping queries on a multiprocessor system. With the availability of parallel execution models, the problem at hand becomes a moldable task scheduling problem where the number of processors needed to execute a task is determined by the scheduler. We propose an online scheduling algorithm to minimize the stretch of the tasks in the system. This metric provides improved fairness to small tasks compared to flow time metric and suits well to the nature of the problem. Experimental evaluation on two workload scenarios indicate that the algorithm results in significantly smaller stretch compared to a recent algorithm and it is more fair to small sized tasks.

  17. Parameter estimation of fractional-order chaotic systems by using quantum parallel particle swarm optimization algorithm.

    PubMed

    Huang, Yu; Guo, Feng; Li, Yongling; Liu, Yufeng

    2015-01-01

    Parameter estimation for fractional-order chaotic systems is an important issue in fractional-order chaotic control and synchronization and could be essentially formulated as a multidimensional optimization problem. A novel algorithm called quantum parallel particle swarm optimization (QPPSO) is proposed to solve the parameter estimation for fractional-order chaotic systems. The parallel characteristic of quantum computing is used in QPPSO. This characteristic increases the calculation of each generation exponentially. The behavior of particles in quantum space is restrained by the quantum evolution equation, which consists of the current rotation angle, individual optimal quantum rotation angle, and global optimal quantum rotation angle. Numerical simulation based on several typical fractional-order systems and comparisons with some typical existing algorithms show the effectiveness and efficiency of the proposed algorithm.

  18. Parameter Estimation of Fractional-Order Chaotic Systems by Using Quantum Parallel Particle Swarm Optimization Algorithm

    PubMed Central

    Huang, Yu; Guo, Feng; Li, Yongling; Liu, Yufeng

    2015-01-01

    Parameter estimation for fractional-order chaotic systems is an important issue in fractional-order chaotic control and synchronization and could be essentially formulated as a multidimensional optimization problem. A novel algorithm called quantum parallel particle swarm optimization (QPPSO) is proposed to solve the parameter estimation for fractional-order chaotic systems. The parallel characteristic of quantum computing is used in QPPSO. This characteristic increases the calculation of each generation exponentially. The behavior of particles in quantum space is restrained by the quantum evolution equation, which consists of the current rotation angle, individual optimal quantum rotation angle, and global optimal quantum rotation angle. Numerical simulation based on several typical fractional-order systems and comparisons with some typical existing algorithms show the effectiveness and efficiency of the proposed algorithm. PMID:25603158

  19. A parallel and incremental algorithm for efficient unique signature discovery on DNA databases

    PubMed Central

    2010-01-01

    Background DNA signatures are distinct short nucleotide sequences that provide valuable information that is used for various purposes, such as the design of Polymerase Chain Reaction primers and microarray experiments. Biologists usually use a discovery algorithm to find unique signatures from DNA databases, and then apply the signatures to microarray experiments. Such discovery algorithms require to set some input factors, such as signature length l and mismatch tolerance d, which affect the discovery results. However, suggestions about how to select proper factor values are rare, especially when an unfamiliar DNA database is used. In most cases, biologists typically select factor values based on experience, or even by guessing. If the discovered result is unsatisfactory, biologists change the input factors of the algorithm to obtain a new result. This process is repeated until a proper result is obtained. Implicit signatures under the discovery condition (l, d) are defined as the signatures of length ≤ l with mismatch tolerance ≥ d. A discovery algorithm that could discover all implicit signatures, such that those that meet the requirements concerning the results, would be more helpful than one that depends on trial and error. However, existing discovery algorithms do not address the need to discover all implicit signatures. Results This work proposes two discovery algorithms - the consecutive multiple discovery (CMD) algorithm and the parallel and incremental signature discovery (PISD) algorithm. The PISD algorithm is designed for efficiently discovering signatures under a certain discovery condition. The algorithm finds new results by using previously discovered results as candidates, rather than by using the whole database. The PISD algorithm further increases discovery efficiency by applying parallel computing. The CMD algorithm is designed to discover implicit signatures efficiently. It uses the PISD algorithm as a kernel routine to discover implicit

  20. Parallel/distributed simulation via event-reservation approach for parametric study of discrete event systems

    NASA Astrophysics Data System (ADS)

    Bhatti, Ghulam M.; Vakili, Pirooz

    1997-06-01

    There are significant opportunities for the development of parallel/distributed simulation algorithms in the context of parametric study of discrete event systems. In such studies, simulation of multiple (often a large number of) parametric variants is required in order to, for example, identify significant parameters (factor screening), determine directions for response improvement (gradient estimation), find optimal parameter settings (response optimization), or construct a model of the response (meta-modeling). The computational burden in this case is to a large extent due to the large number of alternatives that need to be simulated. An effective strategy in this context is to concurrently simulate a number of parametric variants: the structural similarity of the variants often allows for significant amount of sharing of the simulation work, and the code for concurrent simulation of the variants can often be implemented in a parallel/distributed environment. In this paper, we describe two methods of parallel/distributed/concurrent simulation called the standard clock (SC) and the general shared clock (GSC) simulation. Both approaches rely on an event-reservation approach: by contrast to most discrete-event simulation approaches that are based on an event-scheduling approach, in the SC and GSC simulation, the occurrence instances of all events are reserved on the time axis. These instances may or may not be used. This event-reservation approach frees the clock mechanism of the simulation from needing feedback from the state-update mechanism. Due to this autonomy of the clock mechanism, a single clock can be used to drive a number (possibly large) of variants concurrently and in parallel. The autonomy of the clock mechanism is also the key to the different implementation strategies we adopt. To illustrate, we describe the simulation of parametric versions of wireless communication networks on message passing and shared memory environments.

  1. Nexus: An interoperability layer for parallel and distributed computer systems

    SciTech Connect

    Foster, I.; Kesselman, C.; Olson, R.; Tuecke, S.

    1994-05-01

    Nexus is a set of services that can be used to implement various task-parallel languages, data-parallel languages, and message-passing libraries. Nexus is designed to permit the efficient portable implementation of individual parallel programming systems and the interoperability of programs developed with different tools. Nexus supports lightweight threading and active message technology, allowing integration of message passing and threads.

  2. A parallel graded-mesh FDTD algorithm for human-antenna interaction problems.

    PubMed

    Catarinucci, Luca; Tarricone, Luciano

    2009-01-01

    The finite difference time domain method (FDTD) is frequently used for the numerical solution of a wide variety of electromagnetic (EM) problems and, among them, those concerning human exposure to EM fields. In many practical cases related to the assessment of occupational EM exposure, large simulation domains are modeled and high space resolution adopted, so that strong memory and central processing unit power requirements have to be satisfied. To better afford the computational effort, the use of parallel computing is a winning approach; alternatively, subgridding techniques are often implemented. However, the simultaneous use of subgridding schemes and parallel algorithms is very new. In this paper, an easy-to-implement and highly-efficient parallel graded-mesh (GM) FDTD scheme is proposed and applied to human-antenna interaction problems, demonstrating its appropriateness in dealing with complex occupational tasks and showing its capability to guarantee the advantages of a traditional subgridding technique without affecting the parallel FDTD performance.

  3. [Parallel PLS algorithm using MapReduce and its aplication in spectral modeling].

    PubMed

    Yang, Hui-Hua; Du, Ling-Ling; Li, Ling-Qiao; Tang, Tian-Biao; Guo, Tuo; Liang, Qiong-Lin; Wang, Yi-Ming; Luo, Guo-An

    2012-09-01

    Partial least squares (PLS) has been widely used in spectral analysis and modeling, and it is computation-intensive and time-demanding when dealing with massive data To solve this problem effectively, a novel parallel PLS using MapReduce is proposed, which consists of two procedures, the parallelization of data standardizing and the parallelization of principal component computing. Using NIR spectral modeling as an example, experiments were conducted on a Hadoop cluster, which is a collection of ordinary computers. The experimental results demonstrate that the parallel PLS algorithm proposed can handle massive spectra, can significantly cut down the modeling time, and gains a basically linear speedup, and can be easily scaled up.

  4. P-RnaPredict--a parallel evolutionary algorithm for RNA folding: effects of pseudorandom number quality.

    PubMed

    Wiese, Kay C; Hendriks, Andrew; Deschênes, Alain; Ben Youssef, Belgacem

    2005-09-01

    This paper presents a fully parallel version of RnaPredict, a genetic algorithm (GA) for RNA secondary structure prediction. The research presented here builds on previous work and examines the impact of three different pseudorandom number generators (PRNGs) on the GA's performance. The three generators tested are the C standard library PRNG RAND, a parallelized multiplicative congruential generator (MCG), and a parallelized Mersenne Twister (MT). A fully parallel version of RnaPredict using the Message Passing Interface (MPI) was implemented on a 128-node Beowulf cluster. The PRNG comparison tests were performed with known structures whose sequences are 118, 122, 468, 543, and 556 nucleotides in length. The effects of the PRNGs are investigated and the predicted structures are compared to known structures. Results indicate that P-RnaPredict demonstrated good prediction accuracy, particularly so for shorter sequences.

  5. Efficient parallel algorithm of second-order Møller-Plesset perturbation theory with resolution-of-identity approximation (RI-MP2)

    NASA Astrophysics Data System (ADS)

    Katouda, Michio; Nagase, Shigeru

    An efficient parallel algorithm is developed for second-order Møller-Plesset perturbation theory with the resolution-of-identity approximation of two-electron repulsion integrals (RI-MP2) to perform MP2 energy calculations of large molecules on distributed memory processors. Benchmark calculations are carried out for taxol (C47H51NO14), valinomycin (C54H90N6O18), and two-layer nanographene sheets (C96H24)2, which show the high parallel efficiency of the developed algorithm.

  6. A Parallel Newton-Krylov-Schur Algorithm for the Reynolds-Averaged Navier-Stokes Equations

    NASA Astrophysics Data System (ADS)

    Osusky, Michal

    Aerodynamic shape optimization and multidisciplinary optimization algorithms have the potential not only to improve conventional aircraft, but also to enable the design of novel configurations. By their very nature, these algorithms generate and analyze a large number of unique shapes, resulting in high computational costs. In order to improve their efficiency and enable their use in the early stages of the design process, a fast and robust flow solution algorithm is necessary. This thesis presents an efficient parallel Newton-Krylov-Schur flow solution algorithm for the three-dimensional Navier-Stokes equations coupled with the Spalart-Allmaras one-equation turbulence model. The algorithm employs second-order summation-by-parts (SBP) operators on multi-block structured grids with simultaneous approximation terms (SATs) to enforce block interface coupling and boundary conditions. The discrete equations are solved iteratively with an inexact-Newton method, while the linear system at each Newton iteration is solved using the flexible Krylov subspace iterative method GMRES with an approximate-Schur parallel preconditioner. The algorithm is thoroughly verified and validated, highlighting the correspondence of the current algorithm with several established flow solvers. The solution for a transonic flow over a wing on a mesh of medium density (15 million nodes) shows good agreement with experimental results. Using 128 processors, deep convergence is obtained in under 90 minutes. The solution of transonic flow over the Common Research Model wing-body geometry with grids with up to 150 million nodes exhibits the expected grid convergence behavior. This case was completed as part of the Fifth AIAA Drag Prediction Workshop, with the algorithm producing solutions that compare favourably with several widely used flow solvers. The algorithm is shown to scale well on over 6000 processors. The results demonstrate the effectiveness of the SBP-SAT spatial discretization, which can

  7. Large-Scale Parallel Viscous Flow Computations using an Unstructured Multigrid Algorithm

    NASA Technical Reports Server (NTRS)

    Mavriplis, Dimitri J.

    1999-01-01

    The development and testing of a parallel unstructured agglomeration multigrid algorithm for steady-state aerodynamic flows is discussed. The agglomeration multigrid strategy uses a graph algorithm to construct the coarse multigrid levels from the given fine grid, similar to an algebraic multigrid approach, but operates directly on the non-linear system using the FAS (Full Approximation Scheme) approach. The scalability and convergence rate of the multigrid algorithm are examined on the SGI Origin 2000 and the Cray T3E. An argument is given which indicates that the asymptotic scalability of the multigrid algorithm should be similar to that of its underlying single grid smoothing scheme. For medium size problems involving several million grid points, near perfect scalability is obtained for the single grid algorithm, while only a slight drop-off in parallel efficiency is observed for the multigrid V- and W-cycles, using up to 128 processors on the SGI Origin 2000, and up to 512 processors on the Cray T3E. For a large problem using 25 million grid points, good scalability is observed for the multigrid algorithm using up to 1450 processors on a Cray T3E, even when the coarsest grid level contains fewer points than the total number of processors.

  8. Micro-seismic waveform matching inversion based on gravitational search algorithm and parallel computation

    NASA Astrophysics Data System (ADS)

    Jiang, Y.; Xing, H. L.

    2016-12-01

    Micro-seismic events induced by water injection, mining activity or oil/gas extraction are quite informative, the interpretation of which can be applied for the reconstruction of underground stress and monitoring of hydraulic fracturing progress in oil/gas reservoirs. The source characterises and locations are crucial parameters that required for these purposes, which can be obtained through the waveform matching inversion (WMI) method. Therefore it is imperative to develop a WMI algorithm with high accuracy and convergence speed. Heuristic algorithm, as a category of nonlinear method, possesses a very high convergence speed and good capacity to overcome local minimal values, and has been well applied for many areas (e.g. image processing, artificial intelligence). However, its effectiveness for micro-seismic WMI is still poorly investigated; very few literatures exits that addressing this subject. In this research an advanced heuristic algorithm, gravitational search algorithm (GSA) , is proposed to estimate the focal mechanism (angle of strike, dip and rake) and source locations in three dimension. Unlike traditional inversion methods, the heuristic algorithm inversion does not require the approximation of green function. The method directly interacts with a CPU parallelized finite difference forward modelling engine, and updating the model parameters under GSA criterions. The effectiveness of this method is tested with synthetic data form a multi-layered elastic model; the results indicate GSA can be well applied on WMI and has its unique advantages. Keywords: Micro-seismicity, Waveform matching inversion, gravitational search algorithm, parallel computation

  9. Accelerating the Gillespie Exact Stochastic Simulation Algorithm using hybrid parallel execution on graphics processing units.

    PubMed

    Komarov, Ivan; D'Souza, Roshan M

    2012-01-01

    The Gillespie Stochastic Simulation Algorithm (GSSA) and its variants are cornerstone techniques to simulate reaction kinetics in situations where the concentration of the reactant is too low to allow deterministic techniques such as differential equations. The inherent limitations of the GSSA include the time required for executing a single run and the need for multiple runs for parameter sweep exercises due to the stochastic nature of the simulation. Even very efficient variants of GSSA are prohibitively expensive to compute and perform parameter sweeps. Here we present a novel variant of the exact GSSA that is amenable to acceleration by using graphics processing units (GPUs). We parallelize the execution of a single realization across threads in a warp (fine-grained parallelism). A warp is a collection of threads that are executed synchronously on a single multi-processor. Warps executing in parallel on different multi-processors (coarse-grained parallelism) simultaneously generate multiple trajectories. Novel data-structures and algorithms reduce memory traffic, which is the bottleneck in computing the GSSA. Our benchmarks show an 8×-120× performance gain over various state-of-the-art serial algorithms when simulating different types of models.

  10. Accelerating the Gillespie Exact Stochastic Simulation Algorithm Using Hybrid Parallel Execution on Graphics Processing Units

    PubMed Central

    Komarov, Ivan; D'Souza, Roshan M.

    2012-01-01

    The Gillespie Stochastic Simulation Algorithm (GSSA) and its variants are cornerstone techniques to simulate reaction kinetics in situations where the concentration of the reactant is too low to allow deterministic techniques such as differential equations. The inherent limitations of the GSSA include the time required for executing a single run and the need for multiple runs for parameter sweep exercises due to the stochastic nature of the simulation. Even very efficient variants of GSSA are prohibitively expensive to compute and perform parameter sweeps. Here we present a novel variant of the exact GSSA that is amenable to acceleration by using graphics processing units (GPUs). We parallelize the execution of a single realization across threads in a warp (fine-grained parallelism). A warp is a collection of threads that are executed synchronously on a single multi-processor. Warps executing in parallel on different multi-processors (coarse-grained parallelism) simultaneously generate multiple trajectories. Novel data-structures and algorithms reduce memory traffic, which is the bottleneck in computing the GSSA. Our benchmarks show an 8×−120× performance gain over various state-of-the-art serial algorithms when simulating different types of models. PMID:23152751

  11. An efficient parallel algorithm: Poststack and prestack Kirchhoff 3D depth migration using flexi-depth iterations

    NASA Astrophysics Data System (ADS)

    Rastogi, Richa; Srivastava, Abhishek; Khonde, Kiran; Sirasala, Kirannmayi M.; Londhe, Ashutosh; Chavhan, Hitesh

    2015-07-01

    This paper presents an efficient parallel 3D Kirchhoff depth migration algorithm suitable for current class of multicore architecture. The fundamental Kirchhoff depth migration algorithm exhibits inherent parallelism however, when it comes to 3D data migration, as the data size increases the resource requirement of the algorithm also increases. This challenges its practical implementation even on current generation high performance computing systems. Therefore a smart parallelization approach is essential to handle 3D data for migration. The most compute intensive part of Kirchhoff depth migration algorithm is the calculation of traveltime tables due to its resource requirements such as memory/storage and I/O. In the current research work, we target this area and develop a competent parallel algorithm for post and prestack 3D Kirchhoff depth migration, using hybrid MPI+OpenMP programming techniques. We introduce a concept of flexi-depth iterations while depth migrating data in parallel imaging space, using optimized traveltime table computations. This concept provides flexibility to the algorithm by migrating data in a number of depth iterations, which depends upon the available node memory and the size of data to be migrated during runtime. Furthermore, it minimizes the requirements of storage, I/O and inter-node communication, thus making it advantageous over the conventional parallelization approaches. The developed parallel algorithm is demonstrated and analysed on Yuva II, a PARAM series of supercomputers. Optimization, performance and scalability experiment results along with the migration outcome show the effectiveness of the parallel algorithm.

  12. Parallel algorithms for computer vision. Annual report No. 2, 31 August 1986-31 August 1987

    SciTech Connect

    Poggio, T.; Little, J.

    1988-03-01

    Much work during the past year has focused on building the Vision Machine system. The Vision Machine is a testbed for the research on parallel vision algorithms and their integration. The system consists of an input device--a movable two-camera Eye-Head system with six degrees of freedom--and the 16K Connection Machine (CM-1). The authors concentrated on implementing and testing early vision algorithms, and on developing a new sophisticated techniques for their integration. The output of the integration stage will be used for navigation and recognition tasks. From August 31, 1986 to August 31, 1987. The Connection Machine delivered on July 31, 1986 by Thinking Machines Corporation was used. A substantial body of vision software was developed and tested on the machine. Also nearly completed was the development of an integrated Vision Machine that includes several early vision algorithms, and integration stage of middle vision. As outlined in their original proposal, the authors have begun to explore parallel algorithms at the higher level of recognition. They have also studied the performance of alternative, nonconventional architectures for navigation, and worked on the difficult issue of alternative parallel languages for the Connection Machine, in addition to LISP and C. The body of this report gives an overview of the results of the research during the second twelve month of funding.

  13. OpenMP Parallelization and Optimization of Graph-Based Machine Learning Algorithms

    SciTech Connect

    Meng, Zhaoyi; Koniges, Alice; He, Yun Helen; Williams, Samuel; Kurth, Thorsten; Cook, Brandon; Deslippe, Jack; Bertozzi, Andrea L.

    2016-09-21

    In this paper, we investigate the OpenMP parallelization and optimization of two novel data classification algorithms. The new algorithms are based on graph and PDE solution techniques and provide significant accuracy and performance advantages over traditional data classification algorithms in serial mode. The methods leverage the Nystrom extension to calculate eigenvalue/eigenvectors of the graph Laplacian and this is a self-contained module that can be used in conjunction with other graph-Laplacian based methods such as spectral clustering. We use performance tools to collect the hotspots and memory access of the serial codes and use OpenMP as the parallelization language to parallelize the most time-consuming parts. Where possible, we also use library routines. We then optimize the OpenMP implementations and detail the performance on traditional supercomputer nodes (in our case a Cray XC30), and test the optimization steps on emerging testbed systems based on Intel’s Knights Corner and Landing processors. We show both performance improvement and strong scaling behavior. Finally, a large number of optimization techniques and analyses are necessary before the algorithm reaches almost ideal scaling.

  14. A Fast Parallel Algorithm for Selected Inversion of Structured Sparse Matrices with Application to 2D Electronic Structure Calculations

    SciTech Connect

    Lin, Lin; Yang, Chao; Lu, Jiangfeng; Ying, Lexing; E, Weinan

    2009-09-25

    We present an efficient parallel algorithm and its implementation for computing the diagonal of $H^-1$ where $H$ is a 2D Kohn-Sham Hamiltonian discretized on a rectangular domain using a standard second order finite difference scheme. This type of calculation can be used to obtain an accurate approximation to the diagonal of a Fermi-Dirac function of $H$ through a recently developed pole-expansion technique \\cite{LinLuYingE2009}. The diagonal elements are needed in electronic structure calculations for quantum mechanical systems \\citeHohenbergKohn1964, KohnSham 1965,DreizlerGross1990. We show how elimination tree is used to organize the parallel computation and how synchronization overhead is reduced by passing data level by level along this tree using the technique of local buffers and relative indices. We analyze the performance of our implementation by examining its load balance and communication overhead. We show that our implementation exhibits an excellent weak scaling on a large-scale high performance distributed parallel machine. When compared with standard approach for evaluating the diagonal a Fermi-Dirac function of a Kohn-Sham Hamiltonian associated a 2D electron quantum dot, the new pole-expansion technique that uses our algorithm to compute the diagonal of $(H-z_i I)^-1$ for a small number of poles $z_i$ is much faster, especially when the quantum dot contains many electrons.

  15. Distributed machine learning: Scaling up with coarse-grained parallelism

    SciTech Connect

    Provost, F.J.; Hennessy, D.N.

    1994-12-31

    Machine teaming methods are becoming accepted as additions to the biologist`s data-analysis tool kit. However, scaling these techniques up to large data sets, such as those in biological and medical domains, is problematic in terms of both the required computational search effort and required memory (and the detrimental effects of excessive swapping). Our approach to tackling the problem of scaling up to large datasets is to take advantage of the ubiquitous workstation networks that are generally available in scientific and engineering environments. This paper introduces the notion of the invariant-partitioning property--that for certain evaluation criteria it is possible to partition a data set across multiple processors such that any rule that is satisfactory over the entire data set will also be satisfactory on at least one subset. In addition, by taking advantage of cooperation through interprocess communication, it is possible to build distributed learning algorithms such that only rules that are satisfactory over the entire data set will be learned. We describe a distributed learning system, CorPRL, that takes advantage of the invariant-partitioning property to learn from very large data sets, and present results demonstrating CorPRL`s effectiveness in analyzing data from two databases.

  16. Model of stacked long Josephson junctions: Parallel algorithm and numerical results in case of weak coupling

    NASA Astrophysics Data System (ADS)

    Zemlyanaya, E. V.; Bashashin, M. V.; Rahmonov, I. R.; Shukrinov, Yu. M.; Atanasova, P. Kh.; Volokhova, A. V.

    2016-10-01

    We consider a model of system of long Josephson junctions (LJJ) with inductive and capacitive coupling. Corresponding system of nonlinear partial differential equations is solved by means of the standard three-point finite-difference approximation in the spatial coordinate and utilizing the Runge-Kutta method for solution of the resulting Cauchy problem. A parallel algorithm is developed and implemented on a basis of the MPI (Message Passing Interface) technology. Effect of the coupling between the JJs on the properties of LJJ system is demonstrated. Numerical results are discussed from the viewpoint of effectiveness of parallel implementation.

  17. A parallel finite volume algorithm for large-eddy simulation of turbulent flows

    NASA Astrophysics Data System (ADS)

    Bui, Trong Tri

    1998-11-01

    A parallel unstructured finite volume algorithm is developed for large-eddy simulation of compressible turbulent flows. Major components of the algorithm include piecewise linear least-square reconstruction of the unknown variables, trilinear finite element interpolation for the spatial coordinates, Roe flux difference splitting, and second-order MacCormack explicit time marching. The computer code is designed from the start to take full advantage of the additional computational capability provided by the current parallel computer systems. Parallel implementation is done using the message passing programming model and message passing libraries such as the Parallel Virtual Machine (PVM) and Message Passing Interface (MPI). The development of the numerical algorithm is presented in detail. The parallel strategy and issues regarding the implementation of a flow simulation code on the current generation of parallel machines are discussed. The results from parallel performance studies show that the algorithm is well suited for parallel computer systems that use the message passing programming model. Nearly perfect parallel speedup is obtained on MPP systems such as the Cray T3D and IBM SP2. Performance comparison with the older supercomputer systems such as the Cray YMP show that the simulations done on the parallel systems are approximately 10 to 30 times faster. The results of the accuracy and performance studies for the current algorithm are reported. To validate the flow simulation code, a number of Euler and Navier-Stokes simulations are done for internal duct flows. Inviscid Euler simulation of a very small amplitude acoustic wave interacting with a shock wave in a quasi-1D convergent-divergent nozzle shows that the algorithm is capable of simultaneously tracking the very small disturbances of the acoustic wave and capturing the shock wave. Navier-Stokes simulations are made for fully developed laminar flow in a square duct, developing laminar flow in a

  18. Parallelizing Sylvester-like operations on a distributed memory computer

    SciTech Connect

    Hu, D.Y.; Sorensen, D.C.

    1994-12-31

    Discretization of linear operators arising in applied mathematics often leads to matrices with the following structure: M(x) = (D {circle_times} A + B {circle_times} I{sub n} + V)x, where x {element_of} R{sup mn}, B, D {element_of} R{sup nxn}, A {element_of} R{sup mxm} and V {element_of} R{sup mnxmn}; both D and V are diagonal. For the notational convenience, the authors assume that both A and B are symmetric. All the results through this paper can be easily extended to the cases with general A and B. The linear operator on R{sup mn} defined above can be viewed as a generalization of the Sylvester operator: S(x) = (I{sub m} {circle_times} A + B {circle_times} I{sub n})x. The authors therefore refer to it as a Sylvester-like operator. The schemes discussed in this paper therefore also apply to Sylvester operator. In this paper, the authors present the SIMD scheme for parallelization of the Sylvester-like operator on a distributed memory computer. This scheme is designed to approach the best possible efficiency by avoiding unnecessary communication among processors.

  19. Parallel distributed processing: Implications for cognition and development. Technical report

    SciTech Connect

    McClelland, J.L.

    1988-07-11

    This paper provides a brief overview of the connectionist or parallel distributed processing framework for modeling cognitive processes, and considers the application of the connectionist framework to problems of cognitive development. Several aspects of cognitive development might result from the process of learning as it occurs in multi-layer networks. This learning process has the characteristic that it reduces the discrepancy between expected and observed events. As it does this, representations develop on hidden units which dramatically change both the way in which the network represents the environment from which it learns and the expectations that the network generates about environmental events. The learning process exhibits relatively abrupt transitions corresponding to stage shifts in cognitive development. These points are illustrated using a network that learns to anticipate which side of a balance beam will go down, based on the number of weights on each side of the fulcrum and their distance from the fulcrum on each side of the beam. The network is trained in an environment in which weight more frequently governs which side will go down. It recapitulates the states of development seen in children, as well as the stage transitions, as it learns to represent weight and distance information.

  20. A parallel systematic-Monte Carlo algorithm for exploring conformational space.

    PubMed

    Perez-Riverol, Yasset; Vera, Roberto; Mazola, Yuliet; Musacchio, Alexis

    2012-01-01

    Computational algorithms to explore the conformational space of small molecules are complex and computer demand field in chemoinformatics. In this paper a hybrid algorithm to explore the conformational space of organic molecules is presented. This hybrid algorithm is based in a systematic search approach combined with a Monte Carlo based method in order to obtain an ensemble of low-energy conformations simulating the flexibility of small chemical compounds. The Monte Carlo method uses the Metropolis criterion to accept or reject a conformation through an in-house implementation of the MMFF94s force field to calculate the conformational energy. The parallel design of this algorithm, based on the message passing interface (MPI) paradigm, was implemented. The results showed a performance increase in the terms of speed and efficiency.