WorldWideScience

Sample records for parallel computational library

  1. Application Portable Parallel Library

    Science.gov (United States)

    Cole, Gary L.; Blech, Richard A.; Quealy, Angela; Townsend, Scott

    1995-01-01

    Application Portable Parallel Library (APPL) computer program is subroutine-based message-passing software library intended to provide consistent interface to variety of multiprocessor computers on market today. Minimizes effort needed to move application program from one computer to another. User develops application program once and then easily moves application program from parallel computer on which created to another parallel computer. ("Parallel computer" also include heterogeneous collection of networked computers). Written in C language with one FORTRAN 77 subroutine for UNIX-based computers and callable from application programs written in C language or FORTRAN 77.

  2. The specification of Stampi, a message passing library for distributed parallel computing

    International Nuclear Information System (INIS)

    Imamura, Toshiyuki; Takemiya, Hiroshi; Koide, Hiroshi

    2000-03-01

    At CCSE, Center for Promotion of Computational Science and Engineering, a new message passing library for heterogeneous and distributed parallel computing has been developed, and it is called as Stampi. Stampi enables us to communicate between any combination of parallel computers as well as workstations. Currently, a Stampi system is constructed from Stampi library and Stampi/Java. It provides functions to connect a Stampi application with not only those on COMPACS, COMplex Parallel Computer System, but also applets which work on WWW browsers. This report summarizes the specifications of Stampi and details the development of its system. (author)

  3. Portable programming on parallel/networked computers using the Application Portable Parallel Library (APPL)

    Science.gov (United States)

    Quealy, Angela; Cole, Gary L.; Blech, Richard A.

    1993-01-01

    The Application Portable Parallel Library (APPL) is a subroutine-based library of communication primitives that is callable from applications written in FORTRAN or C. APPL provides a consistent programmer interface to a variety of distributed and shared-memory multiprocessor MIMD machines. The objective of APPL is to minimize the effort required to move parallel applications from one machine to another, or to a network of homogeneous machines. APPL encompasses many of the message-passing primitives that are currently available on commercial multiprocessor systems. This paper describes APPL (version 2.3.1) and its usage, reports the status of the APPL project, and indicates possible directions for the future. Several applications using APPL are discussed, as well as performance and overhead results.

  4. Stampi: a message passing library for distributed parallel computing. User's guide

    International Nuclear Information System (INIS)

    Imamura, Toshiyuki; Koide, Hiroshi; Takemiya, Hiroshi

    1998-11-01

    A new message passing library, Stampi, has been developed to realize a computation with different kind of parallel computers arbitrarily and making MPI (Message Passing Interface) as an unique interface for communication. Stampi is based on MPI2 specification. It realizes dynamic process creation to different machines and communication between spawned one within the scope of MPI semantics. Vender implemented MPI as a closed system in one parallel machine and did not support both functions; process creation and communication to external machines. Stampi supports both functions and enables us distributed parallel computing. Currently Stampi has been implemented on COMPACS (COMplex PArallel Computer System) introduced in CCSE, five parallel computers and one graphic workstation, and any communication on them can be processed on. (author)

  5. Stampi: a message passing library for distributed parallel computing. User's guide, second edition

    International Nuclear Information System (INIS)

    Imamura, Toshiyuki; Koide, Hiroshi; Takemiya, Hiroshi

    2000-02-01

    A new message passing library, Stampi, has been developed to realize a computation with different kind of parallel computers arbitrarily and making MPI (Message Passing Interface) as an unique interface for communication. Stampi is based on the MPI2 specification, and it realizes dynamic process creation to different machines and communication between spawned one within the scope of MPI semantics. Main features of Stampi are summarized as follows: (i) an automatic switch function between external- and internal communications, (ii) a message routing/relaying with a routing module, (iii) a dynamic process creation, (iv) a support of two types of connection, Master/Slave and Client/Server, (v) a support of a communication with Java applets. Indeed vendors implemented MPI libraries as a closed system in one parallel machine or their systems, and did not support both functions; process creation and communication to external machines. Stampi supports both functions and enables us distributed parallel computing. Currently Stampi has been implemented on COMPACS (COMplex PArallel Computer System) introduced in CCSE, five parallel computers and one graphic workstation, moreover on eight kinds of parallel machines, totally fourteen systems. Stampi provides us MPI communication functionality on them. This report describes mainly the usage of Stampi. (author)

  6. Parallel computations

    CERN Document Server

    1982-01-01

    Parallel Computations focuses on parallel computation, with emphasis on algorithms used in a variety of numerical and physical applications and for many different types of parallel computers. Topics covered range from vectorization of fast Fourier transforms (FFTs) and of the incomplete Cholesky conjugate gradient (ICCG) algorithm on the Cray-1 to calculation of table lookups and piecewise functions. Single tridiagonal linear systems and vectorized computation of reactive flow are also discussed.Comprised of 13 chapters, this volume begins by classifying parallel computers and describing techn

  7. The ELPA library: scalable parallel eigenvalue solutions for electronic structure theory and computational science.

    Science.gov (United States)

    Marek, A; Blum, V; Johanni, R; Havu, V; Lang, B; Auckenthaler, T; Heinecke, A; Bungartz, H-J; Lederer, H

    2014-05-28

    Obtaining the eigenvalues and eigenvectors of large matrices is a key problem in electronic structure theory and many other areas of computational science. The computational effort formally scales as O(N(3)) with the size of the investigated problem, N (e.g. the electron count in electronic structure theory), and thus often defines the system size limit that practical calculations cannot overcome. In many cases, more than just a small fraction of the possible eigenvalue/eigenvector pairs is needed, so that iterative solution strategies that focus only on a few eigenvalues become ineffective. Likewise, it is not always desirable or practical to circumvent the eigenvalue solution entirely. We here review some current developments regarding dense eigenvalue solvers and then focus on the Eigenvalue soLvers for Petascale Applications (ELPA) library, which facilitates the efficient algebraic solution of symmetric and Hermitian eigenvalue problems for dense matrices that have real-valued and complex-valued matrix entries, respectively, on parallel computer platforms. ELPA addresses standard as well as generalized eigenvalue problems, relying on the well documented matrix layout of the Scalable Linear Algebra PACKage (ScaLAPACK) library but replacing all actual parallel solution steps with subroutines of its own. For these steps, ELPA significantly outperforms the corresponding ScaLAPACK routines and proprietary libraries that implement the ScaLAPACK interface (e.g. Intel's MKL). The most time-critical step is the reduction of the matrix to tridiagonal form and the corresponding backtransformation of the eigenvectors. ELPA offers both a one-step tridiagonalization (successive Householder transformations) and a two-step transformation that is more efficient especially towards larger matrices and larger numbers of CPU cores. ELPA is based on the MPI standard, with an early hybrid MPI-OpenMPI implementation available as well. Scalability beyond 10,000 CPU cores for problem

  8. Starpc: a library for communication among tools on a parallel computer cluster. User's and developer's guide to Starpc

    International Nuclear Information System (INIS)

    Takemiya, Hiroshi; Yamagishi, Nobuhiro

    2000-02-01

    We report on a RPC(Remote Procedure Call)-based communication library, Starpc, for a parallel computer cluster. Starpc supports communication between Java Applets and C programs as well as between C programs. Starpc has the following three features. (1) It enables communication between Java Applets and C programs on an arbitrary computer without security violation, although Java Applets are supposed to communicate only with programs on the specific computer (Web server) in subject to a restriction on security. (2) Diverse network communication protocols are available on Starpc, because of using Nexus communication library developed at Argonne National Laboratory. (3) It works on many kinds of computers including eight parallel computers and four WS servers. In this report, the usage of Starpc and the development of applications using Starpc are described. (author)

  9. The STAPL Parallel Graph Library

    KAUST Repository

    Harshvardhan,; Fidel, Adam; Amato, Nancy M.; Rauchwerger, Lawrence

    2013-01-01

    This paper describes the stapl Parallel Graph Library, a high-level framework that abstracts the user from data-distribution and parallelism details and allows them to concentrate on parallel graph algorithm development. It includes a customizable

  10. Parallel computation

    International Nuclear Information System (INIS)

    Jejcic, A.; Maillard, J.; Maurel, G.; Silva, J.; Wolff-Bacha, F.

    1997-01-01

    The work in the field of parallel processing has developed as research activities using several numerical Monte Carlo simulations related to basic or applied current problems of nuclear and particle physics. For the applications utilizing the GEANT code development or improvement works were done on parts simulating low energy physical phenomena like radiation, transport and interaction. The problem of actinide burning by means of accelerators was approached using a simulation with the GEANT code. A program of neutron tracking in the range of low energies up to the thermal region has been developed. It is coupled to the GEANT code and permits in a single pass the simulation of a hybrid reactor core receiving a proton burst. Other works in this field refers to simulations for nuclear medicine applications like, for instance, development of biological probes, evaluation and characterization of the gamma cameras (collimators, crystal thickness) as well as the method for dosimetric calculations. Particularly, these calculations are suited for a geometrical parallelization approach especially adapted to parallel machines of the TN310 type. Other works mentioned in the same field refer to simulation of the electron channelling in crystals and simulation of the beam-beam interaction effect in colliders. The GEANT code was also used to simulate the operation of germanium detectors designed for natural and artificial radioactivity monitoring of environment

  11. Parallel Computation on Multicore Processors Using Explicit Form of the Finite Element Method and C++ Standard Libraries

    Directory of Open Access Journals (Sweden)

    Rek Václav

    2016-11-01

    Full Text Available In this paper, the form of modifications of the existing sequential code written in C or C++ programming language for the calculation of various kind of structures using the explicit form of the Finite Element Method (Dynamic Relaxation Method, Explicit Dynamics in the NEXX system is introduced. The NEXX system is the core of engineering software NEXIS, Scia Engineer, RFEM and RENEX. It has the possibilities of multithreaded running, which can now be supported at the level of native C++ programming language using standard libraries. Thanks to the high degree of abstraction that a contemporary C++ programming language provides, a respective library created in this way can be very generalized for other purposes of usage of parallelism in computational mechanics.

  12. The STAPL Parallel Graph Library

    KAUST Repository

    Harshvardhan,

    2013-01-01

    This paper describes the stapl Parallel Graph Library, a high-level framework that abstracts the user from data-distribution and parallelism details and allows them to concentrate on parallel graph algorithm development. It includes a customizable distributed graph container and a collection of commonly used parallel graph algorithms. The library introduces pGraph pViews that separate algorithm design from the container implementation. It supports three graph processing algorithmic paradigms, level-synchronous, asynchronous and coarse-grained, and provides common graph algorithms based on them. Experimental results demonstrate improved scalability in performance and data size over existing graph libraries on more than 16,000 cores and on internet-scale graphs containing over 16 billion vertices and 250 billion edges. © Springer-Verlag Berlin Heidelberg 2013.

  13. Library Computing

    Science.gov (United States)

    Library Computing, 1985

    1985-01-01

    Special supplement to "Library Journal" and "School Library Journal" covers topics of interest to school, public, academic, and special libraries planning for automation: microcomputer use, readings in automation, online searching, databases of microcomputer software, public access to microcomputers, circulation, creating a…

  14. Performance Analysis of Parallel Mathematical Subroutine library PARCEL

    International Nuclear Information System (INIS)

    Yamada, Susumu; Shimizu, Futoshi; Kobayashi, Kenichi; Kaburaki, Hideo; Kishida, Norio

    2000-01-01

    The parallel mathematical subroutine library PARCEL (Parallel Computing Elements) has been developed by Japan Atomic Energy Research Institute for easy use of typical parallelized mathematical codes in any application problems on distributed parallel computers. The PARCEL includes routines for linear equations, eigenvalue problems, pseudo-random number generation, and fast Fourier transforms. It is shown that the results of performance for linear equations routines exhibit good parallelization efficiency on vector, as well as scalar, parallel computers. A comparison of the efficiency results with the PETSc (Portable Extensible Tool kit for Scientific Computations) library has been reported. (author)

  15. Parallel computing works!

    CERN Document Server

    Fox, Geoffrey C; Messina, Guiseppe C

    2014-01-01

    A clear illustration of how parallel computers can be successfully appliedto large-scale scientific computations. This book demonstrates how avariety of applications in physics, biology, mathematics and other scienceswere implemented on real parallel computers to produce new scientificresults. It investigates issues of fine-grained parallelism relevant forfuture supercomputers with particular emphasis on hypercube architecture. The authors describe how they used an experimental approach to configuredifferent massively parallel machines, design and implement basic systemsoftware, and develop

  16. Parallel computing works

    Energy Technology Data Exchange (ETDEWEB)

    1991-10-23

    An account of the Caltech Concurrent Computation Program (C{sup 3}P), a five year project that focused on answering the question: Can parallel computers be used to do large-scale scientific computations '' As the title indicates, the question is answered in the affirmative, by implementing numerous scientific applications on real parallel computers and doing computations that produced new scientific results. In the process of doing so, C{sup 3}P helped design and build several new computers, designed and implemented basic system software, developed algorithms for frequently used mathematical computations on massively parallel machines, devised performance models and measured the performance of many computers, and created a high performance computing facility based exclusively on parallel computers. While the initial focus of C{sup 3}P was the hypercube architecture developed by C. Seitz, many of the methods developed and lessons learned have been applied successfully on other massively parallel architectures.

  17. SCELib2: the new revision of SCELib, the parallel computational library of molecular properties in the single center approach

    Science.gov (United States)

    Sanna, N.; Morelli, G.

    2004-09-01

    In this paper we present the new version of the SCELib program (CPC Catalogue identifier ADMG) a full numerical implementation of the Single Center Expansion (SCE) method. The physics involved is that of producing the SCE description of molecular electronic densities, of molecular electrostatic potentials and of molecular perturbed potentials due to a point negative or positive charge. This new revision of the program has been optimized to run in serial as well as in parallel execution mode, to support a larger set of molecular symmetries and to permit the restart of long-lasting calculations. To measure the performance of this new release, a comparative study has been carried out on the most powerful computing architectures in serial and parallel runs. The results of the calculations reported in this paper refer to real cases medium to large molecular systems and they are reported in full details to benchmark at best the parallel architectures the new SCELib code will run on. Program summaryTitle of program: SCELib2 Catalogue identifier: ADGU Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADGU Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Reference to previous versions: Comput. Phys. Commun. 128 (2) (2000) 139 (CPC catalogue identifier: ADMG) Does the new version supersede the original program?: Yes Computer for which the program is designed and others on which it has been tested: HP ES45 and rx2600, SUN ES4500, IBM SP and any single CPU workstation based on Alpha, SPARC, POWER, Itanium2 and X86 processors Installations: CASPUR, local Operating systems under which the program has been tested: HP Tru64 V5.X, SUNOS V5.8, IBM AIX V5.X, Linux RedHat V8.0 Programming language used: C Memory required to execute with typical data: 10 Mwords. Up to 2000 Mwords depending on the molecular system and runtime parameters No. of bits in a word: 64 No. of processors used: 1 to 32 Has the code been vectorized or parallelized?: Yes

  18. Parallelism in matrix computations

    CERN Document Server

    Gallopoulos, Efstratios; Sameh, Ahmed H

    2016-01-01

    This book is primarily intended as a research monograph that could also be used in graduate courses for the design of parallel algorithms in matrix computations. It assumes general but not extensive knowledge of numerical linear algebra, parallel architectures, and parallel programming paradigms. The book consists of four parts: (I) Basics; (II) Dense and Special Matrix Computations; (III) Sparse Matrix Computations; and (IV) Matrix functions and characteristics. Part I deals with parallel programming paradigms and fundamental kernels, including reordering schemes for sparse matrices. Part II is devoted to dense matrix computations such as parallel algorithms for solving linear systems, linear least squares, the symmetric algebraic eigenvalue problem, and the singular-value decomposition. It also deals with the development of parallel algorithms for special linear systems such as banded ,Vandermonde ,Toeplitz ,and block Toeplitz systems. Part III addresses sparse matrix computations: (a) the development of pa...

  19. Practical parallel computing

    CERN Document Server

    Morse, H Stephen

    1994-01-01

    Practical Parallel Computing provides information pertinent to the fundamental aspects of high-performance parallel processing. This book discusses the development of parallel applications on a variety of equipment.Organized into three parts encompassing 12 chapters, this book begins with an overview of the technology trends that converge to favor massively parallel hardware over traditional mainframes and vector machines. This text then gives a tutorial introduction to parallel hardware architectures. Other chapters provide worked-out examples of programs using several parallel languages. Thi

  20. Algorithmically specialized parallel computers

    CERN Document Server

    Snyder, Lawrence; Gannon, Dennis B

    1985-01-01

    Algorithmically Specialized Parallel Computers focuses on the concept and characteristics of an algorithmically specialized computer.This book discusses the algorithmically specialized computers, algorithmic specialization using VLSI, and innovative architectures. The architectures and algorithms for digital signal, speech, and image processing and specialized architectures for numerical computations are also elaborated. Other topics include the model for analyzing generalized inter-processor, pipelined architecture for search tree maintenance, and specialized computer organization for raster

  1. Parallel reservoir simulator computations

    International Nuclear Information System (INIS)

    Hemanth-Kumar, K.; Young, L.C.

    1995-01-01

    The adaptation of a reservoir simulator for parallel computations is described. The simulator was originally designed for vector processors. It performs approximately 99% of its calculations in vector/parallel mode and relative to scalar calculations it achieves speedups of 65 and 81 for black oil and EOS simulations, respectively on the CRAY C-90

  2. Design considerations for parallel graphics libraries

    Science.gov (United States)

    Crockett, Thomas W.

    1994-01-01

    Applications which run on parallel supercomputers are often characterized by massive datasets. Converting these vast collections of numbers to visual form has proven to be a powerful aid to comprehension. For a variety of reasons, it may be desirable to provide this visual feedback at runtime. One way to accomplish this is to exploit the available parallelism to perform graphics operations in place. In order to do this, we need appropriate parallel rendering algorithms and library interfaces. This paper provides a tutorial introduction to some of the issues which arise in designing parallel graphics libraries and their underlying rendering algorithms. The focus is on polygon rendering for distributed memory message-passing systems. We illustrate our discussion with examples from PGL, a parallel graphics library which has been developed on the Intel family of parallel systems.

  3. Algorithms for parallel computers

    International Nuclear Information System (INIS)

    Churchhouse, R.F.

    1985-01-01

    Until relatively recently almost all the algorithms for use on computers had been designed on the (usually unstated) assumption that they were to be run on single processor, serial machines. With the introduction of vector processors, array processors and interconnected systems of mainframes, minis and micros, however, various forms of parallelism have become available. The advantage of parallelism is that it offers increased overall processing speed but it also raises some fundamental questions, including: (i) which, if any, of the existing 'serial' algorithms can be adapted for use in the parallel mode. (ii) How close to optimal can such adapted algorithms be and, where relevant, what are the convergence criteria. (iii) How can we design new algorithms specifically for parallel systems. (iv) For multi-processor systems how can we handle the software aspects of the interprocessor communications. Aspects of these questions illustrated by examples are considered in these lectures. (orig.)

  4. Parallel Computing in SCALE

    International Nuclear Information System (INIS)

    DeHart, Mark D.; Williams, Mark L.; Bowman, Stephen M.

    2010-01-01

    The SCALE computational architecture has remained basically the same since its inception 30 years ago, although constituent modules and capabilities have changed significantly. This SCALE concept was intended to provide a framework whereby independent codes can be linked to provide a more comprehensive capability than possible with the individual programs - allowing flexibility to address a wide variety of applications. However, the current system was designed originally for mainframe computers with a single CPU and with significantly less memory than today's personal computers. It has been recognized that the present SCALE computation system could be restructured to take advantage of modern hardware and software capabilities, while retaining many of the modular features of the present system. Preliminary work is being done to define specifications and capabilities for a more advanced computational architecture. This paper describes the state of current SCALE development activities and plans for future development. With the release of SCALE 6.1 in 2010, a new phase of evolutionary development will be available to SCALE users within the TRITON and NEWT modules. The SCALE (Standardized Computer Analyses for Licensing Evaluation) code system developed by Oak Ridge National Laboratory (ORNL) provides a comprehensive and integrated package of codes and nuclear data for a wide range of applications in criticality safety, reactor physics, shielding, isotopic depletion and decay, and sensitivity/uncertainty (S/U) analysis. Over the last three years, since the release of version 5.1 in 2006, several important new codes have been introduced within SCALE, and significant advances applied to existing codes. Many of these new features became available with the release of SCALE 6.0 in early 2009. However, beginning with SCALE 6.1, a first generation of parallel computing is being introduced. In addition to near-term improvements, a plan for longer term SCALE enhancement

  5. Applied Parallel Computing Industrial Computation and Optimization

    DEFF Research Database (Denmark)

    Madsen, Kaj; NA NA NA Olesen, Dorte

    Proceedings and the Third International Workshop on Applied Parallel Computing in Industrial Problems and Optimization (PARA96)......Proceedings and the Third International Workshop on Applied Parallel Computing in Industrial Problems and Optimization (PARA96)...

  6. Computers in Academic Architecture Libraries.

    Science.gov (United States)

    Willis, Alfred; And Others

    1992-01-01

    Computers are widely used in architectural research and teaching in U.S. schools of architecture. A survey of libraries serving these schools sought information on the emphasis placed on computers by the architectural curriculum, accessibility of computers to library staff, and accessibility of computers to library patrons. Survey results and…

  7. A high-speed linear algebra library with automatic parallelism

    Science.gov (United States)

    Boucher, Michael L.

    1994-01-01

    Parallel or distributed processing is key to getting highest performance workstations. However, designing and implementing efficient parallel algorithms is difficult and error-prone. It is even more difficult to write code that is both portable to and efficient on many different computers. Finally, it is harder still to satisfy the above requirements and include the reliability and ease of use required of commercial software intended for use in a production environment. As a result, the application of parallel processing technology to commercial software has been extremely small even though there are numerous computationally demanding programs that would significantly benefit from application of parallel processing. This paper describes DSSLIB, which is a library of subroutines that perform many of the time-consuming computations in engineering and scientific software. DSSLIB combines the high efficiency and speed of parallel computation with a serial programming model that eliminates many undesirable side-effects of typical parallel code. The result is a simple way to incorporate the power of parallel processing into commercial software without compromising maintainability, reliability, or ease of use. This gives significant advantages over less powerful non-parallel entries in the market.

  8. Event monitoring of parallel computations

    Directory of Open Access Journals (Sweden)

    Gruzlikov Alexander M.

    2015-06-01

    Full Text Available The paper considers the monitoring of parallel computations for detection of abnormal events. It is assumed that computations are organized according to an event model, and monitoring is based on specific test sequences

  9. GASPRNG: GPU accelerated scalable parallel random number generator library

    Science.gov (United States)

    Gao, Shuang; Peterson, Gregory D.

    2013-04-01

    Graphics processors represent a promising technology for accelerating computational science applications. Many computational science applications require fast and scalable random number generation with good statistical properties, so they use the Scalable Parallel Random Number Generators library (SPRNG). We present the GPU Accelerated SPRNG library (GASPRNG) to accelerate SPRNG in GPU-based high performance computing systems. GASPRNG includes code for a host CPU and CUDA code for execution on NVIDIA graphics processing units (GPUs) along with a programming interface to support various usage models for pseudorandom numbers and computational science applications executing on the CPU, GPU, or both. This paper describes the implementation approach used to produce high performance and also describes how to use the programming interface. The programming interface allows a user to be able to use GASPRNG the same way as SPRNG on traditional serial or parallel computers as well as to develop tightly coupled programs executing primarily on the GPU. We also describe how to install GASPRNG and use it. To help illustrate linking with GASPRNG, various demonstration codes are included for the different usage models. GASPRNG on a single GPU shows up to 280x speedup over SPRNG on a single CPU core and is able to scale for larger systems in the same manner as SPRNG. Because GASPRNG generates identical streams of pseudorandom numbers as SPRNG, users can be confident about the quality of GASPRNG for scalable computational science applications. Catalogue identifier: AEOI_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEOI_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: UTK license. No. of lines in distributed program, including test data, etc.: 167900 No. of bytes in distributed program, including test data, etc.: 1422058 Distribution format: tar.gz Programming language: C and CUDA. Computer: Any PC or

  10. SCELib3.0: The new revision of SCELib, the parallel computational library of molecular properties in the Single Center Approach

    Science.gov (United States)

    Sanna, N.; Baccarelli, I.; Morelli, G.

    2009-12-01

    SCELib is a computer program which implements the Single Center Expansion (SCE) method to describe molecular electronic densities and the interaction potentials between a charged projectile (electron or positron) and a target molecular system. The first version (CPC Catalog identifier ADMG_v1_0) was submitted to the CPC Program Library in 2000, and version 2.0 (ADMG_v2_0) was submitted in 2004. We here announce the new release 3.0 which presents additional features with respect to the previous versions aiming at a significative enhance of its capabilities to deal with larger molecular systems. SCELib 3.0 allows for ab initio effective core potential (ECP) calculations of the molecular wavefunctions to be used in the SCE method in addition to the standard all-electron description of the molecule. The list of supported architectures has been updated and the code has been ported to platforms based on accelerating coprocessors, such as the NVIDIA GPGPU and the new parallel model adopted is able to efficiently run on a mixed many-core computing system. Program summaryProgram title: SCELib3.0 Catalogue identifier: ADMG_v3_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADMG_v3_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 2 018 862 No. of bytes in distributed program, including test data, etc.: 4 955 014 Distribution format: tar.gz Programming language: C Compilers used: xlc V8.x, Intel C V10.x, Portland Group V7.x, nvcc V2.x Computer: All SMP platforms based on AIX, Linux and SUNOS operating systems over SPARC, POWER, Intel Itanium2, X86, em64t and Opteron processors Operating system: SUNOS, IBM AIX, Linux RedHat (Enterprise), Linux SuSE (SLES) Has the code been vectorized or parallelized?: Yes. 1 to 32 (CPU or GPU) used RAM: Up to 32 GB depending on the molecular

  11. Massively parallel quantum computer simulator

    NARCIS (Netherlands)

    De Raedt, K.; Michielsen, K.; De Raedt, H.; Trieu, B.; Arnold, G.; Richter, M.; Lippert, Th.; Watanabe, H.; Ito, N.

    2007-01-01

    We describe portable software to simulate universal quantum computers on massive parallel Computers. We illustrate the use of the simulation software by running various quantum algorithms on different computer architectures, such as a IBM BlueGene/L, a IBM Regatta p690+, a Hitachi SR11000/J1, a Cray

  12. Applications of the parallel computing system using network

    International Nuclear Information System (INIS)

    Ido, Shunji; Hasebe, Hiroki

    1994-01-01

    Parallel programming is applied to multiple processors connected in Ethernet. Data exchanges between tasks located in each processing element are realized by two ways. One is socket which is standard library on recent UNIX operating systems. Another is a network connecting software, named as Parallel Virtual Machine (PVM) which is a free software developed by ORNL, to use many workstations connected to network as a parallel computer. This paper discusses the availability of parallel computing using network and UNIX workstations and comparison between specialized parallel systems (Transputer and iPSC/860) in a Monte Carlo simulation which generally shows high parallelization ratio. (author)

  13. Parallel evolutionary computation in bioinformatics applications.

    Science.gov (United States)

    Pinho, Jorge; Sobral, João Luis; Rocha, Miguel

    2013-05-01

    A large number of optimization problems within the field of Bioinformatics require methods able to handle its inherent complexity (e.g. NP-hard problems) and also demand increased computational efforts. In this context, the use of parallel architectures is a necessity. In this work, we propose ParJECoLi, a Java based library that offers a large set of metaheuristic methods (such as Evolutionary Algorithms) and also addresses the issue of its efficient execution on a wide range of parallel architectures. The proposed approach focuses on the easiness of use, making the adaptation to distinct parallel environments (multicore, cluster, grid) transparent to the user. Indeed, this work shows how the development of the optimization library can proceed independently of its adaptation for several architectures, making use of Aspect-Oriented Programming. The pluggable nature of parallelism related modules allows the user to easily configure its environment, adding parallelism modules to the base source code when needed. The performance of the platform is validated with two case studies within biological model optimization. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

  14. Efficient Parallel Engineering Computing on Linux Workstations

    Science.gov (United States)

    Lou, John Z.

    2010-01-01

    A C software module has been developed that creates lightweight processes (LWPs) dynamically to achieve parallel computing performance in a variety of engineering simulation and analysis applications to support NASA and DoD project tasks. The required interface between the module and the application it supports is simple, minimal and almost completely transparent to the user applications, and it can achieve nearly ideal computing speed-up on multi-CPU engineering workstations of all operating system platforms. The module can be integrated into an existing application (C, C++, Fortran and others) either as part of a compiled module or as a dynamically linked library (DLL).

  15. Parallel algorithms and cluster computing

    CERN Document Server

    Hoffmann, Karl Heinz

    2007-01-01

    This book presents major advances in high performance computing as well as major advances due to high performance computing. It contains a collection of papers in which results achieved in the collaboration of scientists from computer science, mathematics, physics, and mechanical engineering are presented. From the science problems to the mathematical algorithms and on to the effective implementation of these algorithms on massively parallel and cluster computers we present state-of-the-art methods and technology as well as exemplary results in these fields. This book shows that problems which seem superficially distinct become intimately connected on a computational level.

  16. COSMOS: Python library for massively parallel workflows.

    Science.gov (United States)

    Gafni, Erik; Luquette, Lovelace J; Lancaster, Alex K; Hawkins, Jared B; Jung, Jae-Yoon; Souilmi, Yassine; Wall, Dennis P; Tonellato, Peter J

    2014-10-15

    Efficient workflows to shepherd clinically generated genomic data through the multiple stages of a next-generation sequencing pipeline are of critical importance in translational biomedical science. Here we present COSMOS, a Python library for workflow management that allows formal description of pipelines and partitioning of jobs. In addition, it includes a user interface for tracking the progress of jobs, abstraction of the queuing system and fine-grained control over the workflow. Workflows can be created on traditional computing clusters as well as cloud-based services. Source code is available for academic non-commercial research purposes. Links to code and documentation are provided at http://lpm.hms.harvard.edu and http://wall-lab.stanford.edu. dpwall@stanford.edu or peter_tonellato@hms.harvard.edu. Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press.

  17. Wakefield calculations on parallel computers

    International Nuclear Information System (INIS)

    Schoessow, P.

    1990-01-01

    The use of parallelism in the solution of wakefield problems is illustrated for two different computer architectures (SIMD and MIMD). Results are given for finite difference codes which have been implemented on a Connection Machine and an Alliant FX/8 and which are used to compute wakefields in dielectric loaded structures. Benchmarks on code performance are presented for both cases. 4 refs., 3 figs., 2 tabs

  18. Parallel R-matrix computation

    International Nuclear Information System (INIS)

    Heggarty, J.W.

    1999-06-01

    For almost thirty years, sequential R-matrix computation has been used by atomic physics research groups, from around the world, to model collision phenomena involving the scattering of electrons or positrons with atomic or molecular targets. As considerable progress has been made in the understanding of fundamental scattering processes, new data, obtained from more complex calculations, is of current interest to experimentalists. Performing such calculations, however, places considerable demands on the computational resources to be provided by the target machine, in terms of both processor speed and memory requirement. Indeed, in some instances the computational requirements are so great that the proposed R-matrix calculations are intractable, even when utilising contemporary classic supercomputers. Historically, increases in the computational requirements of R-matrix computation were accommodated by porting the problem codes to a more powerful classic supercomputer. Although this approach has been successful in the past, it is no longer considered to be a satisfactory solution due to the limitations of current (and future) Von Neumann machines. As a consequence, there has been considerable interest in the high performance multicomputers, that have emerged over the last decade which appear to offer the computational resources required by contemporary R-matrix research. Unfortunately, developing codes for these machines is not as simple a task as it was to develop codes for successive classic supercomputers. The difficulty arises from the considerable differences in the computing models that exist between the two types of machine and results in the programming of multicomputers to be widely acknowledged as a difficult, time consuming and error-prone task. Nevertheless, unless parallel R-matrix computation is realised, important theoretical and experimental atomic physics research will continue to be hindered. This thesis describes work that was undertaken in

  19. Parallel computing and networking; Heiretsu keisanki to network

    Energy Technology Data Exchange (ETDEWEB)

    Asakawa, E; Tsuru, T [Japan National Oil Corp., Tokyo (Japan); Matsuoka, T [Japan Petroleum Exploration Co. Ltd., Tokyo (Japan)

    1996-05-01

    This paper describes the trend of parallel computers used in geophysical exploration. Around 1993 was the early days when the parallel computers began to be used for geophysical exploration. Classification of these computers those days was mainly MIMD (multiple instruction stream, multiple data stream), SIMD (single instruction stream, multiple data stream) and the like. Parallel computers were publicized in the 1994 meeting of the Geophysical Exploration Society as a `high precision imaging technology`. Concerning the library of parallel computers, there was a shift to PVM (parallel virtual machine) in 1993 and to MPI (message passing interface) in 1995. In addition, the compiler of FORTRAN90 was released with support implemented for data parallel and vector computers. In 1993, networks used were Ethernet, FDDI, CDDI and HIPPI. In 1995, the OC-3 products under ATM began to propagate. However, ATM remains to be an interoffice high speed network because the ATM service has not spread yet for the public network. 1 ref.

  20. An object-oriented bulk synchronous parallel library for multicore programming

    NARCIS (Netherlands)

    Yzelman, A.N.; Bisseling, R.H.

    2012-01-01

    We show that the bulk synchronous parallel (BSP) model, originally designed for distributed-memory systems, is also applicable for shared-memory multicore systems and, furthermore, that BSP libraries are useful in scientific computing on these systems. A proof-of-concept MulticoreBSP library has

  1. Parallel computing: numerics, applications, and trends

    National Research Council Canada - National Science Library

    Trobec, Roman; Vajteršic, Marián; Zinterhof, Peter

    2009-01-01

    ... and/or distributed systems. The contributions to this book are focused on topics most concerned in the trends of today's parallel computing. These range from parallel algorithmics, programming, tools, network computing to future parallel computing. Particular attention is paid to parallel numerics: linear algebra, differential equations, numerica...

  2. The numerical parallel computing of photon transport

    International Nuclear Information System (INIS)

    Huang Qingnan; Liang Xiaoguang; Zhang Lifa

    1998-12-01

    The parallel computing of photon transport is investigated, the parallel algorithm and the parallelization of programs on parallel computers both with shared memory and with distributed memory are discussed. By analyzing the inherent law of the mathematics and physics model of photon transport according to the structure feature of parallel computers, using the strategy of 'to divide and conquer', adjusting the algorithm structure of the program, dissolving the data relationship, finding parallel liable ingredients and creating large grain parallel subtasks, the sequential computing of photon transport into is efficiently transformed into parallel and vector computing. The program was run on various HP parallel computers such as the HY-1 (PVP), the Challenge (SMP) and the YH-3 (MPP) and very good parallel speedup has been gotten

  3. Parallel computation of rotating flows

    DEFF Research Database (Denmark)

    Lundin, Lars Kristian; Barker, Vincent A.; Sørensen, Jens Nørkær

    1999-01-01

    This paper deals with the simulation of 3‐D rotating flows based on the velocity‐vorticity formulation of the Navier‐Stokes equations in cylindrical coordinates. The governing equations are discretized by a finite difference method. The solution is advanced to a new time level by a two‐step process...... is that of solving a singular, large, sparse, over‐determined linear system of equations, and the iterative method CGLS is applied for this purpose. We discuss some of the mathematical and numerical aspects of this procedure and report on the performance of our software on a wide range of parallel computers. Darbe...

  4. Parallel computing in enterprise modeling.

    Energy Technology Data Exchange (ETDEWEB)

    Goldsby, Michael E.; Armstrong, Robert C.; Shneider, Max S.; Vanderveen, Keith; Ray, Jaideep; Heath, Zach; Allan, Benjamin A.

    2008-08-01

    This report presents the results of our efforts to apply high-performance computing to entity-based simulations with a multi-use plugin for parallel computing. We use the term 'Entity-based simulation' to describe a class of simulation which includes both discrete event simulation and agent based simulation. What simulations of this class share, and what differs from more traditional models, is that the result sought is emergent from a large number of contributing entities. Logistic, economic and social simulations are members of this class where things or people are organized or self-organize to produce a solution. Entity-based problems never have an a priori ergodic principle that will greatly simplify calculations. Because the results of entity-based simulations can only be realized at scale, scalable computing is de rigueur for large problems. Having said that, the absence of a spatial organizing principal makes the decomposition of the problem onto processors problematic. In addition, practitioners in this domain commonly use the Java programming language which presents its own problems in a high-performance setting. The plugin we have developed, called the Parallel Particle Data Model, overcomes both of these obstacles and is now being used by two Sandia frameworks: the Decision Analysis Center, and the Seldon social simulation facility. While the ability to engage U.S.-sized problems is now available to the Decision Analysis Center, this plugin is central to the success of Seldon. Because Seldon relies on computationally intensive cognitive sub-models, this work is necessary to achieve the scale necessary for realistic results. With the recent upheavals in the financial markets, and the inscrutability of terrorist activity, this simulation domain will likely need a capability with ever greater fidelity. High-performance computing will play an important part in enabling that greater fidelity.

  5. The computer library of experimental neutron data

    International Nuclear Information System (INIS)

    Bychkov, V.M.; Manokhin, V.N.; Surgutanov, V.V.

    1976-05-01

    The paper describes the computer library of experimental neutron data at the Obninsk Nuclear Data Centre. The format of the library (EXFOR) and the system of programmes for supplying the library are briefly described. (author)

  6. An Introduction to Parallel Computation R

    Indian Academy of Sciences (India)

    How are they programmed? This article provides an introduction. A parallel computer is a network of processors built for ... and have been used to solve problems much faster than a single ... in parallel computer design is to select an organization which ..... The most ambitious approach to parallel computing is to develop.

  7. Advances in randomized parallel computing

    CERN Document Server

    Rajasekaran, Sanguthevar

    1999-01-01

    The technique of randomization has been employed to solve numerous prob­ lems of computing both sequentially and in parallel. Examples of randomized algorithms that are asymptotically better than their deterministic counterparts in solving various fundamental problems abound. Randomized algorithms have the advantages of simplicity and better performance both in theory and often in practice. This book is a collection of articles written by renowned experts in the area of randomized parallel computing. A brief introduction to randomized algorithms In the aflalysis of algorithms, at least three different measures of performance can be used: the best case, the worst case, and the average case. Often, the average case run time of an algorithm is much smaller than the worst case. 2 For instance, the worst case run time of Hoare's quicksort is O(n ), whereas its average case run time is only O( n log n). The average case analysis is conducted with an assumption on the input space. The assumption made to arrive at t...

  8. OpenMP Issues Arising in the Development of Parallel BLAS and LAPACK Libraries

    Directory of Open Access Journals (Sweden)

    C. Addison

    2003-01-01

    Full Text Available Dense linear algebra libraries need to cope efficiently with a range of input problem sizes and shapes. Inherently this means that parallel implementations have to exploit parallelism wherever it is present. While OpenMP allows relatively fine grain parallelism to be exploited in a shared memory environment it currently lacks features to make it easy to partition computation over multiple array indices or to overlap sequential and parallel computations. The inherent flexible nature of shared memory paradigms such as OpenMP poses other difficulties when it becomes necessary to optimise performance across successive parallel library calls. Notions borrowed from distributed memory paradigms, such as explicit data distributions help address some of these problems, but the focus on data rather than work distribution appears misplaced in an SMP context.

  9. Parallel Computing for Brain Simulation.

    Science.gov (United States)

    Pastur-Romay, L A; Porto-Pazos, A B; Cedron, F; Pazos, A

    2017-01-01

    The human brain is the most complex system in the known universe, it is therefore one of the greatest mysteries. It provides human beings with extraordinary abilities. However, until now it has not been understood yet how and why most of these abilities are produced. For decades, researchers have been trying to make computers reproduce these abilities, focusing on both understanding the nervous system and, on processing data in a more efficient way than before. Their aim is to make computers process information similarly to the brain. Important technological developments and vast multidisciplinary projects have allowed creating the first simulation with a number of neurons similar to that of a human brain. This paper presents an up-to-date review about the main research projects that are trying to simulate and/or emulate the human brain. They employ different types of computational models using parallel computing: digital models, analog models and hybrid models. This review includes the current applications of these works, as well as future trends. It is focused on various works that look for advanced progress in Neuroscience and still others which seek new discoveries in Computer Science (neuromorphic hardware, machine learning techniques). Their most outstanding characteristics are summarized and the latest advances and future plans are presented. In addition, this review points out the importance of considering not only neurons: Computational models of the brain should also include glial cells, given the proven importance of astrocytes in information processing. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  10. Aspects of computation on asynchronous parallel processors

    International Nuclear Information System (INIS)

    Wright, M.

    1989-01-01

    The increasing availability of asynchronous parallel processors has provided opportunities for original and useful work in scientific computing. However, the field of parallel computing is still in a highly volatile state, and researchers display a wide range of opinion about many fundamental questions such as models of parallelism, approaches for detecting and analyzing parallelism of algorithms, and tools that allow software developers and users to make effective use of diverse forms of complex hardware. This volume collects the work of researchers specializing in different aspects of parallel computing, who met to discuss the framework and the mechanics of numerical computing. The far-reaching impact of high-performance asynchronous systems is reflected in the wide variety of topics, which include scientific applications (e.g. linear algebra, lattice gauge simulation, ordinary and partial differential equations), models of parallelism, parallel language features, task scheduling, automatic parallelization techniques, tools for algorithm development in parallel environments, and system design issues

  11. Eighth SIAM conference on parallel processing for scientific computing: Final program and abstracts

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1997-12-31

    This SIAM conference is the premier forum for developments in parallel numerical algorithms, a field that has seen very lively and fruitful developments over the past decade, and whose health is still robust. Themes for this conference were: combinatorial optimization; data-parallel languages; large-scale parallel applications; message-passing; molecular modeling; parallel I/O; parallel libraries; parallel software tools; parallel compilers; particle simulations; problem-solving environments; and sparse matrix computations.

  12. Parallel Computing Using Web Servers and "Servlets".

    Science.gov (United States)

    Lo, Alfred; Bloor, Chris; Choi, Y. K.

    2000-01-01

    Describes parallel computing and presents inexpensive ways to implement a virtual parallel computer with multiple Web servers. Highlights include performance measurement of parallel systems; models for using Java and intranet technology including single server, multiple clients and multiple servers, single client; and a comparison of CGI (common…

  13. Broadcasting a message in a parallel computer

    Science.gov (United States)

    Berg, Jeremy E [Rochester, MN; Faraj, Ahmad A [Rochester, MN

    2011-08-02

    Methods, systems, and products are disclosed for broadcasting a message in a parallel computer. The parallel computer includes a plurality of compute nodes connected together using a data communications network. The data communications network optimized for point to point data communications and is characterized by at least two dimensions. The compute nodes are organized into at least one operational group of compute nodes for collective parallel operations of the parallel computer. One compute node of the operational group assigned to be a logical root. Broadcasting a message in a parallel computer includes: establishing a Hamiltonian path along all of the compute nodes in at least one plane of the data communications network and in the operational group; and broadcasting, by the logical root to the remaining compute nodes, the logical root's message along the established Hamiltonian path.

  14. Fluorous Parallel Synthesis of A Hydantoin/Thiohydantoin Library

    OpenAIRE

    Lu, Yimin; Zhang, Wei

    2005-01-01

    Fluorous tagging strategy is applied to solution-phase parallel synthesis of a library containing hydantoin and thiohydantoin analogs. Two perfluoroalkyl (Rf)-tagged α-amino esters each react with 6 aromatic aldehydes under reductive amination conditions. Twelve amino esters then each react with 10 isocyanates and isothiocyanates in parallel. The resulting 120 ureas and thioureas undergo spontaneous cyclization to form the corresponding hydantoins and thiohydantoins. The intermediate and fina...

  15. Template based parallel checkpointing in a massively parallel computer system

    Science.gov (United States)

    Archer, Charles Jens [Rochester, MN; Inglett, Todd Alan [Rochester, MN

    2009-01-13

    A method and apparatus for a template based parallel checkpoint save for a massively parallel super computer system using a parallel variation of the rsync protocol, and network broadcast. In preferred embodiments, the checkpoint data for each node is compared to a template checkpoint file that resides in the storage and that was previously produced. Embodiments herein greatly decrease the amount of data that must be transmitted and stored for faster checkpointing and increased efficiency of the computer system. Embodiments are directed to a parallel computer system with nodes arranged in a cluster with a high speed interconnect that can perform broadcast communication. The checkpoint contains a set of actual small data blocks with their corresponding checksums from all nodes in the system. The data blocks may be compressed using conventional non-lossy data compression algorithms to further reduce the overall checkpoint size.

  16. Parallel computing by Monte Carlo codes MVP/GMVP

    International Nuclear Information System (INIS)

    Nagaya, Yasunobu; Nakagawa, Masayuki; Mori, Takamasa

    2001-01-01

    General-purpose Monte Carlo codes MVP/GMVP are well-vectorized and thus enable us to perform high-speed Monte Carlo calculations. In order to achieve more speedups, we parallelized the codes on the different types of parallel computing platforms or by using a standard parallelization library MPI. The platforms used for benchmark calculations are a distributed-memory vector-parallel computer Fujitsu VPP500, a distributed-memory massively parallel computer Intel paragon and a distributed-memory scalar-parallel computer Hitachi SR2201, IBM SP2. As mentioned generally, linear speedup could be obtained for large-scale problems but parallelization efficiency decreased as the batch size per a processing element(PE) was smaller. It was also found that the statistical uncertainty for assembly powers was less than 0.1% by the PWR full-core calculation with more than 10 million histories and it took about 1.5 hours by massively parallel computing. (author)

  17. Compiler Technology for Parallel Scientific Computation

    Directory of Open Access Journals (Sweden)

    Can Özturan

    1994-01-01

    Full Text Available There is a need for compiler technology that, given the source program, will generate efficient parallel codes for different architectures with minimal user involvement. Parallel computation is becoming indispensable in solving large-scale problems in science and engineering. Yet, the use of parallel computation is limited by the high costs of developing the needed software. To overcome this difficulty we advocate a comprehensive approach to the development of scalable architecture-independent software for scientific computation based on our experience with equational programming language (EPL. Our approach is based on a program decomposition, parallel code synthesis, and run-time support for parallel scientific computation. The program decomposition is guided by the source program annotations provided by the user. The synthesis of parallel code is based on configurations that describe the overall computation as a set of interacting components. Run-time support is provided by the compiler-generated code that redistributes computation and data during object program execution. The generated parallel code is optimized using techniques of data alignment, operator placement, wavefront determination, and memory optimization. In this article we discuss annotations, configurations, parallel code generation, and run-time support suitable for parallel programs written in the functional parallel programming language EPL and in Fortran.

  18. CUBESIM, Hypercube and Denelcor Hep Parallel Computer Simulation

    International Nuclear Information System (INIS)

    Dunigan, T.H.

    1988-01-01

    1 - Description of program or function: CUBESIM is a set of subroutine libraries and programs for the simulation of message-passing parallel computers and shared-memory parallel computers. Subroutines are supplied to simulate the Intel hypercube and the Denelcor HEP parallel computers. The system permits a user to develop and test parallel programs written in C or FORTRAN on a single processor. The user may alter such hypercube parameters as message startup times, packet size, and the computation-to-communication ratio. The simulation generates a trace file that can be used for debugging, performance analysis, or graphical display. 2 - Method of solution: The CUBESIM simulator is linked with the user's parallel application routines to run as a single UNIX process. The simulator library provides a small operating system to perform process and message management. 3 - Restrictions on the complexity of the problem: Up to 128 processors can be simulated with a virtual memory limit of 6 million bytes. Up to 1000 processes can be simulated

  19. Parallel algorithms for mapping pipelined and parallel computations

    Science.gov (United States)

    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.

  20. Massively parallel evolutionary computation on GPGPUs

    CERN Document Server

    Tsutsui, Shigeyoshi

    2013-01-01

    Evolutionary algorithms (EAs) are metaheuristics that learn from natural collective behavior and are applied to solve optimization problems in domains such as scheduling, engineering, bioinformatics, and finance. Such applications demand acceptable solutions with high-speed execution using finite computational resources. Therefore, there have been many attempts to develop platforms for running parallel EAs using multicore machines, massively parallel cluster machines, or grid computing environments. Recent advances in general-purpose computing on graphics processing units (GPGPU) have opened u

  1. Fluorous Parallel Synthesis of A Hydantoin/Thiohydantoin Library

    Science.gov (United States)

    Lu, Yimin; Zhang, Wei

    2007-01-01

    Fluorous tagging strategy is applied to solution-phase parallel synthesis of a library containing hydantoin and thiohydantoin analogs. Two perfluoroalkyl (Rf)-tagged α-amino esters each react with 6 aromatic aldehydes under reductive amination conditions. Twelve amino esters then each react with 10 isocyanates and isothiocyanates in parallel. The resulting 120 ureas and thioureas undergo spontaneous cyclization to form the corresponding hydantoins and thiohydantoins. The intermediate and final product purifications are performed with solid-phase extraction (SPE) over FluoroFlash™ cartridges, no chromatography is required. Using standard instruments and straightforward SPE technique, one chemist accomplished the 120-member library synthesis in less than 5 working days, including starting material synthesis and product analysis. PMID:15789556

  2. Computer Science Professionals and Greek Library Science

    Science.gov (United States)

    Dendrinos, Markos N.

    2008-01-01

    This paper attempts to present the current state of computer science penetration into librarianship in terms of both workplace and education issues. The shift from material libraries into digital libraries is mirrored in the corresponding shift from librarians into information scientists. New library data and metadata, as well as new automated…

  3. Parallel Element Agglomeration Algebraic Multigrid and Upscaling Library

    Energy Technology Data Exchange (ETDEWEB)

    2017-10-24

    ParELAG is a parallel C++ library for numerical upscaling of finite element discretizations and element-based algebraic multigrid solvers. It provides optimal complexity algorithms to build multilevel hierarchies and solvers that can be used for solving a wide class of partial differential equations (elliptic, hyperbolic, saddle point problems) on general unstructured meshes. Additionally, a novel multilevel solver for saddle point problems with divergence constraint is implemented.

  4. How to Build an AppleSeed: A Parallel Macintosh Cluster for Numerically Intensive Computing

    Science.gov (United States)

    Decyk, V. K.; Dauger, D. E.

    We have constructed a parallel cluster consisting of a mixture of Apple Macintosh G3 and G4 computers running the Mac OS, and have achieved very good performance on numerically intensive, parallel plasma particle-incell simulations. A subset of the MPI message-passing library was implemented in Fortran77 and C. This library enabled us to port code, without modification, from other parallel processors to the Macintosh cluster. Unlike Unix-based clusters, no special expertise in operating systems is required to build and run the cluster. This enables us to move parallel computing from the realm of experts to the main stream of computing.

  5. COMPUTER TRAINING AND PROFESSIONAL LIBRARY

    African Journals Online (AJOL)

    professional library activities of the subject (R = 0.28507, P < 0.05). Suggestions ... hold great value for Strategic planning. ... In Pakistan for example, the Pakistan Library ..... OECD, A report on management of marketing information. OASIS ...

  6. Collectively loading an application in a parallel computer

    Science.gov (United States)

    Aho, Michael E.; Attinella, John E.; Gooding, Thomas M.; Miller, Samuel J.; Mundy, Michael B.

    2016-01-05

    Collectively loading an application in a parallel computer, the parallel computer comprising a plurality of compute nodes, including: identifying, by a parallel computer control system, a subset of compute nodes in the parallel computer to execute a job; selecting, by the parallel computer control system, one of the subset of compute nodes in the parallel computer as a job leader compute node; retrieving, by the job leader compute node from computer memory, an application for executing the job; and broadcasting, by the job leader to the subset of compute nodes in the parallel computer, the application for executing the job.

  7. Parallel Computing Strategies for Irregular Algorithms

    Science.gov (United States)

    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.

  8. Massively Parallel Computing: A Sandia Perspective

    Energy Technology Data Exchange (ETDEWEB)

    Dosanjh, Sudip S.; Greenberg, David S.; Hendrickson, Bruce; Heroux, Michael A.; Plimpton, Steve J.; Tomkins, James L.; Womble, David E.

    1999-05-06

    The computing power available to scientists and engineers has increased dramatically in the past decade, due in part to progress in making massively parallel computing practical and available. The expectation for these machines has been great. The reality is that progress has been slower than expected. Nevertheless, massively parallel computing is beginning to realize its potential for enabling significant break-throughs in science and engineering. This paper provides a perspective on the state of the field, colored by the authors' experiences using large scale parallel machines at Sandia National Laboratories. We address trends in hardware, system software and algorithms, and we also offer our view of the forces shaping the parallel computing industry.

  9. Domain decomposition methods and parallel computing

    International Nuclear Information System (INIS)

    Meurant, G.

    1991-01-01

    In this paper, we show how to efficiently solve large linear systems on parallel computers. These linear systems arise from discretization of scientific computing problems described by systems of partial differential equations. We show how to get a discrete finite dimensional system from the continuous problem and the chosen conjugate gradient iterative algorithm is briefly described. Then, the different kinds of parallel architectures are reviewed and their advantages and deficiencies are emphasized. We sketch the problems found in programming the conjugate gradient method on parallel computers. For this algorithm to be efficient on parallel machines, domain decomposition techniques are introduced. We give results of numerical experiments showing that these techniques allow a good rate of convergence for the conjugate gradient algorithm as well as computational speeds in excess of a billion of floating point operations per second. (author). 5 refs., 11 figs., 2 tabs., 1 inset

  10. Computing NLTE Opacities -- Node Level Parallel Calculation

    Energy Technology Data Exchange (ETDEWEB)

    Holladay, Daniel [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2015-09-11

    Presentation. The goal: to produce a robust library capable of computing reasonably accurate opacities inline with the assumption of LTE relaxed (non-LTE). Near term: demonstrate acceleration of non-LTE opacity computation. Far term (if funded): connect to application codes with in-line capability and compute opacities. Study science problems. Use efficient algorithms that expose many levels of parallelism and utilize good memory access patterns for use on advanced architectures. Portability to multiple types of hardware including multicore processors, manycore processors such as KNL, GPUs, etc. Easily coupled to radiation hydrodynamics and thermal radiative transfer codes.

  11. Parallel quantum computing in a single ensemble quantum computer

    International Nuclear Information System (INIS)

    Long Guilu; Xiao, L.

    2004-01-01

    We propose a parallel quantum computing mode for ensemble quantum computer. In this mode, some qubits are in pure states while other qubits are in mixed states. It enables a single ensemble quantum computer to perform 'single-instruction-multidata' type of parallel computation. Parallel quantum computing can provide additional speedup in Grover's algorithm and Shor's algorithm. In addition, it also makes a fuller use of qubit resources in an ensemble quantum computer. As a result, some qubits discarded in the preparation of an effective pure state in the Schulman-Varizani and the Cleve-DiVincenzo algorithms can be reutilized

  12. Structured Parallel Programming Patterns for Efficient Computation

    CERN Document Server

    McCool, Michael; Robison, Arch

    2012-01-01

    Programming is now parallel programming. Much as structured programming revolutionized traditional serial programming decades ago, a new kind of structured programming, based on patterns, is relevant to parallel programming today. Parallel computing experts and industry insiders Michael McCool, Arch Robison, and James Reinders describe how to design and implement maintainable and efficient parallel algorithms using a pattern-based approach. They present both theory and practice, and give detailed concrete examples using multiple programming models. Examples are primarily given using two of th

  13. Parallel computation of rotating flows

    DEFF Research Database (Denmark)

    Lundin, Lars Kristian; Barker, Vincent A.; Sørensen, Jens Nørkær

    1999-01-01

    This paper deals with the simulation of 3‐D rotating flows based on the velocity‐vorticity formulation of the Navier‐Stokes equations in cylindrical coordinates. The governing equations are discretized by a finite difference method. The solution is advanced to a new time level by a two‐step process....... In the first step, the vorticity at the new time level is computed using the velocity at the previous time level. In the second step, the velocity at the new time level is computed using the new vorticity. We discuss here the second part which is by far the most time‐consuming. The numerical problem...

  14. Computer-Aided Parallelizer and Optimizer

    Science.gov (United States)

    Jin, Haoqiang

    2011-01-01

    The Computer-Aided Parallelizer and Optimizer (CAPO) automates the insertion of compiler directives (see figure) to facilitate parallel processing on Shared Memory Parallel (SMP) machines. While CAPO currently is integrated seamlessly into CAPTools (developed at the University of Greenwich, now marketed as ParaWise), CAPO was independently developed at Ames Research Center as one of the components for the Legacy Code Modernization (LCM) project. The current version takes serial FORTRAN programs, performs interprocedural data dependence analysis, and generates OpenMP directives. Due to the widely supported OpenMP standard, the generated OpenMP codes have the potential to run on a wide range of SMP machines. CAPO relies on accurate interprocedural data dependence information currently provided by CAPTools. Compiler directives are generated through identification of parallel loops in the outermost level, construction of parallel regions around parallel loops and optimization of parallel regions, and insertion of directives with automatic identification of private, reduction, induction, and shared variables. Attempts also have been made to identify potential pipeline parallelism (implemented with point-to-point synchronization). Although directives are generated automatically, user interaction with the tool is still important for producing good parallel codes. A comprehensive graphical user interface is included for users to interact with the parallelization process.

  15. High performance parallel computers for science

    International Nuclear Information System (INIS)

    Nash, T.; Areti, H.; Atac, R.; Biel, J.; Cook, A.; Deppe, J.; Edel, M.; Fischler, M.; Gaines, I.; Hance, R.

    1989-01-01

    This paper reports that Fermilab's Advanced Computer Program (ACP) has been developing cost effective, yet practical, parallel computers for high energy physics since 1984. The ACP's latest developments are proceeding in two directions. A Second Generation ACP Multiprocessor System for experiments will include $3500 RISC processors each with performance over 15 VAX MIPS. To support such high performance, the new system allows parallel I/O, parallel interprocess communication, and parallel host processes. The ACP Multi-Array Processor, has been developed for theoretical physics. Each $4000 node is a FORTRAN or C programmable pipelined 20 Mflops (peak), 10 MByte single board computer. These are plugged into a 16 port crossbar switch crate which handles both inter and intra crate communication. The crates are connected in a hypercube. Site oriented applications like lattice gauge theory are supported by system software called CANOPY, which makes the hardware virtually transparent to users. A 256 node, 5 GFlop, system is under construction

  16. Parallelizing the QUDA Library for Multi-GPU Calculations in Lattice Quantum Chromodynamics

    International Nuclear Information System (INIS)

    Babich, Ronald; Clark, Michael; Joo, Balint

    2010-01-01

    Graphics Processing Units (GPUs) are having a transformational effect on numerical lattice quantum chromodynamics (LQCD) calculations of importance in nuclear and particle physics. The QUDA library provides a package of mixed precision sparse matrix linear solvers for LQCD applications, supporting single GPUs based on NVIDIA's Compute Unified Device Architecture (CUDA). This library, interfaced to the QDP++/Chroma framework for LQCD calculations, is currently in production use on the '9g' cluster at the Jefferson Laboratory, enabling unprecedented price/performance for a range of problems in LQCD. Nevertheless, memory constraints on current GPU devices limit the problem sizes that can be tackled. In this contribution we describe the parallelization of the QUDA library onto multiple GPUs using MPI, including strategies for the overlapping of communication and computation. We report on both weak and strong scaling for up to 32 GPUs interconnected by InfiniBand, on which we sustain in excess of 4 Tflops.

  17. Parallelizing the QUDA Library for Multi-GPU Calculations in Lattice Quantum Chromodynamics

    Energy Technology Data Exchange (ETDEWEB)

    Ronald Babich, Michael Clark, Balint Joo

    2010-11-01

    Graphics Processing Units (GPUs) are having a transformational effect on numerical lattice quantum chromodynamics (LQCD) calculations of importance in nuclear and particle physics. The QUDA library provides a package of mixed precision sparse matrix linear solvers for LQCD applications, supporting single GPUs based on NVIDIA's Compute Unified Device Architecture (CUDA). This library, interfaced to the QDP++/Chroma framework for LQCD calculations, is currently in production use on the "9g" cluster at the Jefferson Laboratory, enabling unprecedented price/performance for a range of problems in LQCD. Nevertheless, memory constraints on current GPU devices limit the problem sizes that can be tackled. In this contribution we describe the parallelization of the QUDA library onto multiple GPUs using MPI, including strategies for the overlapping of communication and computation. We report on both weak and strong scaling for up to 32 GPUs interconnected by InfiniBand, on which we sustain in excess of 4 Tflops.

  18. Cloud Computing and Your Library

    Science.gov (United States)

    Mitchell, Erik T.

    2010-01-01

    One of the first big shifts in how libraries manage resources was the move from print-journal purchasing models to database-subscription and electronic-journal purchasing models. Libraries found that this transition helped them scale their resources and provide better service just by thinking a bit differently about their services. Likewise,…

  19. Parallel computational in nuclear group constant calculation

    International Nuclear Information System (INIS)

    Su'ud, Zaki; Rustandi, Yaddi K.; Kurniadi, Rizal

    2002-01-01

    In this paper parallel computational method in nuclear group constant calculation using collision probability method will be discuss. The main focus is on the calculation of collision matrix which need large amount of computational time. The geometry treated here is concentric cylinder. The calculation of collision probability matrix is carried out using semi analytic method using Beckley Naylor Function. To accelerate computation speed some computer parallel used to solve the problem. We used LINUX based parallelization using PVM software with C or fortran language. While in windows based we used socket programming using DELPHI or C builder. The calculation results shows the important of optimal weight for each processor in case there area many type of processor speed

  20. Fast parallel tandem mass spectral library searching using GPU hardware acceleration.

    Science.gov (United States)

    Baumgardner, Lydia Ashleigh; Shanmugam, Avinash Kumar; Lam, Henry; Eng, Jimmy K; Martin, Daniel B

    2011-06-03

    Mass spectrometry-based proteomics is a maturing discipline of biologic research that is experiencing substantial growth. Instrumentation has steadily improved over time with the advent of faster and more sensitive instruments collecting ever larger data files. Consequently, the computational process of matching a peptide fragmentation pattern to its sequence, traditionally accomplished by sequence database searching and more recently also by spectral library searching, has become a bottleneck in many mass spectrometry experiments. In both of these methods, the main rate-limiting step is the comparison of an acquired spectrum with all potential matches from a spectral library or sequence database. This is a highly parallelizable process because the core computational element can be represented as a simple but arithmetically intense multiplication of two vectors. In this paper, we present a proof of concept project taking advantage of the massively parallel computing available on graphics processing units (GPUs) to distribute and accelerate the process of spectral assignment using spectral library searching. This program, which we have named FastPaSS (for Fast Parallelized Spectral Searching), is implemented in CUDA (Compute Unified Device Architecture) from NVIDIA, which allows direct access to the processors in an NVIDIA GPU. Our efforts demonstrate the feasibility of GPU computing for spectral assignment, through implementation of the validated spectral searching algorithm SpectraST in the CUDA environment.

  1. Locating hardware faults in a parallel computer

    Science.gov (United States)

    Archer, Charles J.; Megerian, Mark G.; Ratterman, Joseph D.; Smith, Brian E.

    2010-04-13

    Locating hardware faults in a parallel computer, including defining within a tree network of the parallel computer two or more sets of non-overlapping test levels of compute nodes of the network that together include all the data communications links of the network, each non-overlapping test level comprising two or more adjacent tiers of the tree; defining test cells within each non-overlapping test level, each test cell comprising a subtree of the tree including a subtree root compute node and all descendant compute nodes of the subtree root compute node within a non-overlapping test level; performing, separately on each set of non-overlapping test levels, an uplink test on all test cells in a set of non-overlapping test levels; and performing, separately from the uplink tests and separately on each set of non-overlapping test levels, a downlink test on all test cells in a set of non-overlapping test levels.

  2. Impact analysis on a massively parallel computer

    International Nuclear Information System (INIS)

    Zacharia, T.; Aramayo, G.A.

    1994-01-01

    Advanced mathematical techniques and computer simulation play a major role in evaluating and enhancing the design of beverage cans, industrial, and transportation containers for improved performance. Numerical models are used to evaluate the impact requirements of containers used by the Department of Energy (DOE) for transporting radioactive materials. Many of these models are highly compute-intensive. An analysis may require several hours of computational time on current supercomputers despite the simplicity of the models being studied. As computer simulations and materials databases grow in complexity, massively parallel computers have become important tools. Massively parallel computational research at the Oak Ridge National Laboratory (ORNL) and its application to the impact analysis of shipping containers is briefly described in this paper

  3. Internode data communications in a parallel computer

    Science.gov (United States)

    Archer, Charles J.; Blocksome, Michael A.; Miller, Douglas R.; Parker, Jeffrey J.; Ratterman, Joseph D.; Smith, Brian E.

    2013-09-03

    Internode data communications in a parallel computer that includes compute nodes that each include main memory and a messaging unit, the messaging unit including computer memory and coupling compute nodes for data communications, in which, for each compute node at compute node boot time: a messaging unit allocates, in the messaging unit's computer memory, a predefined number of message buffers, each message buffer associated with a process to be initialized on the compute node; receives, prior to initialization of a particular process on the compute node, a data communications message intended for the particular process; and stores the data communications message in the message buffer associated with the particular process. Upon initialization of the particular process, the process establishes a messaging buffer in main memory of the compute node and copies the data communications message from the message buffer of the messaging unit into the message buffer of main memory.

  4. Link failure detection in a parallel computer

    Science.gov (United States)

    Archer, Charles J.; Blocksome, Michael A.; Megerian, Mark G.; Smith, Brian E.

    2010-11-09

    Methods, apparatus, and products are disclosed for link failure detection in a parallel computer including compute nodes connected in a rectangular mesh network, each pair of adjacent compute nodes in the rectangular mesh network connected together using a pair of links, that includes: assigning each compute node to either a first group or a second group such that adjacent compute nodes in the rectangular mesh network are assigned to different groups; sending, by each of the compute nodes assigned to the first group, a first test message to each adjacent compute node assigned to the second group; determining, by each of the compute nodes assigned to the second group, whether the first test message was received from each adjacent compute node assigned to the first group; and notifying a user, by each of the compute nodes assigned to the second group, whether the first test message was received.

  5. Algorithms for computational fluid dynamics n parallel processors

    International Nuclear Information System (INIS)

    Van de Velde, E.F.

    1986-01-01

    A study of parallel algorithms for the numerical solution of partial differential equations arising in computational fluid dynamics is presented. The actual implementation on parallel processors of shared and nonshared memory design is discussed. The performance of these algorithms is analyzed in terms of machine efficiency, communication time, bottlenecks and software development costs. For elliptic equations, a parallel preconditioned conjugate gradient method is described, which has been used to solve pressure equations discretized with high order finite elements on irregular grids. A parallel full multigrid method and a parallel fast Poisson solver are also presented. Hyperbolic conservation laws were discretized with parallel versions of finite difference methods like the Lax-Wendroff scheme and with the Random Choice method. Techniques are developed for comparing the behavior of an algorithm on different architectures as a function of problem size and local computational effort. Effective use of these advanced architecture machines requires the use of machine dependent programming. It is shown that the portability problems can be minimized by introducing high level operations on vectors and matrices structured into program libraries

  6. Implementations of BLAST for parallel computers.

    Science.gov (United States)

    Jülich, A

    1995-02-01

    The BLAST sequence comparison programs have been ported to a variety of parallel computers-the shared memory machine Cray Y-MP 8/864 and the distributed memory architectures Intel iPSC/860 and nCUBE. Additionally, the programs were ported to run on workstation clusters. We explain the parallelization techniques and consider the pros and cons of these methods. The BLAST programs are very well suited for parallelization for a moderate number of processors. We illustrate our results using the program blastp as an example. As input data for blastp, a 799 residue protein query sequence and the protein database PIR were used.

  7. Case Studies in Library Computer Systems.

    Science.gov (United States)

    Palmer, Richard Phillips

    Twenty descriptive case studies of computer applications in a variety of libraries are presented in this book. Computerized circulation, serial and acquisition systems in public, high school, college, university and business libraries are included. Each of the studies discusses: 1) the environment in which the system operates, 2) the objectives of…

  8. A lightweight communication library for distributed computing

    NARCIS (Netherlands)

    Groen, D.; Rieder, S.; Grosso, P.; de Laat, C.; Portegies Zwart, S.

    2010-01-01

    We present MPWide, a platform-independent communication library for performing message passing between computers. Our library allows coupling of several local message passing interface (MPI) applications through a long-distance network and is specifically optimized for such communications. The

  9. The Student/Library Computer Science Collaborative

    Science.gov (United States)

    Hahn, Jim

    2015-01-01

    With funding from an Institute of Museum and Library Services demonstration grant, librarians of the Undergraduate Library at the University of Illinois at Urbana-Champaign partnered with students in computer science courses to design and build student-centered mobile apps. The grant work called for demonstration of student collaboration…

  10. Parallel visualization on leadership computing resources

    Energy Technology Data Exchange (ETDEWEB)

    Peterka, T; Ross, R B [Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439 (United States); Shen, H-W [Department of Computer Science and Engineering, Ohio State University, Columbus, OH 43210 (United States); Ma, K-L [Department of Computer Science, University of California at Davis, Davis, CA 95616 (United States); Kendall, W [Department of Electrical Engineering and Computer Science, University of Tennessee at Knoxville, Knoxville, TN 37996 (United States); Yu, H, E-mail: tpeterka@mcs.anl.go [Sandia National Laboratories, California, Livermore, CA 94551 (United States)

    2009-07-01

    Changes are needed in the way that visualization is performed, if we expect the analysis of scientific data to be effective at the petascale and beyond. By using similar techniques as those used to parallelize simulations, such as parallel I/O, load balancing, and effective use of interprocess communication, the supercomputers that compute these datasets can also serve as analysis and visualization engines for them. Our team is assessing the feasibility of performing parallel scientific visualization on some of the most powerful computational resources of the U.S. Department of Energy's National Laboratories in order to pave the way for analyzing the next generation of computational results. This paper highlights some of the conclusions of that research.

  11. Parallel visualization on leadership computing resources

    International Nuclear Information System (INIS)

    Peterka, T; Ross, R B; Shen, H-W; Ma, K-L; Kendall, W; Yu, H

    2009-01-01

    Changes are needed in the way that visualization is performed, if we expect the analysis of scientific data to be effective at the petascale and beyond. By using similar techniques as those used to parallelize simulations, such as parallel I/O, load balancing, and effective use of interprocess communication, the supercomputers that compute these datasets can also serve as analysis and visualization engines for them. Our team is assessing the feasibility of performing parallel scientific visualization on some of the most powerful computational resources of the U.S. Department of Energy's National Laboratories in order to pave the way for analyzing the next generation of computational results. This paper highlights some of the conclusions of that research.

  12. The new landscape of parallel computer architecture

    Energy Technology Data Exchange (ETDEWEB)

    Shalf, John [NERSC Division, Lawrence Berkeley National Laboratory 1 Cyclotron Road, Berkeley California, 94720 (United States)

    2007-07-15

    The past few years has seen a sea change in computer architecture that will impact every facet of our society as every electronic device from cell phone to supercomputer will need to confront parallelism of unprecedented scale. Whereas the conventional multicore approach (2, 4, and even 8 cores) adopted by the computing industry will eventually hit a performance plateau, the highest performance per watt and per chip area is achieved using manycore technology (hundreds or even thousands of cores). However, fully unleashing the potential of the manycore approach to ensure future advances in sustained computational performance will require fundamental advances in computer architecture and programming models that are nothing short of reinventing computing. In this paper we examine the reasons behind the movement to exponentially increasing parallelism, and its ramifications for system design, applications and programming models.

  13. The new landscape of parallel computer architecture

    International Nuclear Information System (INIS)

    Shalf, John

    2007-01-01

    The past few years has seen a sea change in computer architecture that will impact every facet of our society as every electronic device from cell phone to supercomputer will need to confront parallelism of unprecedented scale. Whereas the conventional multicore approach (2, 4, and even 8 cores) adopted by the computing industry will eventually hit a performance plateau, the highest performance per watt and per chip area is achieved using manycore technology (hundreds or even thousands of cores). However, fully unleashing the potential of the manycore approach to ensure future advances in sustained computational performance will require fundamental advances in computer architecture and programming models that are nothing short of reinventing computing. In this paper we examine the reasons behind the movement to exponentially increasing parallelism, and its ramifications for system design, applications and programming models

  14. Temporal fringe pattern analysis with parallel computing

    International Nuclear Information System (INIS)

    Tuck Wah Ng; Kar Tien Ang; Argentini, Gianluca

    2005-01-01

    Temporal fringe pattern analysis is invaluable in transient phenomena studies but necessitates long processing times. Here we describe a parallel computing strategy based on the single-program multiple-data model and hyperthreading processor technology to reduce the execution time. In a two-node cluster workstation configuration we found that execution periods were reduced by 1.6 times when four virtual processors were used. To allow even lower execution times with an increasing number of processors, the time allocated for data transfer, data read, and waiting should be minimized. Parallel computing is found here to present a feasible approach to reduce execution times in temporal fringe pattern analysis

  15. Endpoint-based parallel data processing in a parallel active messaging interface of a parallel computer

    Science.gov (United States)

    Archer, Charles J.; Blocksome, Michael A.; Ratterman, Joseph D.; Smith, Brian E.

    2014-08-12

    Endpoint-based parallel data processing in a parallel active messaging interface (`PAMI`) of a parallel computer, the PAMI composed of data communications endpoints, each endpoint including a specification of data communications parameters for a thread of execution on a compute node, including specifications of a client, a context, and a task, the compute nodes coupled for data communications through the PAMI, including establishing a data communications geometry, the geometry specifying, for tasks representing processes of execution of the parallel application, a set of endpoints that are used in collective operations of the PAMI including a plurality of endpoints for one of the tasks; receiving in endpoints of the geometry an instruction for a collective operation; and executing the instruction for a collective operation through the endpoints in dependence upon the geometry, including dividing data communications operations among the plurality of endpoints for one of the tasks.

  16. Systematic approach for deriving feasible mappings of parallel algorithms to parallel computing platforms

    NARCIS (Netherlands)

    Arkin, Ethem; Tekinerdogan, Bedir; Imre, Kayhan M.

    2017-01-01

    The need for high-performance computing together with the increasing trend from single processor to parallel computer architectures has leveraged the adoption of parallel computing. To benefit from parallel computing power, usually parallel algorithms are defined that can be mapped and executed

  17. Parallel structures in human and computer memory

    Science.gov (United States)

    Kanerva, Pentti

    1986-08-01

    If we think of our experiences as being recorded continuously on film, then human memory can be compared to a film library that is indexed by the contents of the film strips stored in it. Moreover, approximate retrieval cues suffice to retrieve information stored in this library: We recognize a familiar person in a fuzzy photograph or a familiar tune played on a strange instrument. This paper is about how to construct a computer memory that would allow a computer to recognize patterns and to recall sequences the way humans do. Such a memory is remarkably similar in structure to a conventional computer memory and also to the neural circuits in the cortex of the cerebellum of the human brain. The paper concludes that the frame problem of artificial intelligence could be solved by the use of such a memory if we were able to encode information about the world properly.

  18. Parallel computation of nondeterministic algorithms in VLSI

    Energy Technology Data Exchange (ETDEWEB)

    Hortensius, P D

    1987-01-01

    This work examines parallel VLSI implementations of nondeterministic algorithms. It is demonstrated that conventional pseudorandom number generators are unsuitable for highly parallel applications. Efficient parallel pseudorandom sequence generation can be accomplished using certain classes of elementary one-dimensional cellular automata. The pseudorandom numbers appear in parallel on each clock cycle. Extensive study of the properties of these new pseudorandom number generators is made using standard empirical random number tests, cycle length tests, and implementation considerations. Furthermore, it is shown these particular cellular automata can form the basis of efficient VLSI architectures for computations involved in the Monte Carlo simulation of both the percolation and Ising models from statistical mechanics. Finally, a variation on a Built-In Self-Test technique based upon cellular automata is presented. These Cellular Automata-Logic-Block-Observation (CALBO) circuits improve upon conventional design for testability circuitry.

  19. Frontiers of massively parallel scientific computation

    International Nuclear Information System (INIS)

    Fischer, J.R.

    1987-07-01

    Practical applications using massively parallel computer hardware first appeared during the 1980s. Their development was motivated by the need for computing power orders of magnitude beyond that available today for tasks such as numerical simulation of complex physical and biological processes, generation of interactive visual displays, satellite image analysis, and knowledge based systems. Representative of the first generation of this new class of computers is the Massively Parallel Processor (MPP). A team of scientists was provided the opportunity to test and implement their algorithms on the MPP. The first results are presented. The research spans a broad variety of applications including Earth sciences, physics, signal and image processing, computer science, and graphics. The performance of the MPP was very good. Results obtained using the Connection Machine and the Distributed Array Processor (DAP) are presented

  20. Analysis of parallel computing performance of the code MCNP

    International Nuclear Information System (INIS)

    Wang Lei; Wang Kan; Yu Ganglin

    2006-01-01

    Parallel computing can reduce the running time of the code MCNP effectively. With the MPI message transmitting software, MCNP5 can achieve its parallel computing on PC cluster with Windows operating system. Parallel computing performance of MCNP is influenced by factors such as the type, the complexity level and the parameter configuration of the computing problem. This paper analyzes the parallel computing performance of MCNP regarding with these factors and gives measures to improve the MCNP parallel computing performance. (authors)

  1. Vector and parallel processors in computational science

    International Nuclear Information System (INIS)

    Duff, I.S.; Reid, J.K.

    1985-01-01

    These proceedings contain the articles presented at the named conference. These concern hardware and software for vector and parallel processors, numerical methods and algorithms for the computation on such processors, as well as applications of such methods to different fields of physics and related sciences. See hints under the relevant topics. (HSI)

  2. Contributions to computational stereology and parallel programming

    DEFF Research Database (Denmark)

    Rasmusson, Allan

    rotator, even without the need for isotropic sections. To meet the need for computational power to perform image restoration of virtual tissue sections, parallel programming on GPUs has also been part of the project. This has lead to a significant change in paradigm for a previously developed surgical...

  3. Parallelization of mathematical library for generalized eigenvalue problem for real band matrices

    International Nuclear Information System (INIS)

    Tanaka, Yasuhisa.

    1997-05-01

    This research has focused on a parallelization of the mathematical library for a generalized eigenvalue problem for real band matrices on IBM SP and Hitachi SR2201. The origin of the library is LASO (Lanczos Algorithm with Selective Orthogonalization), which was developed on the basis of Block Lanczos method for standard eigenvalue problem for real band matrices at Texas University. We adopted D.O.F. (Degree Of Freedom) decomposition method for a parallelization of this library, and evaluated its parallel performance. (author)

  4. A massively parallel algorithm for the collision probability calculations in the Apollo-II code using the PVM library

    International Nuclear Information System (INIS)

    Stankovski, Z.

    1995-01-01

    The collision probability method in neutron transport, as applied to 2D geometries, consume a great amount of computer time, for a typical 2D assembly calculation about 90% of the computing time is consumed in the collision probability evaluations. Consequently RZ or 3D calculations became prohibitive. In this paper the author presents a simple but efficient parallel algorithm based on the message passing host/node programmation model. Parallelization was applied to the energy group treatment. Such approach permits parallelization of the existing code, requiring only limited modifications. Sequential/parallel computer portability is preserved, which is a necessary condition for a industrial code. Sequential performances are also preserved. The algorithm is implemented on a CRAY 90 coupled to a 128 processor T3D computer, a 16 processor IBM SPI and a network of workstations, using the Public Domain PVM library. The tests were executed for a 2D geometry with the standard 99-group library. All results were very satisfactory, the best ones with IBM SPI. Because of heterogeneity of the workstation network, the author did not ask high performances for this architecture. The same source code was used for all computers. A more impressive advantage of this algorithm will appear in the calculations of the SAPHYR project (with the future fine multigroup library of about 8000 groups) with a massively parallel computer, using several hundreds of processors

  5. Parallel computing of physical maps--a comparative study in SIMD and MIMD parallelism.

    Science.gov (United States)

    Bhandarkar, S M; Chirravuri, S; Arnold, J

    1996-01-01

    Ordering clones from a genomic library into physical maps of whole chromosomes presents a central computational problem in genetics. Chromosome reconstruction via clone ordering is usually isomorphic to the NP-complete Optimal Linear Arrangement problem. Parallel SIMD and MIMD algorithms for simulated annealing based on Markov chain distribution are proposed and applied to the problem of chromosome reconstruction via clone ordering. Perturbation methods and problem-specific annealing heuristics are proposed and described. The SIMD algorithms are implemented on a 2048 processor MasPar MP-2 system which is an SIMD 2-D toroidal mesh architecture whereas the MIMD algorithms are implemented on an 8 processor Intel iPSC/860 which is an MIMD hypercube architecture. A comparative analysis of the various SIMD and MIMD algorithms is presented in which the convergence, speedup, and scalability characteristics of the various algorithms are analyzed and discussed. On a fine-grained, massively parallel SIMD architecture with a low synchronization overhead such as the MasPar MP-2, a parallel simulated annealing algorithm based on multiple periodically interacting searches performs the best. For a coarse-grained MIMD architecture with high synchronization overhead such as the Intel iPSC/860, a parallel simulated annealing algorithm based on multiple independent searches yields the best results. In either case, distribution of clonal data across multiple processors is shown to exacerbate the tendency of the parallel simulated annealing algorithm to get trapped in a local optimum.

  6. A lightweight communication library for distributed computing

    International Nuclear Information System (INIS)

    Groen, Derek; Rieder, Steven; Zwart, Simon Portegies; Grosso, Paola; Laat, Cees de

    2010-01-01

    We present MPWide, a platform-independent communication library for performing message passing between computers. Our library allows coupling of several local message passing interface (MPI) applications through a long-distance network and is specifically optimized for such communications. The implementation is deliberately kept lightweight and platform independent, and the library can be installed and used without administrative privileges. The only requirements are a C++ compiler and at least one open port to a wide-area network on each site. In this paper we present the library, describe the user interface, present performance tests and apply MPWide in a large-scale cosmological N-body simulation on a network of two computers, one in Amsterdam and the other in Tokyo.

  7. Java parallel secure stream for grid computing

    International Nuclear Information System (INIS)

    Chen, J.; Akers, W.; Chen, Y.; Watson, W.

    2001-01-01

    The emergence of high speed wide area networks makes grid computing a reality. However grid applications that need reliable data transfer still have difficulties to achieve optimal TCP performance due to network tuning of TCP window size to improve the bandwidth and to reduce latency on a high speed wide area network. The authors present a pure Java package called JPARSS (Java Parallel Secure Stream) that divides data into partitions that are sent over several parallel Java streams simultaneously and allows Java or Web applications to achieve optimal TCP performance in a gird environment without the necessity of tuning the TCP window size. Several experimental results are provided to show that using parallel stream is more effective than tuning TCP window size. In addition X.509 certificate based single sign-on mechanism and SSL based connection establishment are integrated into this package. Finally a few applications using this package will be discussed

  8. A massively parallel algorithm for the collision probability calculations in the Apollo-II code using the PVM library

    International Nuclear Information System (INIS)

    Stankovski, Z.

    1995-01-01

    The collision probability method in neutron transport, as applied to 2D geometries, consume a great amount of computer time, for a typical 2D assembly calculation evaluations. Consequently RZ or 3D calculations became prohibitive. In this paper we present a simple but efficient parallel algorithm based on the message passing host/node programing model. Parallelization was applied to the energy group treatment. Such approach permits parallelization of the existing code, requiring only limited modifications. Sequential/parallel computer portability is preserved, witch is a necessary condition for a industrial code. Sequential performances are also preserved. The algorithm is implemented on a CRAY 90 coupled to a 128 processor T3D computer, a 16 processor IBM SP1 and a network of workstations, using the Public Domain PVM library. The tests were executed for a 2D geometry with the standard 99-group library. All results were very satisfactory, the best ones with IBM SP1. Because of heterogeneity of the workstation network, we did ask high performances for this architecture. The same source code was used for all computers. A more impressive advantage of this algorithm will appear in the calculations of the SAPHYR project (with the future fine multigroup library of about 8000 groups) with a massively parallel computer, using several hundreds of processors. (author). 5 refs., 6 figs., 2 tabs

  9. Intranode data communications in a parallel computer

    Science.gov (United States)

    Archer, Charles J; Blocksome, Michael A; Miller, Douglas R; Ratterman, Joseph D; Smith, Brian E

    2014-01-07

    Intranode data communications in a parallel computer that includes compute nodes configured to execute processes, where the data communications include: allocating, upon initialization of a first process of a computer node, a region of shared memory; establishing, by the first process, a predefined number of message buffers, each message buffer associated with a process to be initialized on the compute node; sending, to a second process on the same compute node, a data communications message without determining whether the second process has been initialized, including storing the data communications message in the message buffer of the second process; and upon initialization of the second process: retrieving, by the second process, a pointer to the second process's message buffer; and retrieving, by the second process from the second process's message buffer in dependence upon the pointer, the data communications message sent by the first process.

  10. Intranode data communications in a parallel computer

    Science.gov (United States)

    Archer, Charles J; Blocksome, Michael A; Miller, Douglas R; Ratterman, Joseph D; Smith, Brian E

    2013-07-23

    Intranode data communications in a parallel computer that includes compute nodes configured to execute processes, where the data communications include: allocating, upon initialization of a first process of a compute node, a region of shared memory; establishing, by the first process, a predefined number of message buffers, each message buffer associated with a process to be initialized on the compute node; sending, to a second process on the same compute node, a data communications message without determining whether the second process has been initialized, including storing the data communications message in the message buffer of the second process; and upon initialization of the second process: retrieving, by the second process, a pointer to the second process's message buffer; and retrieving, by the second process from the second process's message buffer in dependence upon the pointer, the data communications message sent by the first process.

  11. Parallel computers and three-dimensional computational electromagnetics

    International Nuclear Information System (INIS)

    Madsen, N.K.

    1994-01-01

    The authors have continued to enhance their ability to use new massively parallel processing computers to solve time-domain electromagnetic problems. New vectorization techniques have improved the performance of their code DSI3D by factors of 5 to 15, depending on the computer used. New radiation boundary conditions and far-field transformations now allow the computation of radar cross-section values for complex objects. A new parallel-data extraction code has been developed that allows the extraction of data subsets from large problems, which have been run on parallel computers, for subsequent post-processing on workstations with enhanced graphics capabilities. A new charged-particle-pushing version of DSI3D is under development. Finally, DSI3D has become a focal point for several new Cooperative Research and Development Agreement activities with industrial companies such as Lockheed Advanced Development Company, Varian, Hughes Electron Dynamics Division, General Atomic, and Cray

  12. Computationally efficient implementation of combustion chemistry in parallel PDF calculations

    International Nuclear Information System (INIS)

    Lu Liuyan; Lantz, Steven R.; Ren Zhuyin; Pope, Stephen B.

    2009-01-01

    In parallel calculations of combustion processes with realistic chemistry, the serial in situ adaptive tabulation (ISAT) algorithm [S.B. Pope, Computationally efficient implementation of combustion chemistry using in situ adaptive tabulation, Combustion Theory and Modelling, 1 (1997) 41-63; L. Lu, S.B. Pope, An improved algorithm for in situ adaptive tabulation, Journal of Computational Physics 228 (2009) 361-386] substantially speeds up the chemistry calculations on each processor. To improve the parallel efficiency of large ensembles of such calculations in parallel computations, in this work, the ISAT algorithm is extended to the multi-processor environment, with the aim of minimizing the wall clock time required for the whole ensemble. Parallel ISAT strategies are developed by combining the existing serial ISAT algorithm with different distribution strategies, namely purely local processing (PLP), uniformly random distribution (URAN), and preferential distribution (PREF). The distribution strategies enable the queued load redistribution of chemistry calculations among processors using message passing. They are implemented in the software x2f m pi, which is a Fortran 95 library for facilitating many parallel evaluations of a general vector function. The relative performance of the parallel ISAT strategies is investigated in different computational regimes via the PDF calculations of multiple partially stirred reactors burning methane/air mixtures. The results show that the performance of ISAT with a fixed distribution strategy strongly depends on certain computational regimes, based on how much memory is available and how much overlap exists between tabulated information on different processors. No one fixed strategy consistently achieves good performance in all the regimes. Therefore, an adaptive distribution strategy, which blends PLP, URAN and PREF, is devised and implemented. It yields consistently good performance in all regimes. In the adaptive parallel

  13. Overview of Parallel Platforms for Common High Performance Computing

    Directory of Open Access Journals (Sweden)

    T. Fryza

    2012-04-01

    Full Text Available The paper deals with various parallel platforms used for high performance computing in the signal processing domain. More precisely, the methods exploiting the multicores central processing units such as message passing interface and OpenMP are taken into account. The properties of the programming methods are experimentally proved in the application of a fast Fourier transform and a discrete cosine transform and they are compared with the possibilities of MATLAB's built-in functions and Texas Instruments digital signal processors with very long instruction word architectures. New FFT and DCT implementations were proposed and tested. The implementation phase was compared with CPU based computing methods and with possibilities of the Texas Instruments digital signal processing library on C6747 floating-point DSPs. The optimal combination of computing methods in the signal processing domain and new, fast routines' implementation is proposed as well.

  14. On synchronous parallel computations with independent probabilistic choice

    International Nuclear Information System (INIS)

    Reif, J.H.

    1984-01-01

    This paper introduces probabilistic choice to synchronous parallel machine models; in particular parallel RAMs. The power of probabilistic choice in parallel computations is illustrate by parallelizing some known probabilistic sequential algorithms. The authors characterize the computational complexity of time, space, and processor bounded probabilistic parallel RAMs in terms of the computational complexity of probabilistic sequential RAMs. They show that parallelism uniformly speeds up time bounded probabilistic sequential RAM computations by nearly a quadratic factor. They also show that probabilistic choice can be eliminated from parallel computations by introducing nonuniformity

  15. The Parallel C++ Statistical Library ‘QUESO’: Quantification of Uncertainty for Estimation, Simulation and Optimization

    KAUST Repository

    Prudencio, Ernesto E.

    2012-01-01

    QUESO is a collection of statistical algorithms and programming constructs supporting research into the uncertainty quantification (UQ) of models and their predictions. It has been designed with three objectives: it should (a) be sufficiently abstract in order to handle a large spectrum of models, (b) be algorithmically extensible, allowing an easy insertion of new and improved algorithms, and (c) take advantage of parallel computing, in order to handle realistic models. Such objectives demand a combination of an object-oriented design with robust software engineering practices. QUESO is written in C++, uses MPI, and leverages libraries already available to the scientific community. We describe some UQ concepts, present QUESO, and list planned enhancements.

  16. The Adoption of Cloud Computing Technology for Library Services ...

    African Journals Online (AJOL)

    The study investigated the rationales for the adoption of cloud computing technology for library services in NOUN Library. Issues related to the existing computer network available in NOUN library such as LAN, WAN, rationales for the adoption of cloud computing in NOUN library such as the need to disclose their collections ...

  17. Computational chaos in massively parallel neural networks

    Science.gov (United States)

    Barhen, Jacob; Gulati, Sandeep

    1989-01-01

    A fundamental issue which directly impacts the scalability of current theoretical neural network models to massively parallel embodiments, in both software as well as hardware, is the inherent and unavoidable concurrent asynchronicity of emerging fine-grained computational ensembles and the possible emergence of chaotic manifestations. Previous analyses attributed dynamical instability to the topology of the interconnection matrix, to parasitic components or to propagation delays. However, researchers have observed the existence of emergent computational chaos in a concurrently asynchronous framework, independent of the network topology. Researcher present a methodology enabling the effective asynchronous operation of large-scale neural networks. Necessary and sufficient conditions guaranteeing concurrent asynchronous convergence are established in terms of contracting operators. Lyapunov exponents are computed formally to characterize the underlying nonlinear dynamics. Simulation results are presented to illustrate network convergence to the correct results, even in the presence of large delays.

  18. Electromagnetic Physics Models for Parallel Computing Architectures

    International Nuclear Information System (INIS)

    Amadio, G; Bianchini, C; Iope, R; Ananya, A; Apostolakis, J; Aurora, A; Bandieramonte, M; Brun, R; Carminati, F; Gheata, A; Gheata, M; Goulas, I; Nikitina, T; Bhattacharyya, A; Mohanty, A; Canal, P; Elvira, D; Jun, S Y; Lima, G; Duhem, L

    2016-01-01

    The recent emergence of hardware architectures characterized by many-core or accelerated processors has opened new opportunities for concurrent programming models taking advantage of both SIMD and SIMT architectures. GeantV, a next generation detector simulation, has been designed to exploit both the vector capability of mainstream CPUs and multi-threading capabilities of coprocessors including NVidia GPUs and Intel Xeon Phi. The characteristics of these architectures are very different in terms of the vectorization depth and type of parallelization needed to achieve optimal performance. In this paper we describe implementation of electromagnetic physics models developed for parallel computing architectures as a part of the GeantV project. Results of preliminary performance evaluation and physics validation are presented as well. (paper)

  19. Electromagnetic Physics Models for Parallel Computing Architectures

    Science.gov (United States)

    Amadio, G.; Ananya, A.; Apostolakis, J.; Aurora, A.; Bandieramonte, M.; Bhattacharyya, A.; Bianchini, C.; Brun, R.; Canal, P.; Carminati, F.; Duhem, L.; Elvira, D.; Gheata, A.; Gheata, M.; Goulas, I.; Iope, R.; Jun, S. Y.; Lima, G.; Mohanty, A.; Nikitina, T.; Novak, M.; Pokorski, W.; Ribon, A.; Seghal, R.; Shadura, O.; Vallecorsa, S.; Wenzel, S.; Zhang, Y.

    2016-10-01

    The recent emergence of hardware architectures characterized by many-core or accelerated processors has opened new opportunities for concurrent programming models taking advantage of both SIMD and SIMT architectures. GeantV, a next generation detector simulation, has been designed to exploit both the vector capability of mainstream CPUs and multi-threading capabilities of coprocessors including NVidia GPUs and Intel Xeon Phi. The characteristics of these architectures are very different in terms of the vectorization depth and type of parallelization needed to achieve optimal performance. In this paper we describe implementation of electromagnetic physics models developed for parallel computing architectures as a part of the GeantV project. Results of preliminary performance evaluation and physics validation are presented as well.

  20. (Nearly) portable PIC code for parallel computers

    International Nuclear Information System (INIS)

    Decyk, V.K.

    1993-01-01

    As part of the Numerical Tokamak Project, the author has developed a (nearly) portable, one dimensional version of the GCPIC algorithm for particle-in-cell codes on parallel computers. This algorithm uses a spatial domain decomposition for the fields, and passes particles from one domain to another as the particles move spatially. With only minor changes, the code has been run in parallel on the Intel Delta, the Cray C-90, the IBM ES/9000 and a cluster of workstations. After a line by line translation into cmfortran, the code was also run on the CM-200. Impressive speeds have been achieved, both on the Intel Delta and the Cray C-90, around 30 nanoseconds per particle per time step. In addition, the author was able to isolate the data management modules, so that the physics modules were not changed much from their sequential version, and the data management modules can be used as open-quotes black boxes.close quotes

  1. Computation and parallel implementation for early vision

    Science.gov (United States)

    Gualtieri, J. Anthony

    1990-01-01

    The problem of early vision is to transform one or more retinal illuminance images-pixel arrays-to image representations built out of such primitive visual features such as edges, regions, disparities, and clusters. These transformed representations form the input to later vision stages that perform higher level vision tasks including matching and recognition. Researchers developed algorithms for: (1) edge finding in the scale space formulation; (2) correlation methods for computing matches between pairs of images; and (3) clustering of data by neural networks. These algorithms are formulated for parallel implementation of SIMD machines, such as the Massively Parallel Processor, a 128 x 128 array processor with 1024 bits of local memory per processor. For some cases, researchers can show speedups of three orders of magnitude over serial implementations.

  2. Parallel computing techniques for rotorcraft aerodynamics

    Science.gov (United States)

    Ekici, Kivanc

    The modification of unsteady three-dimensional Navier-Stokes codes for application on massively parallel and distributed computing environments is investigated. The Euler/Navier-Stokes code TURNS (Transonic Unsteady Rotor Navier-Stokes) was chosen as a test bed because of its wide use by universities and industry. For the efficient implementation of TURNS on parallel computing systems, two algorithmic changes are developed. First, main modifications to the implicit operator, Lower-Upper Symmetric Gauss Seidel (LU-SGS) originally used in TURNS, is performed. Second, application of an inexact Newton method, coupled with a Krylov subspace iterative method (Newton-Krylov method) is carried out. Both techniques have been tried previously for the Euler equations mode of the code. In this work, we have extended the methods to the Navier-Stokes mode. Several new implicit operators were tried because of convergence problems of traditional operators with the high cell aspect ratio (CAR) grids needed for viscous calculations on structured grids. Promising results for both Euler and Navier-Stokes cases are presented for these operators. For the efficient implementation of Newton-Krylov methods to the Navier-Stokes mode of TURNS, efficient preconditioners must be used. The parallel implicit operators used in the previous step are employed as preconditioners and the results are compared. The Message Passing Interface (MPI) protocol has been used because of its portability to various parallel architectures. It should be noted that the proposed methodology is general and can be applied to several other CFD codes (e.g. OVERFLOW).

  3. Computationally designed libraries for rapid enzyme stabilization

    NARCIS (Netherlands)

    Wijma, Hein J.; Floor, Robert J.; Jekel, Peter A.; Baker, David; Marrink, Siewert J.; Janssen, Dick B.

    The ability to engineer enzymes and other proteins to any desired stability would have wide-ranging applications. Here, we demonstrate that computational design of a library with chemically diverse stabilizing mutations allows the engineering of drastically stabilized and fully functional variants

  4. AstroCV: Astronomy computer vision library

    Science.gov (United States)

    González, Roberto E.; Muñoz, Roberto P.; Hernández, Cristian A.

    2018-04-01

    AstroCV processes and analyzes big astronomical datasets, and is intended to provide a community repository of high performance Python and C++ algorithms used for image processing and computer vision. The library offers methods for object recognition, segmentation and classification, with emphasis in the automatic detection and classification of galaxies.

  5. Computational fluid dynamics on a massively parallel computer

    Science.gov (United States)

    Jespersen, Dennis C.; Levit, Creon

    1989-01-01

    A finite difference code was implemented for the compressible Navier-Stokes equations on the Connection Machine, a massively parallel computer. The code is based on the ARC2D/ARC3D program and uses the implicit factored algorithm of Beam and Warming. The codes uses odd-even elimination to solve linear systems. Timings and computation rates are given for the code, and a comparison is made with a Cray XMP.

  6. MulticoreBSP for C : A high-performance library for shared-memory parallel programming

    NARCIS (Netherlands)

    Yzelman, A. N.; Bisseling, R. H.; Roose, D.; Meerbergen, K.

    2014-01-01

    The bulk synchronous parallel (BSP) model, as well as parallel programming interfaces based on BSP, classically target distributed-memory parallel architectures. In earlier work, Yzelman and Bisseling designed a MulticoreBSP for Java library specifically for shared-memory architectures. In the

  7. Lemon : An MPI parallel I/O library for data encapsulation using LIME

    NARCIS (Netherlands)

    Deuzeman, Albert; Reker, Siebren; Urbach, Carsten

    We introduce Lemon, an MPI parallel I/O library that provides efficient parallel I/O of both binary and metadata on massively parallel architectures. Motivated by the demands of the lattice Quantum Chromodynamics community, the data is stored in the SciDAC Lattice QCD Interchange Message

  8. Climate models on massively parallel computers

    International Nuclear Information System (INIS)

    Vitart, F.; Rouvillois, P.

    1993-01-01

    First results got on massively parallel computers (Multiple Instruction Multiple Data and Simple Instruction Multiple Data) allow to consider building of coupled models with high resolutions. This would make possible simulation of thermoaline circulation and other interaction phenomena between atmosphere and ocean. The increasing of computers powers, and then the improvement of resolution will go us to revise our approximations. Then hydrostatic approximation (in ocean circulation) will not be valid when the grid mesh will be of a dimension lower than a few kilometers: We shall have to find other models. The expert appraisement got in numerical analysis at the Center of Limeil-Valenton (CEL-V) will be used again to imagine global models taking in account atmosphere, ocean, ice floe and biosphere, allowing climate simulation until a regional scale

  9. Massively parallel computation of conservation laws

    Energy Technology Data Exchange (ETDEWEB)

    Garbey, M [Univ. Claude Bernard, Villeurbanne (France); Levine, D [Argonne National Lab., IL (United States)

    1990-01-01

    The authors present a new method for computing solutions of conservation laws based on the use of cellular automata with the method of characteristics. The method exploits the high degree of parallelism available with cellular automata and retains important features of the method of characteristics. It yields high numerical accuracy and extends naturally to adaptive meshes and domain decomposition methods for perturbed conservation laws. They describe the method and its implementation for a Dirichlet problem with a single conservation law for the one-dimensional case. Numerical results for the one-dimensional law with the classical Burgers nonlinearity or the Buckley-Leverett equation show good numerical accuracy outside the neighborhood of the shocks. The error in the area of the shocks is of the order of the mesh size. The algorithm is well suited for execution on both massively parallel computers and vector machines. They present timing results for an Alliant FX/8, Connection Machine Model 2, and CRAY X-MP.

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

    Science.gov (United States)

    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.

  11. External parallel sorting with multiprocessor computers

    International Nuclear Information System (INIS)

    Comanceau, S.I.

    1984-01-01

    This article describes methods of external sorting in which the entire main computer memory is used for the internal sorting of entries, forming out of them sorted segments of the greatest possible size, and outputting them to external memories. The obtained segments are merged into larger segments until all entries form one ordered segment. The described methods are suitable for sequential files stored on magnetic tape. The needs of the sorting algorithm can be met by using the relatively slow peripheral storage devices (e.g., tapes, disks, drums). The efficiency of the external sorting methods is determined by calculating the total sorting time as a function of the number of entries to be sorted and the number of parallel processors participating in the sorting process

  12. Contact-impact algorithms on parallel computers

    International Nuclear Information System (INIS)

    Zhong Zhihua; Nilsson, Larsgunnar

    1994-01-01

    Contact-impact algorithms on parallel computers are discussed within the context of explicit finite element analysis. The algorithms concerned include a contact searching algorithm and an algorithm for contact force calculations. The contact searching algorithm is based on the territory concept of the general HITA algorithm. However, no distinction is made between different contact bodies, or between different contact surfaces. All contact segments from contact boundaries are taken as a single set. Hierarchy territories and contact territories are expanded. A three-dimensional bucket sort algorithm is used to sort contact nodes. The defence node algorithm is used in the calculation of contact forces. Both the contact searching algorithm and the defence node algorithm are implemented on the connection machine CM-200. The performance of the algorithms is examined under different circumstances, and numerical results are presented. ((orig.))

  13. Distributed Memory Parallel Computing with SEAWAT

    Science.gov (United States)

    Verkaik, J.; Huizer, S.; van Engelen, J.; Oude Essink, G.; Ram, R.; Vuik, K.

    2017-12-01

    Fresh groundwater reserves in coastal aquifers are threatened by sea-level rise, extreme weather conditions, increasing urbanization and associated groundwater extraction rates. To counteract these threats, accurate high-resolution numerical models are required to optimize the management of these precious reserves. The major model drawbacks are long run times and large memory requirements, limiting the predictive power of these models. Distributed memory parallel computing is an efficient technique for reducing run times and memory requirements, where the problem is divided over multiple processor cores. A new Parallel Krylov Solver (PKS) for SEAWAT is presented. PKS has recently been applied to MODFLOW and includes Conjugate Gradient (CG) and Biconjugate Gradient Stabilized (BiCGSTAB) linear accelerators. Both accelerators are preconditioned by an overlapping additive Schwarz preconditioner in a way that: a) subdomains are partitioned using Recursive Coordinate Bisection (RCB) load balancing, b) each subdomain uses local memory only and communicates with other subdomains by Message Passing Interface (MPI) within the linear accelerator, c) it is fully integrated in SEAWAT. Within SEAWAT, the PKS-CG solver replaces the Preconditioned Conjugate Gradient (PCG) solver for solving the variable-density groundwater flow equation and the PKS-BiCGSTAB solver replaces the Generalized Conjugate Gradient (GCG) solver for solving the advection-diffusion equation. PKS supports the third-order Total Variation Diminishing (TVD) scheme for computing advection. Benchmarks were performed on the Dutch national supercomputer (https://userinfo.surfsara.nl/systems/cartesius) using up to 128 cores, for a synthetic 3D Henry model (100 million cells) and the real-life Sand Engine model ( 10 million cells). The Sand Engine model was used to investigate the potential effect of the long-term morphological evolution of a large sand replenishment and climate change on fresh groundwater resources

  14. Schnek: A C++ library for the development of parallel simulation codes on regular grids

    Science.gov (United States)

    Schmitz, Holger

    2018-05-01

    A large number of algorithms across the field of computational physics are formulated on grids with a regular topology. We present Schnek, a library that enables fast development of parallel simulations on regular grids. Schnek contains a number of easy-to-use modules that greatly reduce the amount of administrative code for large-scale simulation codes. The library provides an interface for reading simulation setup files with a hierarchical structure. The structure of the setup file is translated into a hierarchy of simulation modules that the developer can specify. The reader parses and evaluates mathematical expressions and initialises variables or grid data. This enables developers to write modular and flexible simulation codes with minimal effort. Regular grids of arbitrary dimension are defined as well as mechanisms for defining physical domain sizes, grid staggering, and ghost cells on these grids. Ghost cells can be exchanged between neighbouring processes using MPI with a simple interface. The grid data can easily be written into HDF5 files using serial or parallel I/O.

  15. Distributed and cloud computing from parallel processing to the Internet of Things

    CERN Document Server

    Hwang, Kai; Fox, Geoffrey C

    2012-01-01

    Distributed and Cloud Computing, named a 2012 Outstanding Academic Title by the American Library Association's Choice publication, explains how to create high-performance, scalable, reliable systems, exposing the design principles, architecture, and innovative applications of parallel, distributed, and cloud computing systems. Starting with an overview of modern distributed models, the book provides comprehensive coverage of distributed and cloud computing, including: Facilitating management, debugging, migration, and disaster recovery through virtualization Clustered systems for resear

  16. Automatic Parallelization Tool: Classification of Program Code for Parallel Computing

    Directory of Open Access Journals (Sweden)

    Mustafa Basthikodi

    2016-04-01

    Full Text Available Performance growth of single-core processors has come to a halt in the past decade, but was re-enabled by the introduction of parallelism in processors. Multicore frameworks along with Graphical Processing Units empowered to enhance parallelism broadly. Couples of compilers are updated to developing challenges forsynchronization and threading issues. Appropriate program and algorithm classifications will have advantage to a great extent to the group of software engineers to get opportunities for effective parallelization. In present work we investigated current species for classification of algorithms, in that related work on classification is discussed along with the comparison of issues that challenges the classification. The set of algorithms are chosen which matches the structure with different issues and perform given task. We have tested these algorithms utilizing existing automatic species extraction toolsalong with Bones compiler. We have added functionalities to existing tool, providing a more detailed characterization. The contributions of our work include support for pointer arithmetic, conditional and incremental statements, user defined types, constants and mathematical functions. With this, we can retain significant data which is not captured by original speciesof algorithms. We executed new theories into the device, empowering automatic characterization of program code.

  17. Broadcasting collective operation contributions throughout a parallel computer

    Science.gov (United States)

    Faraj, Ahmad [Rochester, MN

    2012-02-21

    Methods, systems, and products are disclosed for broadcasting collective operation contributions throughout a parallel computer. The parallel computer includes a plurality of compute nodes connected together through a data communications network. Each compute node has a plurality of processors for use in collective parallel operations on the parallel computer. Broadcasting collective operation contributions throughout a parallel computer according to embodiments of the present invention includes: transmitting, by each processor on each compute node, that processor's collective operation contribution to the other processors on that compute node using intra-node communications; and transmitting on a designated network link, by each processor on each compute node according to a serial processor transmission sequence, that processor's collective operation contribution to the other processors on the other compute nodes using inter-node communications.

  18. Accelerating Astronomy & Astrophysics in the New Era of Parallel Computing: GPUs, Phi and Cloud Computing

    Science.gov (United States)

    Ford, Eric B.; Dindar, Saleh; Peters, Jorg

    2015-08-01

    The realism of astrophysical simulations and statistical analyses of astronomical data are set by the available computational resources. Thus, astronomers and astrophysicists are constantly pushing the limits of computational capabilities. For decades, astronomers benefited from massive improvements in computational power that were driven primarily by increasing clock speeds and required relatively little attention to details of the computational hardware. For nearly a decade, increases in computational capabilities have come primarily from increasing the degree of parallelism, rather than increasing clock speeds. Further increases in computational capabilities will likely be led by many-core architectures such as Graphical Processing Units (GPUs) and Intel Xeon Phi. Successfully harnessing these new architectures, requires significantly more understanding of the hardware architecture, cache hierarchy, compiler capabilities and network network characteristics.I will provide an astronomer's overview of the opportunities and challenges provided by modern many-core architectures and elastic cloud computing. The primary goal is to help an astronomical audience understand what types of problems are likely to yield more than order of magnitude speed-ups and which problems are unlikely to parallelize sufficiently efficiently to be worth the development time and/or costs.I will draw on my experience leading a team in developing the Swarm-NG library for parallel integration of large ensembles of small n-body systems on GPUs, as well as several smaller software projects. I will share lessons learned from collaborating with computer scientists, including both technical and soft skills. Finally, I will discuss the challenges of training the next generation of astronomers to be proficient in this new era of high-performance computing, drawing on experience teaching a graduate class on High-Performance Scientific Computing for Astrophysics and organizing a 2014 advanced summer

  19. PCG: A software package for the iterative solution of linear systems on scalar, vector and parallel computers

    Energy Technology Data Exchange (ETDEWEB)

    Joubert, W. [Los Alamos National Lab., NM (United States); Carey, G.F. [Univ. of Texas, Austin, TX (United States)

    1994-12-31

    A great need exists for high performance numerical software libraries transportable across parallel machines. This talk concerns the PCG package, which solves systems of linear equations by iterative methods on parallel computers. The features of the package are discussed, as well as techniques used to obtain high performance as well as transportability across architectures. Representative numerical results are presented for several machines including the Connection Machine CM-5, Intel Paragon and Cray T3D parallel computers.

  20. From parallel to distributed computing for reactive scattering calculations

    International Nuclear Information System (INIS)

    Lagana, A.; Gervasi, O.; Baraglia, R.

    1994-01-01

    Some reactive scattering codes have been ported on different innovative computer architectures ranging from massively parallel machines to clustered workstations. The porting has required a drastic restructuring of the codes to single out computationally decoupled cpu intensive subsections. The suitability of different theoretical approaches for parallel and distributed computing restructuring is discussed and the efficiency of related algorithms evaluated

  1. Model-driven product line engineering for mapping parallel algorithms to parallel computing platforms

    NARCIS (Netherlands)

    Arkin, Ethem; Tekinerdogan, Bedir

    2016-01-01

    Mapping parallel algorithms to parallel computing platforms requires several activities such as the analysis of the parallel algorithm, the definition of the logical configuration of the platform, the mapping of the algorithm to the logical configuration platform and the implementation of the

  2. The Library Macintosh at SCIL [Small Computers in Libraries]'88.

    Science.gov (United States)

    Valauskas, Edward J.; And Others

    1988-01-01

    The first of three papers describes the role of Macintosh workstations in a library. The second paper explains why the Macintosh was selected for end-user searching in an academic library, and the third discusses advantages and disadvantages of desktop publishing for librarians. (8 references) (MES)

  3. Data communications in a parallel active messaging interface of a parallel computer

    Science.gov (United States)

    Archer, Charles J; Blocksome, Michael A; Ratterman, Joseph D; Smith, Brian E

    2013-11-12

    Data communications in a parallel active messaging interface (`PAMI`) of a parallel computer composed of compute nodes that execute a parallel application, each compute node including application processors that execute the parallel application and at least one management processor dedicated to gathering information regarding data communications. The PAMI is composed of data communications endpoints, each endpoint composed of a specification of data communications parameters for a thread of execution on a compute node, including specifications of a client, a context, and a task, the compute nodes and the endpoints coupled for data communications through the PAMI and through data communications resources. Embodiments function by gathering call site statistics describing data communications resulting from execution of data communications instructions and identifying in dependence upon the call cite statistics a data communications algorithm for use in executing a data communications instruction at a call site in the parallel application.

  4. Parallel Computing for Terrestrial Ecosystem Carbon Modeling

    International Nuclear Information System (INIS)

    Wang, Dali; Post, Wilfred M.; Ricciuto, Daniel M.; Berry, Michael

    2011-01-01

    Terrestrial ecosystems are a primary component of research on global environmental change. Observational and modeling research on terrestrial ecosystems at the global scale, however, has lagged behind their counterparts for oceanic and atmospheric systems, largely because the unique challenges associated with the tremendous diversity and complexity of terrestrial ecosystems. There are 8 major types of terrestrial ecosystem: tropical rain forest, savannas, deserts, temperate grassland, deciduous forest, coniferous forest, tundra, and chaparral. The carbon cycle is an important mechanism in the coupling of terrestrial ecosystems with climate through biological fluxes of CO 2 . The influence of terrestrial ecosystems on atmospheric CO 2 can be modeled via several means at different timescales. Important processes include plant dynamics, change in land use, as well as ecosystem biogeography. Over the past several decades, many terrestrial ecosystem models (see the 'Model developments' section) have been developed to understand the interactions between terrestrial carbon storage and CO 2 concentration in the atmosphere, as well as the consequences of these interactions. Early TECMs generally adapted simple box-flow exchange models, in which photosynthetic CO 2 uptake and respiratory CO 2 release are simulated in an empirical manner with a small number of vegetation and soil carbon pools. Demands on kinds and amount of information required from global TECMs have grown. Recently, along with the rapid development of parallel computing, spatially explicit TECMs with detailed process based representations of carbon dynamics become attractive, because those models can readily incorporate a variety of additional ecosystem processes (such as dispersal, establishment, growth, mortality etc.) and environmental factors (such as landscape position, pest populations, disturbances, resource manipulations, etc.), and provide information to frame policy options for climate change

  5. Parallel Libraries to support High-Level Programming

    DEFF Research Database (Denmark)

    Larsen, Morten Nørgaard

    and the Microsoft .NET iv framework. Normally, one would not directly think of the .NET framework when talking scientific applications, but Microsoft has in the last couple of versions of .NET introduce a number of tools for writing parallel and high performance code. The first section examines how programmers can...

  6. Fast parallel computation of polynomials using few processors

    DEFF Research Database (Denmark)

    Valiant, Leslie; Skyum, Sven

    1981-01-01

    It is shown that any multivariate polynomial that can be computed sequentially in C steps and has degree d can be computed in parallel in 0((log d) (log C + log d)) steps using only (Cd)0(1) processors....

  7. Prototyping and Simulating Parallel, Distributed Computations with VISA

    National Research Council Canada - National Science Library

    Demeure, Isabelle M; Nutt, Gary J

    1989-01-01

    ...] to support the design, prototyping, and simulation of parallel, distributed computations. In particular, VISA is meant to guide the choice of partitioning and communication strategies for such computations, based on their performance...

  8. Solving the Stokes problem on a massively parallel computer

    DEFF Research Database (Denmark)

    Axelsson, Owe; Barker, Vincent A.; Neytcheva, Maya

    2001-01-01

    boundary value problem for each velocity component, are solved by the conjugate gradient method with a preconditioning based on the algebraic multi‐level iteration (AMLI) technique. The velocity is found from the computed pressure. The method is optimal in the sense that the computational work...... is proportional to the number of unknowns. Further, it is designed to exploit a massively parallel computer with distributed memory architecture. Numerical experiments on a Cray T3E computer illustrate the parallel performance of the method....

  9. Automatic Thread-Level Parallelization in the Chombo AMR Library

    Energy Technology Data Exchange (ETDEWEB)

    Christen, Matthias; Keen, Noel; Ligocki, Terry; Oliker, Leonid; Shalf, John; Van Straalen, Brian; Williams, Samuel

    2011-05-26

    The increasing on-chip parallelism has some substantial implications for HPC applications. Currently, hybrid programming models (typically MPI+OpenMP) are employed for mapping software to the hardware in order to leverage the hardware?s architectural features. In this paper, we present an approach that automatically introduces thread level parallelism into Chombo, a parallel adaptive mesh refinement framework for finite difference type PDE solvers. In Chombo, core algorithms are specified in the ChomboFortran, a macro language extension to F77 that is part of the Chombo framework. This domain-specific language forms an already used target language for an automatic migration of the large number of existing algorithms into a hybrid MPI+OpenMP implementation. It also provides access to the auto-tuning methodology that enables tuning certain aspects of an algorithm to hardware characteristics. Performance measurements are presented for a few of the most relevant kernels with respect to a specific application benchmark using this technique as well as benchmark results for the entire application. The kernel benchmarks show that, using auto-tuning, up to a factor of 11 in performance was gained with 4 threads with respect to the serial reference implementation.

  10. Numerical discrepancy between serial and MPI parallel computations

    Directory of Open Access Journals (Sweden)

    Sang Bong Lee

    2016-09-01

    Full Text Available Numerical simulations of 1D Burgers equation and 2D sloshing problem were carried out to study numerical discrepancy between serial and parallel computations. The numerical domain was decomposed into 2 and 4 subdomains for parallel computations with message passing interface. The numerical solution of Burgers equation disclosed that fully explicit boundary conditions used on subdomains of parallel computation was responsible for the numerical discrepancy of transient solution between serial and parallel computations. Two dimensional sloshing problems in a rectangular domain were solved using OpenFOAM. After a lapse of initial transient time sloshing patterns of water were significantly different in serial and parallel computations although the same numerical conditions were given. Based on the histograms of pressure measured at two points near the wall the statistical characteristics of numerical solution was not affected by the number of subdomains as much as the transient solution was dependent on the number of subdomains.

  11. Parallel computation for solving the tridiagonal linear system of equations

    International Nuclear Information System (INIS)

    Ishiguro, Misako; Harada, Hiroo; Fujii, Minoru; Fujimura, Toichiro; Nakamura, Yasuhiro; Nanba, Katsumi.

    1981-09-01

    Recently, applications of parallel computation for scientific calculations have increased from the need of the high speed calculation of large scale programs. At the JAERI computing center, an array processor FACOM 230-75 APU has installed to study the applicability of parallel computation for nuclear codes. We made some numerical experiments by using the APU on the methods of solution of tridiagonal linear equation which is an important problem in scientific calculations. Referring to the recent papers with parallel methods, we investigate eight ones. These are Gauss elimination method, Parallel Gauss method, Accelerated parallel Gauss method, Jacobi method, Recursive doubling method, Cyclic reduction method, Chebyshev iteration method, and Conjugate gradient method. The computing time and accuracy were compared among the methods on the basis of the numerical experiments. As the result, it is found that the Cyclic reduction method is best both in computing time and accuracy and the Gauss elimination method is the second one. (author)

  12. NDL-v2.0: A new version of the numerical differentiation library for parallel architectures

    Science.gov (United States)

    Hadjidoukas, P. E.; Angelikopoulos, P.; Voglis, C.; Papageorgiou, D. G.; Lagaris, I. E.

    2014-07-01

    We present a new version of the numerical differentiation library (NDL) used for the numerical estimation of first and second order partial derivatives of a function by finite differencing. In this version we have restructured the serial implementation of the code so as to achieve optimal task-based parallelization. The pure shared-memory parallelization of the library has been based on the lightweight OpenMP tasking model allowing for the full extraction of the available parallelism and efficient scheduling of multiple concurrent library calls. On multicore clusters, parallelism is exploited by means of TORC, an MPI-based multi-threaded tasking library. The new MPI implementation of NDL provides optimal performance in terms of function calls and, furthermore, supports asynchronous execution of multiple library calls within legacy MPI programs. In addition, a Python interface has been implemented for all cases, exporting the functionality of our library to sequential Python codes. Catalog identifier: AEDG_v2_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEDG_v2_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 63036 No. of bytes in distributed program, including test data, etc.: 801872 Distribution format: tar.gz Programming language: ANSI Fortran-77, ANSI C, Python. Computer: Distributed systems (clusters), shared memory systems. Operating system: Linux, Unix. Has the code been vectorized or parallelized?: Yes. RAM: The library uses O(N) internal storage, N being the dimension of the problem. It can use up to O(N2) internal storage for Hessian calculations, if a task throttling factor has not been set by the user. Classification: 4.9, 4.14, 6.5. Catalog identifier of previous version: AEDG_v1_0 Journal reference of previous version: Comput. Phys. Comm. 180

  13. Solution-phase parallel synthesis of a library of delta(2)-pyrazolines.

    Science.gov (United States)

    Manyem, Shankar; Sibi, Mukund P; Lushington, Gerald H; Neuenswander, Benjamin; Schoenen, Frank; Aubé, Jeffrey

    2007-01-01

    A parallel synthesis of a library (80 members) of 2-pyrazolines in solution phase is described. The 2-pyrazoline core was accessed through the [3 + 2] cycloaddition of nitrilimines with enoyl oxazolidinones. The cycloaddition provided two regioisomers, the major product being the C regioisomer. The oxazolidinone moiety was further reduced to the primary alcohol, producing another library of 5-hydroxymethyl-2-pyrazolines. The Lipinski profiles and calculated ADME properties of the compounds are also reported.

  14. The Research of the Parallel Computing Development from the Angle of Cloud Computing

    Science.gov (United States)

    Peng, Zhensheng; Gong, Qingge; Duan, Yanyu; Wang, Yun

    2017-10-01

    Cloud computing is the development of parallel computing, distributed computing and grid computing. The development of cloud computing makes parallel computing come into people’s lives. Firstly, this paper expounds the concept of cloud computing and introduces two several traditional parallel programming model. Secondly, it analyzes and studies the principles, advantages and disadvantages of OpenMP, MPI and Map Reduce respectively. Finally, it takes MPI, OpenMP models compared to Map Reduce from the angle of cloud computing. The results of this paper are intended to provide a reference for the development of parallel computing.

  15. Data communications in a parallel active messaging interface of a parallel computer

    Science.gov (United States)

    Archer, Charles J; Blocksome, Michael A; Ratterman, Joseph D; Smith, Brian E

    2013-10-29

    Data communications in a parallel active messaging interface (`PAMI`) of a parallel computer, the parallel computer including a plurality of compute nodes that execute a parallel application, the PAMI composed of data communications endpoints, each endpoint including a specification of data communications parameters for a thread of execution on a compute node, including specifications of a client, a context, and a task, the compute nodes and the endpoints coupled for data communications through the PAMI and through data communications resources, including receiving in an origin endpoint of the PAMI a data communications instruction, the instruction characterized by an instruction type, the instruction specifying a transmission of transfer data from the origin endpoint to a target endpoint and transmitting, in accordance with the instruction type, the transfer data from the origin endpoint to the target endpoint.

  16. The ongoing investigation of high performance parallel computing in HEP

    CERN Document Server

    Peach, Kenneth J; Böck, R K; Dobinson, Robert W; Hansroul, M; Norton, Alan Robert; Willers, Ian Malcolm; Baud, J P; Carminati, F; Gagliardi, F; McIntosh, E; Metcalf, M; Robertson, L; CERN. Geneva. Detector Research and Development Committee

    1993-01-01

    Past and current exploitation of parallel computing in High Energy Physics is summarized and a list of R & D projects in this area is presented. The applicability of new parallel hardware and software to physics problems is investigated, in the light of the requirements for computing power of LHC experiments and the current trends in the computer industry. Four main themes are discussed (possibilities for a finer grain of parallelism; fine-grain communication mechanism; usable parallel programming environment; different programming models and architectures, using standard commercial products). Parallel computing technology is potentially of interest for offline and vital for real time applications in LHC. A substantial investment in applications development and evaluation of state of the art hardware and software products is needed. A solid development environment is required at an early stage, before mainline LHC program development begins.

  17. Hypergraph partitioning implementation for parallelizing matrix-vector multiplication using CUDA GPU-based parallel computing

    Science.gov (United States)

    Murni, Bustamam, A.; Ernastuti, Handhika, T.; Kerami, D.

    2017-07-01

    Calculation of the matrix-vector multiplication in the real-world problems often involves large matrix with arbitrary size. Therefore, parallelization is needed to speed up the calculation process that usually takes a long time. Graph partitioning techniques that have been discussed in the previous studies cannot be used to complete the parallelized calculation of matrix-vector multiplication with arbitrary size. This is due to the assumption of graph partitioning techniques that can only solve the square and symmetric matrix. Hypergraph partitioning techniques will overcome the shortcomings of the graph partitioning technique. This paper addresses the efficient parallelization of matrix-vector multiplication through hypergraph partitioning techniques using CUDA GPU-based parallel computing. CUDA (compute unified device architecture) is a parallel computing platform and programming model that was created by NVIDIA and implemented by the GPU (graphics processing unit).

  18. Vector and parallel processors in computational science

    International Nuclear Information System (INIS)

    Duff, I.S.; Reid, J.K.

    1985-01-01

    This book presents the papers given at a conference which reviewed the new developments in parallel and vector processing. Topics considered at the conference included hardware (array processors, supercomputers), programming languages, software aids, numerical methods (e.g., Monte Carlo algorithms, iterative methods, finite elements, optimization), and applications (e.g., neutron transport theory, meteorology, image processing)

  19. Partitions in languages and parallel computations

    Energy Technology Data Exchange (ETDEWEB)

    Burgin, M S; Burgina, E S

    1982-05-01

    Partitions of entries (linguistic structures) are studied that are intended for parallel data processing. The representations of formal languages with the aid of such structures is examined, and the relationships are considered between partitions of entries and abstract families of languages and automata. 18 references.

  20. Heuristic framework for parallel sorting computations | Nwanze ...

    African Journals Online (AJOL)

    Parallel sorting techniques have become of practical interest with the advent of new multiprocessor architectures. The decreasing cost of these processors will probably in the future, make the solutions that are derived thereof to be more appealing. Efficient algorithms for sorting scheme that are encountered in a number of ...

  1. Algorithms for parallel and vector computations

    Science.gov (United States)

    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.

  2. Parallel computing, failure recovery, and extreme values

    DEFF Research Database (Denmark)

    Andersen, Lars Nørvang; Asmussen, Søren

    A task of random size T is split into M subtasks of lengths T1, . . . , TM, each of which is sent to one out of M parallel processors. Each processor may fail at a random time before completing its allocated task, and then has to restart it from the beginning. If X1, . . . ,XM are the total task ...

  3. Simultaneous digital quantification and fluorescence-based size characterization of massively parallel sequencing libraries.

    Science.gov (United States)

    Laurie, Matthew T; Bertout, Jessica A; Taylor, Sean D; Burton, Joshua N; Shendure, Jay A; Bielas, Jason H

    2013-08-01

    Due to the high cost of failed runs and suboptimal data yields, quantification and determination of fragment size range are crucial steps in the library preparation process for massively parallel sequencing (or next-generation sequencing). Current library quality control methods commonly involve quantification using real-time quantitative PCR and size determination using gel or capillary electrophoresis. These methods are laborious and subject to a number of significant limitations that can make library calibration unreliable. Herein, we propose and test an alternative method for quality control of sequencing libraries using droplet digital PCR (ddPCR). By exploiting a correlation we have discovered between droplet fluorescence and amplicon size, we achieve the joint quantification and size determination of target DNA with a single ddPCR assay. We demonstrate the accuracy and precision of applying this method to the preparation of sequencing libraries.

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

    Science.gov (United States)

    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.

  5. Highly parallel machines and future of scientific computing

    International Nuclear Information System (INIS)

    Singh, G.S.

    1992-01-01

    Computing requirement of large scale scientific computing has always been ahead of what state of the art hardware could supply in the form of supercomputers of the day. And for any single processor system the limit to increase in the computing power was realized a few years back itself. Now with the advent of parallel computing systems the availability of machines with the required computing power seems a reality. In this paper the author tries to visualize the future large scale scientific computing in the penultimate decade of the present century. The author summarized trends in parallel computers and emphasize the need for a better programming environment and software tools for optimal performance. The author concludes this paper with critique on parallel architectures, software tools and algorithms. (author). 10 refs., 2 tabs

  6. Cloud Computing in KAUST Library: Beyond Remote Hosting

    KAUST Repository

    Yu, Yi

    2013-12-01

    Enterprise computing is the key strategic approach for KAUST to build its modern IT landscape. In such a strategic direction and technical environment, the library tries to establish library technology by catching new trends which help to make the library more efficient and sufficient. This paper focuses on the cloud computing development in the KAUST library, by using real world scenarios and first-hand experiences to describe what cloud computing means for KAUST library. It addresses the difficulties that were met by the library during the implementation process, how cloud computing affects the functional performance and work procedure of the library, how it impacts the style and modal of the library’s technical service and systems administration, how it changes the relationships and cooperation among the involved players (the library, campus IT and vendors), and what the benefits and disadvantages are. The story of cloud computing at KAUST will share the knowledge and lessons that the KAUST library learnt during its development, and will also point out the future direction of cloud computing at KAUST.

  7. Parallel computing in genomic research: advances and applications

    Directory of Open Access Journals (Sweden)

    Ocaña K

    2015-11-01

    Full Text Available Kary Ocaña,1 Daniel de Oliveira2 1National Laboratory of Scientific Computing, Petrópolis, Rio de Janeiro, 2Institute of Computing, Fluminense Federal University, Niterói, Brazil Abstract: Today's genomic experiments have to process the so-called "biological big data" that is now reaching the size of Terabytes and Petabytes. To process this huge amount of data, scientists may require weeks or months if they use their own workstations. Parallelism techniques and high-performance computing (HPC environments can be applied for reducing the total processing time and to ease the management, treatment, and analyses of this data. However, running bioinformatics experiments in HPC environments such as clouds, grids, clusters, and graphics processing unit requires the expertise from scientists to integrate computational, biological, and mathematical techniques and technologies. Several solutions have already been proposed to allow scientists for processing their genomic experiments using HPC capabilities and parallelism techniques. This article brings a systematic review of literature that surveys the most recently published research involving genomics and parallel computing. Our objective is to gather the main characteristics, benefits, and challenges that can be considered by scientists when running their genomic experiments to benefit from parallelism techniques and HPC capabilities. Keywords: high-performance computing, genomic research, cloud computing, grid computing, cluster computing, parallel computing

  8. Basic design of parallel computational program for probabilistic structural analysis

    International Nuclear Information System (INIS)

    Kaji, Yoshiyuki; Arai, Taketoshi; Gu, Wenwei; Nakamura, Hitoshi

    1999-06-01

    In our laboratory, for 'development of damage evaluation method of structural brittle materials by microscopic fracture mechanics and probabilistic theory' (nuclear computational science cross-over research) we examine computational method related to super parallel computation system which is coupled with material strength theory based on microscopic fracture mechanics for latent cracks and continuum structural model to develop new structural reliability evaluation methods for ceramic structures. This technical report is the review results regarding probabilistic structural mechanics theory, basic terms of formula and program methods of parallel computation which are related to principal terms in basic design of computational mechanics program. (author)

  9. Basic design of parallel computational program for probabilistic structural analysis

    Energy Technology Data Exchange (ETDEWEB)

    Kaji, Yoshiyuki; Arai, Taketoshi [Japan Atomic Energy Research Inst., Tokai, Ibaraki (Japan). Tokai Research Establishment; Gu, Wenwei; Nakamura, Hitoshi

    1999-06-01

    In our laboratory, for `development of damage evaluation method of structural brittle materials by microscopic fracture mechanics and probabilistic theory` (nuclear computational science cross-over research) we examine computational method related to super parallel computation system which is coupled with material strength theory based on microscopic fracture mechanics for latent cracks and continuum structural model to develop new structural reliability evaluation methods for ceramic structures. This technical report is the review results regarding probabilistic structural mechanics theory, basic terms of formula and program methods of parallel computation which are related to principal terms in basic design of computational mechanics program. (author)

  10. Cloud computing: An innovative tool for library services

    OpenAIRE

    Sahu, R.

    2015-01-01

    Cloud computing is a new technique of information communication technology because of its potential benefits such as reduced cost, accessible anywhere any time as well as its elasticity and flexibility. In this Paper defines cloud Computing, definition, essential characteristics, model of cloud computing, components of cloud, advantages & drawbacks of cloud computing and also describe cloud computing in libraries.

  11. Parallel computing in plasma physics: Nonlinear instabilities

    International Nuclear Information System (INIS)

    Pohn, E.; Kamelander, G.; Shoucri, M.

    2000-01-01

    A Vlasov-Poisson-system is used for studying the time evolution of the charge-separation at a spatial one- as well as a two-dimensional plasma-edge. Ions are advanced in time using the Vlasov-equation. The whole three-dimensional velocity-space is considered leading to very time-consuming four-resp. five-dimensional fully kinetic simulations. In the 1D simulations electrons are assumed to behave adiabatic, i.e. they are Boltzmann-distributed, leading to a nonlinear Poisson-equation. In the 2D simulations a gyro-kinetic approximation is used for the electrons. The plasma is assumed to be initially neutral. The simulations are performed at an equidistant grid. A constant time-step is used for advancing the density-distribution function in time. The time-evolution of the distribution function is performed using a splitting scheme. Each dimension (x, y, υ x , υ y , υ z ) of the phase-space is advanced in time separately. The value of the distribution function for the next time is calculated from the value of an - in general - interstitial point at the present time (fractional shift). One-dimensional cubic-spline interpolation is used for calculating the interstitial function values. After the fractional shifts are performed for each dimension of the phase-space, a whole time-step for advancing the distribution function is finished. Afterwards the charge density is calculated, the Poisson-equation is solved and the electric field is calculated before the next time-step is performed. The fractional shift method sketched above was parallelized for p processors as follows. Considering first the shifts in y-direction, a proper parallelization strategy is to split the grid into p disjoint υ z -slices, which are sub-grids, each containing a different 1/p-th part of the υ z range but the whole range of all other dimensions. Each processor is responsible for performing the y-shifts on a different slice, which can be done in parallel without any communication between

  12. Research in Parallel Algorithms and Software for Computational Aerosciences

    Science.gov (United States)

    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.

  13. Performance of Air Pollution Models on Massively Parallel Computers

    DEFF Research Database (Denmark)

    Brown, John; Hansen, Per Christian; Wasniewski, Jerzy

    1996-01-01

    To compare the performance and use of three massively parallel SIMD computers, we implemented a large air pollution model on the computers. Using a realistic large-scale model, we gain detailed insight about the performance of the three computers when used to solve large-scale scientific problems...

  14. Parallel computing solution of Boltzmann neutron transport equation

    International Nuclear Information System (INIS)

    Ansah-Narh, T.

    2010-01-01

    The focus of the research was on developing parallel computing algorithm for solving Eigen-values of the Boltzmam Neutron Transport Equation (BNTE) in a slab geometry using multi-grid approach. In response to the problem of slow execution of serial computing when solving large problems, such as BNTE, the study was focused on the design of parallel computing systems which was an evolution of serial computing that used multiple processing elements simultaneously to solve complex physical and mathematical problems. Finite element method (FEM) was used for the spatial discretization scheme, while angular discretization was accomplished by expanding the angular dependence in terms of Legendre polynomials. The eigenvalues representing the multiplication factors in the BNTE were determined by the power method. MATLAB Compiler Version 4.1 (R2009a) was used to compile the MATLAB codes of BNTE. The implemented parallel algorithms were enabled with matlabpool, a Parallel Computing Toolbox function. The option UseParallel was set to 'always' and the default value of the option was 'never'. When those conditions held, the solvers computed estimated gradients in parallel. The parallel computing system was used to handle all the bottlenecks in the matrix generated from the finite element scheme and each domain of the power method generated. The parallel algorithm was implemented on a Symmetric Multi Processor (SMP) cluster machine, which had Intel 32 bit quad-core x 86 processors. Convergence rates and timings for the algorithm on the SMP cluster machine were obtained. Numerical experiments indicated the designed parallel algorithm could reach perfect speedup and had good stability and scalability. (au)

  15. Fluid dynamics parallel computer development at NASA Langley Research Center

    Science.gov (United States)

    Townsend, James C.; Zang, Thomas A.; Dwoyer, Douglas L.

    1987-01-01

    To accomplish more detailed simulations of highly complex flows, such as the transition to turbulence, fluid dynamics research requires computers much more powerful than any available today. Only parallel processing on multiple-processor computers offers hope for achieving the required effective speeds. Looking ahead to the use of these machines, the fluid dynamicist faces three issues: algorithm development for near-term parallel computers, architecture development for future computer power increases, and assessment of possible advantages of special purpose designs. Two projects at NASA Langley address these issues. Software development and algorithm exploration is being done on the FLEX/32 Parallel Processing Research Computer. New architecture features are being explored in the special purpose hardware design of the Navier-Stokes Computer. These projects are complementary and are producing promising results.

  16. CFDLIB05, Computational Fluid Dynamics Library

    International Nuclear Information System (INIS)

    Kashiwa, B.A.; Padial, N.T.; Rauenzahn, R.M.; VanderHeyden, W.B.

    2007-01-01

    1 - Description of program or function: CFDLib05 is the Los Alamos Computational Fluid Dynamics Library. This is a collection of hydro-codes using a common data structure and a common numerical method, for problems ranging from single-field, incompressible flow, to multi-species, multi-field, compressible flow. The data structure is multi-block, with a so-called structured grid in each block. The numerical method is a Finite-Volume scheme employing a state vector that is fully cell-centered. This means that the integral form of the conversation laws is solved on the physical domain that is represented by a mesh of control volumes. The typical control volume is an arbitrary quadrilateral in 2D and an arbitrary hexahedron in 3D. The Finite-Volume scheme is for time-unsteady flow and remains well coupled by means of time and space centered fluxes; if a steady state solution is required, the problem is integrated forward in time until the user is satisfied that the state is stationary. 2 - Methods: Cells-centered Implicit Continuous-fluid Eulerian (ICE) method

  17. Climate Ocean Modeling on Parallel Computers

    Science.gov (United States)

    Wang, P.; Cheng, B. N.; Chao, Y.

    1998-01-01

    Ocean modeling plays an important role in both understanding the current climatic conditions and predicting future climate change. However, modeling the ocean circulation at various spatial and temporal scales is a very challenging computational task.

  18. History Matching in Parallel Computational Environments

    Energy Technology Data Exchange (ETDEWEB)

    Steven Bryant; Sanjay Srinivasan; Alvaro Barrera; Sharad Yadav

    2004-08-31

    In the probabilistic approach for history matching, the information from the dynamic data is merged with the prior geologic information in order to generate permeability models consistent with the observed dynamic data as well as the prior geology. The relationship between dynamic response data and reservoir attributes may vary in different regions of the reservoir due to spatial variations in reservoir attributes, fluid properties, well configuration, flow constrains on wells etc. This implies probabilistic approach should then update different regions of the reservoir in different ways. This necessitates delineation of multiple reservoir domains in order to increase the accuracy of the approach. The research focuses on a probabilistic approach to integrate dynamic data that ensures consistency between reservoir models developed from one stage to the next. The algorithm relies on efficient parameterization of the dynamic data integration problem and permits rapid assessment of the updated reservoir model at each stage. The report also outlines various domain decomposition schemes from the perspective of increasing the accuracy of probabilistic approach of history matching. Research progress in three important areas of the project are discussed: {lg_bullet}Validation and testing the probabilistic approach to incorporating production data in reservoir models. {lg_bullet}Development of a robust scheme for identifying reservoir regions that will result in a more robust parameterization of the history matching process. {lg_bullet}Testing commercial simulators for parallel capability and development of a parallel algorithm for history matching.

  19. Parallel computing for event reconstruction in high-energy physics

    International Nuclear Information System (INIS)

    Wolbers, S.

    1993-01-01

    Parallel computing has been recognized as a solution to large computing problems. In High Energy Physics offline event reconstruction of detector data is a very large computing problem that has been solved with parallel computing techniques. A review of the parallel programming package CPS (Cooperative Processes Software) developed and used at Fermilab for offline reconstruction of Terabytes of data requiring the delivery of hundreds of Vax-Years per experiment is given. The Fermilab UNIX farms, consisting of 180 Silicon Graphics workstations and 144 IBM RS6000 workstations, are used to provide the computing power for the experiments. Fermilab has had a long history of providing production parallel computing starting with the ACP (Advanced Computer Project) Farms in 1986. The Fermilab UNIX Farms have been in production for over 2 years with 24 hour/day service to experimental user groups. Additional tools for management, control and monitoring these large systems will be described. Possible future directions for parallel computing in High Energy Physics will be given

  20. Parallelism, fractal geometry and other aspects of computational mathematics

    International Nuclear Information System (INIS)

    Churchhouse, R.F.

    1991-01-01

    In some fields such as meteorology, theoretical physics, quantum chemistry and hydrodynamics there are problems which involve so much computation that computers of the power of a thousand times a Cray 2 could be fully utilised if they were available. Since it is unlikely that uniprocessors of such power will be available, such large scale problems could be solved by using systems of computers running in parallel. This approach, of course, requires to find appropriate algorithms for the solution of such problems which can efficiently make use of a large number of computers working in parallel. 11 refs, 10 figs, 1 tab

  1. Parallel Computing:. Some Activities in High Energy Physics

    Science.gov (United States)

    Willers, Ian

    This paper examines some activities in High Energy Physics that utilise parallel computing. The topic includes all computing from the proposed SIMD front end detectors, the farming applications, high-powered RISC processors and the large machines in the computer centers. We start by looking at the motivation behind using parallelism for general purpose computing. The developments around farming are then described from its simplest form to the more complex system in Fermilab. Finally, there is a list of some developments that are happening close to the experiments.

  2. Parallel ray tracing for one-dimensional discrete ordinate computations

    International Nuclear Information System (INIS)

    Jarvis, R.D.; Nelson, P.

    1996-01-01

    The ray-tracing sweep in discrete-ordinates, spatially discrete numerical approximation methods applied to the linear, steady-state, plane-parallel, mono-energetic, azimuthally symmetric, neutral-particle transport equation can be reduced to a parallel prefix computation. In so doing, the often severe penalty in convergence rate of the source iteration, suffered by most current parallel algorithms using spatial domain decomposition, can be avoided while attaining parallelism in the spatial domain to whatever extent desired. In addition, the reduction implies parallel algorithm complexity limits for the ray-tracing sweep. The reduction applies to all closed, linear, one-cell functional (CLOF) spatial approximation methods, which encompasses most in current popular use. Scalability test results of an implementation of the algorithm on a 64-node nCube-2S hypercube-connected, message-passing, multi-computer are described. (author)

  3. Parallel computer calculation of quantum spin lattices

    International Nuclear Information System (INIS)

    Lamarcq, J.

    1998-01-01

    Numerical simulation allows the theorists to convince themselves about the validity of the models they use. Particularly by simulating the spin lattices one can judge about the validity of a conjecture. Simulating a system defined by a large number of degrees of freedom requires highly sophisticated machines. This study deals with modelling the magnetic interactions between the ions of a crystal. Many exact results have been found for spin 1/2 systems but not for systems of other spins for which many simulation have been carried out. The interest for simulations has been renewed by the Haldane's conjecture stipulating the existence of a energy gap between the ground state and the first excited states of a spin 1 lattice. The existence of this gap has been experimentally demonstrated. This report contains the following four chapters: 1. Spin systems; 2. Calculation of eigenvalues; 3. Programming; 4. Parallel calculation

  4. Misleading Performance Claims in Parallel Computations

    Energy Technology Data Exchange (ETDEWEB)

    Bailey, David H.

    2009-05-29

    In a previous humorous note entitled 'Twelve Ways to Fool the Masses,' I outlined twelve common ways in which performance figures for technical computer systems can be distorted. In this paper and accompanying conference talk, I give a reprise of these twelve 'methods' and give some actual examples that have appeared in peer-reviewed literature in years past. I then propose guidelines for reporting performance, the adoption of which would raise the level of professionalism and reduce the level of confusion, not only in the world of device simulation but also in the larger arena of technical computing.

  5. Global seismic tomography and modern parallel computers

    Directory of Open Access Journals (Sweden)

    A. Piersanti

    2006-06-01

    Full Text Available A fast technological progress is providing seismic tomographers with computers of rapidly increasing speed and RAM, that are not always properly taken advantage of. Large computers with both shared-memory and distributedmemory architectures have made it possible to approach the tomographic inverse problem more accurately. For example, resolution can be quantified from the resolution matrix rather than checkerboard tests; the covariance matrix can be calculated to evaluate the propagation of errors from data to model parameters; the L-curve method can be applied to determine a range of acceptable regularization schemes. We show how these exercises can be implemented efficiently on different hardware architectures.

  6. Integrated computer network high-speed parallel interface

    International Nuclear Information System (INIS)

    Frank, R.B.

    1979-03-01

    As the number and variety of computers within Los Alamos Scientific Laboratory's Central Computer Facility grows, the need for a standard, high-speed intercomputer interface has become more apparent. This report details the development of a High-Speed Parallel Interface from conceptual through implementation stages to meet current and future needs for large-scle network computing within the Integrated Computer Network. 4 figures

  7. Parallel algorithms and archtectures for computational structural mechanics

    Science.gov (United States)

    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.

  8. Finite element electromagnetic field computation on the Sequent Symmetry 81 parallel computer

    International Nuclear Information System (INIS)

    Ratnajeevan, S.; Hoole, H.

    1990-01-01

    Finite element field analysis algorithms lend themselves to parallelization and this fact is exploited in this paper to implement a finite element analysis program for electromagnetic field computation on the Sequent Symmetry 81 parallel computer with three processors. In terms of waiting time, the maximum gains are to be made in matrix solution and therefore this paper concentrates on the gains in parallelizing the solution part of finite element analysis. An outline of how parallelization could be exploited in most finite element operations is given in this paper although the actual implemention of parallelism on the Sequent Symmetry 81 parallel computer was in sparsity computation, matrix assembly and the matrix solution areas. In all cases, the algorithms were modified suit the parallel programming application rather than allowing the compiler to parallelize on existing algorithms

  9. A microeconomic scheduler for parallel computers

    Science.gov (United States)

    Stoica, Ion; Abdel-Wahab, Hussein; Pothen, Alex

    1995-01-01

    We describe a scheduler based on the microeconomic paradigm for scheduling on-line a set of parallel jobs in a multiprocessor system. In addition to the classical objectives of increasing the system throughput and reducing the response time, we consider fairness in allocating system resources among the users, and providing the user with control over the relative performances of his jobs. We associate with every user a savings account in which he receives money at a constant rate. When a user wants to run a job, he creates an expense account for that job to which he transfers money from his savings account. The job uses the funds in its expense account to obtain the system resources it needs for execution. The share of the system resources allocated to the user is directly related to the rate at which the user receives money; the rate at which the user transfers money into a job expense account controls the job's performance. We prove that starvation is not possible in our model. Simulation results show that our scheduler improves both system and user performances in comparison with two different variable partitioning policies. It is also shown to be effective in guaranteeing fairness and providing control over the performance of jobs.

  10. Subroutine library for error estimation of matrix computation (Ver. 1.0)

    International Nuclear Information System (INIS)

    Ichihara, Kiyoshi; Shizawa, Yoshihisa; Kishida, Norio

    1999-03-01

    'Subroutine Library for Error Estimation of Matrix Computation' is a subroutine library which aids the users in obtaining the error ranges of the linear system's solutions or the Hermitian matrices' eigenvalues. This library contains routines for both sequential computers and parallel computers. The subroutines for linear system error estimation calculate norms of residual vectors, matrices's condition numbers, error bounds of solutions and so on. The subroutines for error estimation of Hermitian matrix eigenvalues derive the error ranges of the eigenvalues according to the Korn-Kato's formula. The test matrix generators supply the matrices appeared in the mathematical research, the ones randomly generated and the ones appeared in the application programs. This user's manual contains a brief mathematical background of error analysis on linear algebra and usage of the subroutines. (author)

  11. Efficient Parallel Kernel Solvers for Computational Fluid Dynamics Applications

    Science.gov (United States)

    Sun, Xian-He

    1997-01-01

    Distributed-memory parallel computers dominate today's parallel computing arena. These machines, such as Intel Paragon, IBM SP2, and Cray Origin2OO, have successfully delivered high performance computing power for solving some of the so-called "grand-challenge" problems. Despite initial success, parallel machines have not been widely accepted in production engineering environments due to the complexity of parallel programming. On a parallel computing system, a task has to be partitioned and distributed appropriately among processors to reduce communication cost and to attain load balance. More importantly, even with careful partitioning and mapping, the performance of an algorithm may still be unsatisfactory, since conventional sequential algorithms may be serial in nature and may not be implemented efficiently on parallel machines. In many cases, new algorithms have to be introduced to increase parallel performance. In order to achieve optimal performance, in addition to partitioning and mapping, a careful performance study should be conducted for a given application to find a good algorithm-machine combination. This process, however, is usually painful and elusive. The goal of this project is to design and develop efficient parallel algorithms for highly accurate Computational Fluid Dynamics (CFD) simulations and other engineering applications. The work plan is 1) developing highly accurate parallel numerical algorithms, 2) conduct preliminary testing to verify the effectiveness and potential of these algorithms, 3) incorporate newly developed algorithms into actual simulation packages. The work plan has well achieved. Two highly accurate, efficient Poisson solvers have been developed and tested based on two different approaches: (1) Adopting a mathematical geometry which has a better capacity to describe the fluid, (2) Using compact scheme to gain high order accuracy in numerical discretization. The previously developed Parallel Diagonal Dominant (PDD) algorithm

  12. History Matching in Parallel Computational Environments

    Energy Technology Data Exchange (ETDEWEB)

    Steven Bryant; Sanjay Srinivasan; Alvaro Barrera; Sharad Yadav

    2005-10-01

    A novel methodology for delineating multiple reservoir domains for the purpose of history matching in a distributed computing environment has been proposed. A fully probabilistic approach to perturb permeability within the delineated zones is implemented. The combination of robust schemes for identifying reservoir zones and distributed computing significantly increase the accuracy and efficiency of the probabilistic approach. The information pertaining to the permeability variations in the reservoir that is contained in dynamic data is calibrated in terms of a deformation parameter rD. This information is merged with the prior geologic information in order to generate permeability models consistent with the observed dynamic data as well as the prior geology. The relationship between dynamic response data and reservoir attributes may vary in different regions of the reservoir due to spatial variations in reservoir attributes, well configuration, flow constrains etc. The probabilistic approach then has to account for multiple r{sub D} values in different regions of the reservoir. In order to delineate reservoir domains that can be characterized with different rD parameters, principal component analysis (PCA) of the Hessian matrix has been done. The Hessian matrix summarizes the sensitivity of the objective function at a given step of the history matching to model parameters. It also measures the interaction of the parameters in affecting the objective function. The basic premise of PC analysis is to isolate the most sensitive and least correlated regions. The eigenvectors obtained during the PCA are suitably scaled and appropriate grid block volume cut-offs are defined such that the resultant domains are neither too large (which increases interactions between domains) nor too small (implying ineffective history matching). The delineation of domains requires calculation of Hessian, which could be computationally costly and as well as restricts the current approach to

  13. A compositional reservoir simulator on distributed memory parallel computers

    International Nuclear Information System (INIS)

    Rame, M.; Delshad, M.

    1995-01-01

    This paper presents the application of distributed memory parallel computes to field scale reservoir simulations using a parallel version of UTCHEM, The University of Texas Chemical Flooding Simulator. The model is a general purpose highly vectorized chemical compositional simulator that can simulate a wide range of displacement processes at both field and laboratory scales. The original simulator was modified to run on both distributed memory parallel machines (Intel iPSC/960 and Delta, Connection Machine 5, Kendall Square 1 and 2, and CRAY T3D) and a cluster of workstations. A domain decomposition approach has been taken towards parallelization of the code. A portion of the discrete reservoir model is assigned to each processor by a set-up routine that attempts a data layout as even as possible from the load-balance standpoint. Each of these subdomains is extended so that data can be shared between adjacent processors for stencil computation. The added routines that make parallel execution possible are written in a modular fashion that makes the porting to new parallel platforms straight forward. Results of the distributed memory computing performance of Parallel simulator are presented for field scale applications such as tracer flood and polymer flood. A comparison of the wall-clock times for same problems on a vector supercomputer is also presented

  14. Models of parallel computation :a survey and classification

    Institute of Scientific and Technical Information of China (English)

    ZHANG Yunquan; CHEN Guoliang; SUN Guangzhong; MIAO Qiankun

    2007-01-01

    In this paper,the state-of-the-art parallel computational model research is reviewed.We will introduce various models that were developed during the past decades.According to their targeting architecture features,especially memory organization,we classify these parallel computational models into three generations.These models and their characteristics are discussed based on three generations classification.We believe that with the ever increasing speed gap between the CPU and memory systems,incorporating non-uniform memory hierarchy into computational models will become unavoidable.With the emergence of multi-core CPUs,the parallelism hierarchy of current computing platforms becomes more and more complicated.Describing this complicated parallelism hierarchy in future computational models becomes more and more important.A semi-automatic toolkit that can extract model parameters and their values on real computers can reduce the model analysis complexity,thus allowing more complicated models with more parameters to be adopted.Hierarchical memory and hierarchical parallelism will be two very important features that should be considered in future model design and research.

  15. Identifying failure in a tree network of a parallel computer

    Science.gov (United States)

    Archer, Charles J.; Pinnow, Kurt W.; Wallenfelt, Brian P.

    2010-08-24

    Methods, parallel computers, and products are provided for identifying failure in a tree network of a parallel computer. The parallel computer includes one or more processing sets including an I/O node and a plurality of compute nodes. For each processing set embodiments include selecting a set of test compute nodes, the test compute nodes being a subset of the compute nodes of the processing set; measuring the performance of the I/O node of the processing set; measuring the performance of the selected set of test compute nodes; calculating a current test value in dependence upon the measured performance of the I/O node of the processing set, the measured performance of the set of test compute nodes, and a predetermined value for I/O node performance; and comparing the current test value with a predetermined tree performance threshold. If the current test value is below the predetermined tree performance threshold, embodiments include selecting another set of test compute nodes. If the current test value is not below the predetermined tree performance threshold, embodiments include selecting from the test compute nodes one or more potential problem nodes and testing individually potential problem nodes and links to potential problem nodes.

  16. Fast Parallel Computation of Polynomials Using Few Processors

    DEFF Research Database (Denmark)

    Valiant, Leslie G.; Skyum, Sven; Berkowitz, S.

    1983-01-01

    It is shown that any multivariate polynomial of degree $d$ that can be computed sequentially in $C$ steps can be computed in parallel in $O((\\log d)(\\log C + \\log d))$ steps using only $(Cd)^{O(1)} $ processors....

  17. Tutorial: Parallel Computing of Simulation Models for Risk Analysis.

    Science.gov (United States)

    Reilly, Allison C; Staid, Andrea; Gao, Michael; Guikema, Seth D

    2016-10-01

    Simulation models are widely used in risk analysis to study the effects of uncertainties on outcomes of interest in complex problems. Often, these models are computationally complex and time consuming to run. This latter point may be at odds with time-sensitive evaluations or may limit the number of parameters that are considered. In this article, we give an introductory tutorial focused on parallelizing simulation code to better leverage modern computing hardware, enabling risk analysts to better utilize simulation-based methods for quantifying uncertainty in practice. This article is aimed primarily at risk analysts who use simulation methods but do not yet utilize parallelization to decrease the computational burden of these models. The discussion is focused on conceptual aspects of embarrassingly parallel computer code and software considerations. Two complementary examples are shown using the languages MATLAB and R. A brief discussion of hardware considerations is located in the Appendix. © 2016 Society for Risk Analysis.

  18. Data-flow oriented visual programming libraries for scientific computing

    NARCIS (Netherlands)

    Maubach, J.M.L.; Drenth, W.D.; Sloot, P.M.A.

    2002-01-01

    The growing release of scientific computational software does not seem to aid the implementation of complex numerical algorithms. Released libraries lack a common standard interface with regard to for instance finite element, difference or volume discretizations. And, libraries written in standard

  19. Evaluation of computer-based library services at Kenneth Dike ...

    African Journals Online (AJOL)

    This study evaluated computer-based library services/routines at Kenneth Dike Library, University of Ibadan. Four research questions were developed and answered. A survey research design was adopted; using questionnaire as the instrument for data collection. A total of 200 respondents randomly selected from 10 ...

  20. Employing Virtualization in Library Computing: Use Cases and Lessons Learned

    Directory of Open Access Journals (Sweden)

    Arwen Hutt

    2009-09-01

    Full Text Available This paper provides a broad overview of virtualization technology and describes several examples of its use at the University of California, San Diego Libraries. Libraries can leverage virtualization to address many long-standing library computing challenges, but careful planning is needed to determine if this technology is the right solution for a specific need. This paper outlines both technical and usability considerations, and concludes with a discussion of potential enterprise impacts on the library infrastructure.

  1. Application of parallel computing to seismic damage process simulation of an arch dam

    International Nuclear Information System (INIS)

    Zhong Hong; Lin Gao; Li Jianbo

    2010-01-01

    The simulation of damage process of high arch dam subjected to strong earthquake shocks is significant to the evaluation of its performance and seismic safety, considering the catastrophic effect of dam failure. However, such numerical simulation requires rigorous computational capacity. Conventional serial computing falls short of that and parallel computing is a fairly promising solution to this problem. The parallel finite element code PDPAD was developed for the damage prediction of arch dams utilizing the damage model with inheterogeneity of concrete considered. Developed with programming language Fortran, the code uses a master/slave mode for programming, domain decomposition method for allocation of tasks, MPI (Message Passing Interface) for communication and solvers from AZTEC library for solution of large-scale equations. Speedup test showed that the performance of PDPAD was quite satisfactory. The code was employed to study the damage process of a being-built arch dam on a 4-node PC Cluster, with more than one million degrees of freedom considered. The obtained damage mode was quite similar to that of shaking table test, indicating that the proposed procedure and parallel code PDPAD has a good potential in simulating seismic damage mode of arch dams. With the rapidly growing need for massive computation emerged from engineering problems, parallel computing will find more and more applications in pertinent areas.

  2. DMG-α--a computational geometry library for multimolecular systems.

    Science.gov (United States)

    Szczelina, Robert; Murzyn, Krzysztof

    2014-11-24

    The DMG-α library grants researchers in the field of computational biology, chemistry, and biophysics access to an open-sourced, easy to use, and intuitive software for performing fine-grained geometric analysis of molecular systems. The library is capable of computing power diagrams (weighted Voronoi diagrams) in three dimensions with 3D periodic boundary conditions, computing approximate projective 2D Voronoi diagrams on arbitrarily defined surfaces, performing shape properties recognition using α-shape theory and can do exact Solvent Accessible Surface Area (SASA) computation. The software is written mainly as a template-based C++ library for greater performance, but a rich Python interface (pydmga) is provided as a convenient way to manipulate the DMG-α routines. To illustrate possible applications of the DMG-α library, we present results of sample analyses which allowed to determine nontrivial geometric properties of two Escherichia coli-specific lipids as emerging from molecular dynamics simulations of relevant model bilayers.

  3. News from the Library: A one-stop-shop for computing literature: ACM Digital Library

    CERN Multimedia

    CERN Library

    2011-01-01

    The Association for Computing Machinery, ACM, is the world’s largest educational and scientific computing society. Among others, the ACM provides the computing field's premier Digital Library and serves its members and the computing profession with leading-edge publications, conferences, and career resources.   ACM Digital Library is available to the CERN community. The most popular journal here at CERN is Communications of the ACM. However, the collection offers access to a series of other valuable important academic journals such as Journal of the ACM and even fulltext of a series of classical books. In addition, users have access to the ACM Guide to Computing Literature, the most comprehensive bibliographic database focusing on computing, integrated with ACM’s full-text articles and including features such as ACM Author Profile Pages - which provides bibliographic and bibliometric data for over 1,000,000 authors in the field. ACM Digital Library is an excellent com...

  4. Dynamic grid refinement for partial differential equations on parallel computers

    International Nuclear Information System (INIS)

    Mccormick, S.; Quinlan, D.

    1989-01-01

    The fast adaptive composite grid method (FAC) is an algorithm that uses various levels of uniform grids to provide adaptive resolution and fast solution of PDEs. An asynchronous version of FAC, called AFAC, that completely eliminates the bottleneck to parallelism is presented. This paper describes the advantage that this algorithm has in adaptive refinement for moving singularities on multiprocessor computers. This work is applicable to the parallel solution of two- and three-dimensional shock tracking problems. 6 refs

  5. RAMA: A file system for massively parallel computers

    Science.gov (United States)

    Miller, Ethan L.; Katz, Randy H.

    1993-01-01

    This paper describes a file system design for massively parallel computers which makes very efficient use of a few disks per processor. This overcomes the traditional I/O bottleneck of massively parallel machines by storing the data on disks within the high-speed interconnection network. In addition, the file system, called RAMA, requires little inter-node synchronization, removing another common bottleneck in parallel processor file systems. Support for a large tertiary storage system can easily be integrated in lo the file system; in fact, RAMA runs most efficiently when tertiary storage is used.

  6. Parallel grid generation algorithm for distributed memory computers

    Science.gov (United States)

    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.

  7. Processing data communications events by awakening threads in parallel active messaging interface of a parallel computer

    Science.gov (United States)

    Archer, Charles J.; Blocksome, Michael A.; Ratterman, Joseph D.; Smith, Brian E.

    2016-03-15

    Processing data communications events in a parallel active messaging interface (`PAMI`) of a parallel computer that includes compute nodes that execute a parallel application, with the PAMI including data communications endpoints, and the endpoints are coupled for data communications through the PAMI and through other data communications resources, including determining by an advance function that there are no actionable data communications events pending for its context, placing by the advance function its thread of execution into a wait state, waiting for a subsequent data communications event for the context; responsive to occurrence of a subsequent data communications event for the context, awakening by the thread from the wait state; and processing by the advance function the subsequent data communications event now pending for the context.

  8. IPython: components for interactive and parallel computing across disciplines. (Invited)

    Science.gov (United States)

    Perez, F.; Bussonnier, M.; Frederic, J. D.; Froehle, B. M.; Granger, B. E.; Ivanov, P.; Kluyver, T.; Patterson, E.; Ragan-Kelley, B.; Sailer, Z.

    2013-12-01

    Scientific computing is an inherently exploratory activity that requires constantly cycling between code, data and results, each time adjusting the computations as new insights and questions arise. To support such a workflow, good interactive environments are critical. The IPython project (http://ipython.org) provides a rich architecture for interactive computing with: 1. Terminal-based and graphical interactive consoles. 2. A web-based Notebook system with support for code, text, mathematical expressions, inline plots and other rich media. 3. Easy to use, high performance tools for parallel computing. Despite its roots in Python, the IPython architecture is designed in a language-agnostic way to facilitate interactive computing in any language. This allows users to mix Python with Julia, R, Octave, Ruby, Perl, Bash and more, as well as to develop native clients in other languages that reuse the IPython clients. In this talk, I will show how IPython supports all stages in the lifecycle of a scientific idea: 1. Individual exploration. 2. Collaborative development. 3. Production runs with parallel resources. 4. Publication. 5. Education. In particular, the IPython Notebook provides an environment for "literate computing" with a tight integration of narrative and computation (including parallel computing). These Notebooks are stored in a JSON-based document format that provides an "executable paper": notebooks can be version controlled, exported to HTML or PDF for publication, and used for teaching.

  9. 7th International Workshop on Parallel Tools for High Performance Computing

    CERN Document Server

    Gracia, José; Nagel, Wolfgang; Resch, Michael

    2014-01-01

    Current advances in High Performance Computing (HPC) increasingly impact efficient software development workflows. Programmers for HPC applications need to consider trends such as increased core counts, multiple levels of parallelism, reduced memory per core, and I/O system challenges in order to derive well performing and highly scalable codes. At the same time, the increasing complexity adds further sources of program defects. While novel programming paradigms and advanced system libraries provide solutions for some of these challenges, appropriate supporting tools are indispensable. Such tools aid application developers in debugging, performance analysis, or code optimization and therefore make a major contribution to the development of robust and efficient parallel software. This book introduces a selection of the tools presented and discussed at the 7th International Parallel Tools Workshop, held in Dresden, Germany, September 3-4, 2013.  

  10. Small file aggregation in a parallel computing system

    Science.gov (United States)

    Faibish, Sorin; Bent, John M.; Tzelnic, Percy; Grider, Gary; Zhang, Jingwang

    2014-09-02

    Techniques are provided for small file aggregation in a parallel computing system. An exemplary method for storing a plurality of files generated by a plurality of processes in a parallel computing system comprises aggregating the plurality of files into a single aggregated file; and generating metadata for the single aggregated file. The metadata comprises an offset and a length of each of the plurality of files in the single aggregated file. The metadata can be used to unpack one or more of the files from the single aggregated file.

  11. Computational acceleration for MR image reconstruction in partially parallel imaging.

    Science.gov (United States)

    Ye, Xiaojing; Chen, Yunmei; Huang, Feng

    2011-05-01

    In this paper, we present a fast numerical algorithm for solving total variation and l(1) (TVL1) based image reconstruction with application in partially parallel magnetic resonance imaging. Our algorithm uses variable splitting method to reduce computational cost. Moreover, the Barzilai-Borwein step size selection method is adopted in our algorithm for much faster convergence. Experimental results on clinical partially parallel imaging data demonstrate that the proposed algorithm requires much fewer iterations and/or less computational cost than recently developed operator splitting and Bregman operator splitting methods, which can deal with a general sensing matrix in reconstruction framework, to get similar or even better quality of reconstructed images.

  12. Domain decomposition parallel computing for transient two-phase flow of nuclear reactors

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Jae Ryong; Yoon, Han Young [KAERI, Daejeon (Korea, Republic of); Choi, Hyoung Gwon [Seoul National University, Seoul (Korea, Republic of)

    2016-05-15

    KAERI (Korea Atomic Energy Research Institute) has been developing a multi-dimensional two-phase flow code named CUPID for multi-physics and multi-scale thermal hydraulics analysis of Light water reactors (LWRs). The CUPID code has been validated against a set of conceptual problems and experimental data. In this work, the CUPID code has been parallelized based on the domain decomposition method with Message passing interface (MPI) library. For domain decomposition, the CUPID code provides both manual and automatic methods with METIS library. For the effective memory management, the Compressed sparse row (CSR) format is adopted, which is one of the methods to represent the sparse asymmetric matrix. CSR format saves only non-zero value and its position (row and column). By performing the verification for the fundamental problem set, the parallelization of the CUPID has been successfully confirmed. Since the scalability of a parallel simulation is generally known to be better for fine mesh system, three different scales of mesh system are considered: 40000 meshes for coarse mesh system, 320000 meshes for mid-size mesh system, and 2560000 meshes for fine mesh system. In the given geometry, both single- and two-phase calculations were conducted. In addition, two types of preconditioners for a matrix solver were compared: Diagonal and incomplete LU preconditioner. In terms of enhancement of the parallel performance, the OpenMP and MPI hybrid parallel computing for a pressure solver was examined. It is revealed that the scalability of hybrid calculation was enhanced for the multi-core parallel computation.

  13. Hybrid parallel computing architecture for multiview phase shifting

    Science.gov (United States)

    Zhong, Kai; Li, Zhongwei; Zhou, Xiaohui; Shi, Yusheng; Wang, Congjun

    2014-11-01

    The multiview phase-shifting method shows its powerful capability in achieving high resolution three-dimensional (3-D) shape measurement. Unfortunately, this ability results in very high computation costs and 3-D computations have to be processed offline. To realize real-time 3-D shape measurement, a hybrid parallel computing architecture is proposed for multiview phase shifting. In this architecture, the central processing unit can co-operate with the graphic processing unit (GPU) to achieve hybrid parallel computing. The high computation cost procedures, including lens distortion rectification, phase computation, correspondence, and 3-D reconstruction, are implemented in GPU, and a three-layer kernel function model is designed to simultaneously realize coarse-grained and fine-grained paralleling computing. Experimental results verify that the developed system can perform 50 fps (frame per second) real-time 3-D measurement with 260 K 3-D points per frame. A speedup of up to 180 times is obtained for the performance of the proposed technique using a NVIDIA GT560Ti graphics card rather than a sequential C in a 3.4 GHZ Inter Core i7 3770.

  14. Parallel computing for homogeneous diffusion and transport equations in neutronics

    International Nuclear Information System (INIS)

    Pinchedez, K.

    1999-06-01

    Parallel computing meets the ever-increasing requirements for neutronic computer code speed and accuracy. In this work, two different approaches have been considered. We first parallelized the sequential algorithm used by the neutronics code CRONOS developed at the French Atomic Energy Commission. The algorithm computes the dominant eigenvalue associated with PN simplified transport equations by a mixed finite element method. Several parallel algorithms have been developed on distributed memory machines. The performances of the parallel algorithms have been studied experimentally by implementation on a T3D Cray and theoretically by complexity models. A comparison of various parallel algorithms has confirmed the chosen implementations. We next applied a domain sub-division technique to the two-group diffusion Eigen problem. In the modal synthesis-based method, the global spectrum is determined from the partial spectra associated with sub-domains. Then the Eigen problem is expanded on a family composed, on the one hand, from eigenfunctions associated with the sub-domains and, on the other hand, from functions corresponding to the contribution from the interface between the sub-domains. For a 2-D homogeneous core, this modal method has been validated and its accuracy has been measured. (author)

  15. Parallelism in computations in quantum and statistical mechanics

    International Nuclear Information System (INIS)

    Clementi, E.; Corongiu, G.; Detrich, J.H.

    1985-01-01

    Often very fundamental biochemical and biophysical problems defy simulations because of limitations in today's computers. We present and discuss a distributed system composed of two IBM 4341 s and/or an IBM 4381 as front-end processors and ten FPS-164 attached array processors. This parallel system - called LCAP - has presently a peak performance of about 110 Mflops; extensions to higher performance are discussed. Presently, the system applications use a modified version of VM/SP as the operating system: description of the modifications is given. Three applications programs have been migrated from sequential to parallel: a molecular quantum mechanical, a Metropolis-Monte Carlo and a molecular dynamics program. Descriptions of the parallel codes are briefly outlined. Use of these parallel codes has already opened up new capabilities for our research. The very positive performance comparisons with today's supercomputers allow us to conclude that parallel computers and programming, of the type we have considered, represent a pragmatic answer to many computationally intensive problems. (orig.)

  16. A Novel Parallel Algorithm for Edit Distance Computation

    Directory of Open Access Journals (Sweden)

    Muhammad Murtaza Yousaf

    2018-01-01

    Full Text Available The edit distance between two sequences is the minimum number of weighted transformation-operations that are required to transform one string into the other. The weighted transformation-operations are insert, remove, and substitute. Dynamic programming solution to find edit distance exists but it becomes computationally intensive when the lengths of strings become very large. This work presents a novel parallel algorithm to solve edit distance problem of string matching. The algorithm is based on resolving dependencies in the dynamic programming solution of the problem and it is able to compute each row of edit distance table in parallel. In this way, it becomes possible to compute the complete table in min(m,n iterations for strings of size m and n whereas state-of-the-art parallel algorithm solves the problem in max(m,n iterations. The proposed algorithm also increases the amount of parallelism in each of its iteration. The algorithm is also capable of exploiting spatial locality while its implementation. Additionally, the algorithm works in a load balanced way that further improves its performance. The algorithm is implemented for multicore systems having shared memory. Implementation of the algorithm in OpenMP shows linear speedup and better execution time as compared to state-of-the-art parallel approach. Efficiency of the algorithm is also proven better in comparison to its competitor.

  17. Analysis of multigrid methods on massively parallel computers: Architectural implications

    Science.gov (United States)

    Matheson, Lesley R.; Tarjan, Robert E.

    1993-01-01

    We study the potential performance of multigrid algorithms running on massively parallel computers with the intent of discovering whether presently envisioned machines will provide an efficient platform for such algorithms. We consider the domain parallel version of the standard V cycle algorithm on model problems, discretized using finite difference techniques in two and three dimensions on block structured grids of size 10(exp 6) and 10(exp 9), respectively. Our models of parallel computation were developed to reflect the computing characteristics of the current generation of massively parallel multicomputers. These models are based on an interconnection network of 256 to 16,384 message passing, 'workstation size' processors executing in an SPMD mode. The first model accomplishes interprocessor communications through a multistage permutation network. The communication cost is a logarithmic function which is similar to the costs in a variety of different topologies. The second model allows single stage communication costs only. Both models were designed with information provided by machine developers and utilize implementation derived parameters. With the medium grain parallelism of the current generation and the high fixed cost of an interprocessor communication, our analysis suggests an efficient implementation requires the machine to support the efficient transmission of long messages, (up to 1000 words) or the high initiation cost of a communication must be significantly reduced through an alternative optimization technique. Furthermore, with variable length message capability, our analysis suggests the low diameter multistage networks provide little or no advantage over a simple single stage communications network.

  18. General-purpose parallel simulator for quantum computing

    International Nuclear Information System (INIS)

    Niwa, Jumpei; Matsumoto, Keiji; Imai, Hiroshi

    2002-01-01

    With current technologies, it seems to be very difficult to implement quantum computers with many qubits. It is therefore of importance to simulate quantum algorithms and circuits on the existing computers. However, for a large-size problem, the simulation often requires more computational power than is available from sequential processing. Therefore, simulation methods for parallel processors are required. We have developed a general-purpose simulator for quantum algorithms/circuits on the parallel computer (Sun Enterprise4500). It can simulate algorithms/circuits with up to 30 qubits. In order to test efficiency of our proposed methods, we have simulated Shor's factorization algorithm and Grover's database search, and we have analyzed robustness of the corresponding quantum circuits in the presence of both decoherence and operational errors. The corresponding results, statistics, and analyses are presented in this paper

  19. Parallel algorithms for computation of the manipulator inertia matrix

    Science.gov (United States)

    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.

  20. Fencing data transfers in a parallel active messaging interface of a parallel computer

    Science.gov (United States)

    Blocksome, Michael A.; Mamidala, Amith R.

    2015-06-02

    Fencing data transfers in a parallel active messaging interface (`PAMI`) of a parallel computer, the PAMI including data communications endpoints, each endpoint including a specification of data communications parameters for a thread of execution on a compute node, including specifications of a client, a context, and a task; the compute nodes coupled for data communications through the PAMI and through data communications resources including at least one segment of shared random access memory; including initiating execution through the PAMI of an ordered sequence of active SEND instructions for SEND data transfers between two endpoints, effecting deterministic SEND data transfers through a segment of shared memory; and executing through the PAMI, with no FENCE accounting for SEND data transfers, an active FENCE instruction, the FENCE instruction completing execution only after completion of all SEND instructions initiated prior to execution of the FENCE instruction for SEND data transfers between the two endpoints.

  1. Element-topology-independent preconditioners for parallel finite element computations

    Science.gov (United States)

    Park, K. C.; Alexander, Scott

    1992-01-01

    A family of preconditioners for the solution of finite element equations are presented, which are element-topology independent and thus can be applicable to element order-free parallel computations. A key feature of the present preconditioners is the repeated use of element connectivity matrices and their left and right inverses. The properties and performance of the present preconditioners are demonstrated via beam and two-dimensional finite element matrices for implicit time integration computations.

  2. Image processing with massively parallel computer Quadrics Q1

    International Nuclear Information System (INIS)

    Della Rocca, A.B.; La Porta, L.; Ferriani, S.

    1995-05-01

    Aimed to evaluate the image processing capabilities of the massively parallel computer Quadrics Q1, a convolution algorithm that has been implemented is described in this report. At first the discrete convolution mathematical definition is recalled together with the main Q1 h/w and s/w features. Then the different codification forms of the algorythm are described and the Q1 performances are compared with those obtained by different computers. Finally, the conclusions report on main results and suggestions

  3. WEKA-G: Parallel data mining on computational grids

    Directory of Open Access Journals (Sweden)

    PIMENTA, A.

    2009-12-01

    Full Text Available Data mining is a technology that can extract useful information from large amounts of data. However, mining a database often requires a high computational power. To resolve this problem, this paper presents a tool (Weka-G, which runs in parallel algorithms used in the mining process data. As the environment for doing so, we use a computational grid by adding several features within a WAN.

  4. Hardware packet pacing using a DMA in a parallel computer

    Science.gov (United States)

    Chen, Dong; Heidelberger, Phillip; Vranas, Pavlos

    2013-08-13

    Method and system for hardware packet pacing using a direct memory access controller in a parallel computer which, in one aspect, keeps track of a total number of bytes put on the network as a result of a remote get operation, using a hardware token counter.

  5. On the efficient parallel computation of Legendre transforms

    NARCIS (Netherlands)

    Inda, M.A.; Bisseling, R.H.; Maslen, D.K.

    2001-01-01

    In this article, we discuss a parallel implementation of efficient algorithms for computation of Legendre polynomial transforms and other orthogonal polynomial transforms. We develop an approach to the Driscoll-Healy algorithm using polynomial arithmetic and present experimental results on the

  6. On the efficient parallel computation of Legendre transforms

    NARCIS (Netherlands)

    Inda, M.A.; Bisseling, R.H.; Maslen, D.K.

    1999-01-01

    In this article we discuss a parallel implementation of efficient algorithms for computation of Legendre polynomial transforms and other orthogonal polynomial transforms. We develop an approach to the Driscoll-Healy algorithm using polynomial arithmetic and present experimental results on the

  7. Introduction of library administration system using an office computer in the smallscale library

    International Nuclear Information System (INIS)

    Itabashi, Keizo; Ishikawa, Masashi

    1984-01-01

    Research Information Center was established in Fusion Research Center at Naka site as a new section of Department of Technical Information of Japan Atomic Energy Research Institute. A library materials management system utilizing an office computer was introduced to provide good services. The system is a total-system centered on services at counter except purchase business and the serviced materials are books, reports, journals and pamphlets. The system has produced good effects on many aspects, e.g. a significantly easy inventory of library materials, and complete removal of user's handwriting for borrowing materials, by using an optical chracter recognition handscanner. Those improvements have resulted in better image of the library. (author)

  8. Parallel Computing Characteristics of CUPID code under MPI and Hybrid environment

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Jae Ryong; Yoon, Han Young [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of); Jeon, Byoung Jin; Choi, Hyoung Gwon [Seoul National Univ. of Science and Technology, Seoul (Korea, Republic of)

    2014-05-15

    In this paper, a characteristic of parallel algorithm is presented for solving an elliptic type equation of CUPID via domain decomposition method using the MPI and the parallel performance is estimated in terms of a scalability which shows the speedup ratio. In addition, the time-consuming pattern of major subroutines is studied. Two different grid systems are taken into account: 40,000 meshes for coarse system and 320,000 meshes for fine system. Since the matrix of the CUPID code differs according to whether the flow is single-phase or two-phase, the effect of matrix shape is evaluated. Finally, the effect of the preconditioner for matrix solver is also investigated. Finally, the hybrid (OpenMP+MPI) parallel algorithm is introduced and discussed in detail for solving pressure solver. Component-scale thermal-hydraulics code, CUPID has been developed for two-phase flow analysis, which adopts a three-dimensional, transient, three-field model, and parallelized to fulfill a recent demand for long-transient and highly resolved multi-phase flow behavior. In this study, the parallel performance of the CUPID code was investigated in terms of scalability. The CUPID code was parallelized with domain decomposition method. The MPI library was adopted to communicate the information at the neighboring domain. For managing the sparse matrix effectively, the CSR storage format is used. To take into account the characteristics of the pressure matrix which turns to be asymmetric for two-phase flow, both single-phase and two-phase calculations were run. In addition, the effect of the matrix size and preconditioning was also investigated. The fine mesh calculation shows better scalability than the coarse mesh because the number of coarse mesh does not need to decompose the computational domain excessively. The fine mesh can be present good scalability when dividing geometry with considering the ratio between computation and communication time. For a given mesh, single-phase flow

  9. Emerging Nanophotonic Applications Explored with Advanced Scientific Parallel Computing

    Science.gov (United States)

    Meng, Xiang

    The domain of nanoscale optical science and technology is a combination of the classical world of electromagnetics and the quantum mechanical regime of atoms and molecules. Recent advancements in fabrication technology allows the optical structures to be scaled down to nanoscale size or even to the atomic level, which are far smaller than the wavelength they are designed for. These nanostructures can have unique, controllable, and tunable optical properties and their interactions with quantum materials can have important near-field and far-field optical response. Undoubtedly, these optical properties can have many important applications, ranging from the efficient and tunable light sources, detectors, filters, modulators, high-speed all-optical switches; to the next-generation classical and quantum computation, and biophotonic medical sensors. This emerging research of nanoscience, known as nanophotonics, is a highly interdisciplinary field requiring expertise in materials science, physics, electrical engineering, and scientific computing, modeling and simulation. It has also become an important research field for investigating the science and engineering of light-matter interactions that take place on wavelength and subwavelength scales where the nature of the nanostructured matter controls the interactions. In addition, the fast advancements in the computing capabilities, such as parallel computing, also become as a critical element for investigating advanced nanophotonic devices. This role has taken on even greater urgency with the scale-down of device dimensions, and the design for these devices require extensive memory and extremely long core hours. Thus distributed computing platforms associated with parallel computing are required for faster designs processes. Scientific parallel computing constructs mathematical models and quantitative analysis techniques, and uses the computing machines to analyze and solve otherwise intractable scientific challenges. In

  10. Computer Programme Library at Ispra: Service to IAEA Member States

    International Nuclear Information System (INIS)

    1974-01-01

    In 1964, in view of the increasingly important role of computers in atomic energy, the Nuclear Energy Agency of the Organization for Economic Co-operation and Development established a Computer Programme Library (CPL) at Ispra, Italy. The original purpose of this Library, then consisting chiefly of programmes for reactor calculations, was to improve communication between the originators of the computer programmes and the scientists and engineers in Member States of the OECD who used them, thus furthering the efficient and economic use of the many large and expensive computers in the countries concerned. During the first few years of the Library's operation, a growing interest in its activities became evident in countries which were not members of the OECD. The Director General of the International Atomic Energy Agency, aware that such countries which were Member States of the IAEA could benefit from the Library's services, concluded an agreement with the Nuclear Energy Agency in 1967 to the effect that these services would be extended to all IAEA Member States. In March 1968, the Director General announced by circular letter that these services were available, and requested the governments of Member States that were not members of OECD to nominate establishments to participate in the activities of the Computer Programme Library. By August 1973, 32 such establishments were regularly using the services of the CPL

  11. A parallelization study of the general purpose Monte Carlo code MCNP4 on a distributed memory highly parallel computer

    International Nuclear Information System (INIS)

    Yamazaki, Takao; Fujisaki, Masahide; Okuda, Motoi; Takano, Makoto; Masukawa, Fumihiro; Naito, Yoshitaka

    1993-01-01

    The general purpose Monte Carlo code MCNP4 has been implemented on the Fujitsu AP1000 distributed memory highly parallel computer. Parallelization techniques developed and studied are reported. A shielding analysis function of the MCNP4 code is parallelized in this study. A technique to map a history to each processor dynamically and to map control process to a certain processor was applied. The efficiency of parallelized code is up to 80% for a typical practical problem with 512 processors. These results demonstrate the advantages of a highly parallel computer to the conventional computers in the field of shielding analysis by Monte Carlo method. (orig.)

  12. Parallel peak pruning for scalable SMP contour tree computation

    Energy Technology Data Exchange (ETDEWEB)

    Carr, Hamish A. [Univ. of Leeds (United Kingdom); Weber, Gunther H. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of California, Davis, CA (United States); Sewell, Christopher M. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Ahrens, James P. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2017-03-09

    As data sets grow to exascale, automated data analysis and visualisation are increasingly important, to intermediate human understanding and to reduce demands on disk storage via in situ analysis. Trends in architecture of high performance computing systems necessitate analysis algorithms to make effective use of combinations of massively multicore and distributed systems. One of the principal analytic tools is the contour tree, which analyses relationships between contours to identify features of more than local importance. Unfortunately, the predominant algorithms for computing the contour tree are explicitly serial, and founded on serial metaphors, which has limited the scalability of this form of analysis. While there is some work on distributed contour tree computation, and separately on hybrid GPU-CPU computation, there is no efficient algorithm with strong formal guarantees on performance allied with fast practical performance. Here in this paper, we report the first shared SMP algorithm for fully parallel contour tree computation, withfor-mal guarantees of O(lgnlgt) parallel steps and O(n lgn) work, and implementations with up to 10x parallel speed up in OpenMP and up to 50x speed up in NVIDIA Thrust.

  13. A hybrid method for the parallel computation of Green's functions

    DEFF Research Database (Denmark)

    Petersen, Dan Erik; Li, Song; Stokbro, Kurt

    2009-01-01

    of the large number of times this calculation needs to be performed, this is computationally very expensive even on supercomputers. The classical approach is based on recurrence formulas which cannot be efficiently parallelized. This practically prevents the solution of large problems with hundreds...... of thousands of atoms. We propose new recurrences for a general class of sparse matrices to calculate Green's and lesser Green's function matrices which extend formulas derived by Takahashi and others. We show that these recurrences may lead to a dramatically reduced computational cost because they only...... require computing a small number of entries of the inverse matrix. Then. we propose a parallelization strategy for block tridiagonal matrices which involves a combination of Schur complement calculations and cyclic reduction. It achieves good scalability even on problems of modest size....

  14. Parallel computing in genomic research: advances and applications.

    Science.gov (United States)

    Ocaña, Kary; de Oliveira, Daniel

    2015-01-01

    Today's genomic experiments have to process the so-called "biological big data" that is now reaching the size of Terabytes and Petabytes. To process this huge amount of data, scientists may require weeks or months if they use their own workstations. Parallelism techniques and high-performance computing (HPC) environments can be applied for reducing the total processing time and to ease the management, treatment, and analyses of this data. However, running bioinformatics experiments in HPC environments such as clouds, grids, clusters, and graphics processing unit requires the expertise from scientists to integrate computational, biological, and mathematical techniques and technologies. Several solutions have already been proposed to allow scientists for processing their genomic experiments using HPC capabilities and parallelism techniques. This article brings a systematic review of literature that surveys the most recently published research involving genomics and parallel computing. Our objective is to gather the main characteristics, benefits, and challenges that can be considered by scientists when running their genomic experiments to benefit from parallelism techniques and HPC capabilities.

  15. Aggregating job exit statuses of a plurality of compute nodes executing a parallel application

    Science.gov (United States)

    Aho, Michael E.; Attinella, John E.; Gooding, Thomas M.; Mundy, Michael B.

    2015-07-21

    Aggregating job exit statuses of a plurality of compute nodes executing a parallel application, including: identifying a subset of compute nodes in the parallel computer to execute the parallel application; selecting one compute node in the subset of compute nodes in the parallel computer as a job leader compute node; initiating execution of the parallel application on the subset of compute nodes; receiving an exit status from each compute node in the subset of compute nodes, where the exit status for each compute node includes information describing execution of some portion of the parallel application by the compute node; aggregating each exit status from each compute node in the subset of compute nodes; and sending an aggregated exit status for the subset of compute nodes in the parallel computer.

  16. High spatial resolution CT image reconstruction using parallel computing

    International Nuclear Information System (INIS)

    Yin Yin; Liu Li; Sun Gongxing

    2003-01-01

    Using the PC cluster system with 16 dual CPU nodes, we accelerate the FBP and OR-OSEM reconstruction of high spatial resolution image (2048 x 2048). Based on the number of projections, we rewrite the reconstruction algorithms into parallel format and dispatch the tasks to each CPU. By parallel computing, the speedup factor is roughly equal to the number of CPUs, which can be up to about 25 times when 25 CPUs used. This technique is very suitable for real-time high spatial resolution CT image reconstruction. (authors)

  17. Interfacing the Paramesh Computational Libraries to the Cactus Computational Framework, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — We will design and implement an interface between the Paramesh computational libraries, developed and used by groups at NASA GSFC, and the Cactus computational...

  18. Quantification of massively parallel sequencing libraries - a comparative study of eight methods

    DEFF Research Database (Denmark)

    Hussing, Christian; Kampmann, Marie-Louise; Mogensen, Helle Smidt

    2018-01-01

    Quantification of massively parallel sequencing libraries is important for acquisition of monoclonal beads or clusters prior to clonal amplification and to avoid large variations in library coverage when multiple samples are included in one sequencing analysis. No gold standard for quantification...... estimates followed by Qubit and electrophoresis-based instruments (Bioanalyzer, TapeStation, GX Touch, and Fragment Analyzer), while SYBR Green and TaqMan based qPCR assays gave the lowest estimates. qPCR gave more accurate predictions of sequencing coverage than Qubit and TapeStation did. Costs, time......-consumption, workflow simplicity, and ability to quantify multiple samples are discussed. Technical specifications, advantages, and disadvantages of the various methods are pointed out....

  19. The NEA computer program library: a possible GDMS application

    International Nuclear Information System (INIS)

    Schuler, W.

    1978-01-01

    NEA Computer Program library maintains a series of eleven sequential computer files, used for linked applications in managing their stock of computer codes for nuclear reactor calculations, storing index and program abstract information, and administering their service to requesters. The high data redundancy beween the files suggests that a data base approach would be valid and this paper suggests a possible 'schema' for an CODASYL GDMS

  20. Prioritizing multiple therapeutic targets in parallel using automated DNA-encoded library screening

    Science.gov (United States)

    Machutta, Carl A.; Kollmann, Christopher S.; Lind, Kenneth E.; Bai, Xiaopeng; Chan, Pan F.; Huang, Jianzhong; Ballell, Lluis; Belyanskaya, Svetlana; Besra, Gurdyal S.; Barros-Aguirre, David; Bates, Robert H.; Centrella, Paolo A.; Chang, Sandy S.; Chai, Jing; Choudhry, Anthony E.; Coffin, Aaron; Davie, Christopher P.; Deng, Hongfeng; Deng, Jianghe; Ding, Yun; Dodson, Jason W.; Fosbenner, David T.; Gao, Enoch N.; Graham, Taylor L.; Graybill, Todd L.; Ingraham, Karen; Johnson, Walter P.; King, Bryan W.; Kwiatkowski, Christopher R.; Lelièvre, Joël; Li, Yue; Liu, Xiaorong; Lu, Quinn; Lehr, Ruth; Mendoza-Losana, Alfonso; Martin, John; McCloskey, Lynn; McCormick, Patti; O'Keefe, Heather P.; O'Keeffe, Thomas; Pao, Christina; Phelps, Christopher B.; Qi, Hongwei; Rafferty, Keith; Scavello, Genaro S.; Steiginga, Matt S.; Sundersingh, Flora S.; Sweitzer, Sharon M.; Szewczuk, Lawrence M.; Taylor, Amy; Toh, May Fern; Wang, Juan; Wang, Minghui; Wilkins, Devan J.; Xia, Bing; Yao, Gang; Zhang, Jean; Zhou, Jingye; Donahue, Christine P.; Messer, Jeffrey A.; Holmes, David; Arico-Muendel, Christopher C.; Pope, Andrew J.; Gross, Jeffrey W.; Evindar, Ghotas

    2017-07-01

    The identification and prioritization of chemically tractable therapeutic targets is a significant challenge in the discovery of new medicines. We have developed a novel method that rapidly screens multiple proteins in parallel using DNA-encoded library technology (ELT). Initial efforts were focused on the efficient discovery of antibacterial leads against 119 targets from Acinetobacter baumannii and Staphylococcus aureus. The success of this effort led to the hypothesis that the relative number of ELT binders alone could be used to assess the ligandability of large sets of proteins. This concept was further explored by screening 42 targets from Mycobacterium tuberculosis. Active chemical series for six targets from our initial effort as well as three chemotypes for DHFR from M. tuberculosis are reported. The findings demonstrate that parallel ELT selections can be used to assess ligandability and highlight opportunities for successful lead and tool discovery.

  1. A discrete ordinate response matrix method for massively parallel computers

    International Nuclear Information System (INIS)

    Hanebutte, U.R.; Lewis, E.E.

    1991-01-01

    A discrete ordinate response matrix method is formulated for the solution of neutron transport problems on massively parallel computers. The response matrix formulation eliminates iteration on the scattering source. The nodal matrices which result from the diamond-differenced equations are utilized in a factored form which minimizes memory requirements and significantly reduces the required number of algorithm utilizes massive parallelism by assigning each spatial node to a processor. The algorithm is accelerated effectively by a synthetic method in which the low-order diffusion equations are also solved by massively parallel red/black iterations. The method has been implemented on a 16k Connection Machine-2, and S 8 and S 16 solutions have been obtained for fixed-source benchmark problems in X--Y geometry

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

    Science.gov (United States)

    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.

  3. Implementation of PHENIX trigger algorithms on massively parallel computers

    International Nuclear Information System (INIS)

    Petridis, A.N.; Wohn, F.K.

    1995-01-01

    The event selection requirements of contemporary high energy and nuclear physics experiments are met by the introduction of on-line trigger algorithms which identify potentially interesting events and reduce the data acquisition rate to levels that are manageable by the electronics. Such algorithms being parallel in nature can be simulated off-line using massively parallel computers. The PHENIX experiment intends to investigate the possible existence of a new phase of matter called the quark gluon plasma which has been theorized to have existed in very early stages of the evolution of the universe by studying collisions of heavy nuclei at ultra-relativistic energies. Such interactions can also reveal important information regarding the structure of the nucleus and mandate a thorough investigation of the simpler proton-nucleus collisions at the same energies. The complexity of PHENIX events and the need to analyze and also simulate them at rates similar to the data collection ones imposes enormous computation demands. This work is a first effort to implement PHENIX trigger algorithms on parallel computers and to study the feasibility of using such machines to run the complex programs necessary for the simulation of the PHENIX detector response. Fine and coarse grain approaches have been studied and evaluated. Depending on the application the performance of a massively parallel computer can be much better or much worse than that of a serial workstation. A comparison between single instruction and multiple instruction computers is also made and possible applications of the single instruction machines to high energy and nuclear physics experiments are outlined. copyright 1995 American Institute of Physics

  4. The 2nd Symposium on the Frontiers of Massively Parallel Computations

    Science.gov (United States)

    Mills, Ronnie (Editor)

    1988-01-01

    Programming languages, computer graphics, neural networks, massively parallel computers, SIMD architecture, algorithms, digital terrain models, sort computation, simulation of charged particle transport on the massively parallel processor and image processing are among the topics discussed.

  5. Time complexity analysis for distributed memory computers: implementation of parallel conjugate gradient method

    NARCIS (Netherlands)

    Hoekstra, A.G.; Sloot, P.M.A.; Haan, M.J.; Hertzberger, L.O.; van Leeuwen, J.

    1991-01-01

    New developments in Computer Science, both hardware and software, offer researchers, such as physicists, unprecedented possibilities to solve their computational intensive problems.However, full exploitation of e.g. new massively parallel computers, parallel languages or runtime environments

  6. Screening of a Brassica napus bacterial artificial chromosome library using highly parallel single nucleotide polymorphism assays

    Science.gov (United States)

    2013-01-01

    Background Efficient screening of bacterial artificial chromosome (BAC) libraries with polymerase chain reaction (PCR)-based markers is feasible provided that a multidimensional pooling strategy is implemented. Single nucleotide polymorphisms (SNPs) can be screened in multiplexed format, therefore this marker type lends itself particularly well for medium- to high-throughput applications. Combining the power of multiplex-PCR assays with a multidimensional pooling system may prove to be especially challenging in a polyploid genome. In polyploid genomes two classes of SNPs need to be distinguished, polymorphisms between accessions (intragenomic SNPs) and those differentiating between homoeologous genomes (intergenomic SNPs). We have assessed whether the highly parallel Illumina GoldenGate® Genotyping Assay is suitable for the screening of a BAC library of the polyploid Brassica napus genome. Results A multidimensional screening platform was developed for a Brassica napus BAC library which is composed of almost 83,000 clones. Intragenomic and intergenomic SNPs were included in Illumina’s GoldenGate® Genotyping Assay and both SNP classes were used successfully for screening of the multidimensional BAC pools of the Brassica napus library. An optimized scoring method is proposed which is especially valuable for SNP calling of intergenomic SNPs. Validation of the genotyping results by independent methods revealed a success of approximately 80% for the multiplex PCR-based screening regardless of whether intra- or intergenomic SNPs were evaluated. Conclusions Illumina’s GoldenGate® Genotyping Assay can be efficiently used for screening of multidimensional Brassica napus BAC pools. SNP calling was specifically tailored for the evaluation of BAC pool screening data. The developed scoring method can be implemented independently of plant reference samples. It is demonstrated that intergenomic SNPs represent a powerful tool for BAC library screening of a polyploid genome

  7. A Parallel Computational Model for Multichannel Phase Unwrapping Problem

    Science.gov (United States)

    Imperatore, Pasquale; Pepe, Antonio; Lanari, Riccardo

    2015-05-01

    In this paper, a parallel model for the solution of the computationally intensive multichannel phase unwrapping (MCh-PhU) problem is proposed. Firstly, the Extended Minimum Cost Flow (EMCF) algorithm for solving MCh-PhU problem is revised within the rigorous mathematical framework of the discrete calculus ; thus permitting to capture its topological structure in terms of meaningful discrete differential operators. Secondly, emphasis is placed on those methodological and practical aspects, which lead to a parallel reformulation of the EMCF algorithm. Thus, a novel dual-level parallel computational model, in which the parallelism is hierarchically implemented at two different (i.e., process and thread) levels, is presented. The validity of our approach has been demonstrated through a series of experiments that have revealed a significant speedup. Therefore, the attained high-performance prototype is suitable for the solution of large-scale phase unwrapping problems in reasonable time frames, with a significant impact on the systematic exploitation of the existing, and rapidly growing, large archives of SAR data.

  8. Executing a gather operation on a parallel computer

    Science.gov (United States)

    Archer, Charles J [Rochester, MN; Ratterman, Joseph D [Rochester, MN

    2012-03-20

    Methods, apparatus, and computer program products are disclosed for executing a gather operation on a parallel computer according to embodiments of the present invention. Embodiments include configuring, by the logical root, a result buffer or the logical root, the result buffer having positions, each position corresponding to a ranked node in the operational group and for storing contribution data gathered from that ranked node. Embodiments also include repeatedly for each position in the result buffer: determining, by each compute node of an operational group, whether the current position in the result buffer corresponds with the rank of the compute node, if the current position in the result buffer corresponds with the rank of the compute node, contributing, by that compute node, the compute node's contribution data, if the current position in the result buffer does not correspond with the rank of the compute node, contributing, by that compute node, a value of zero for the contribution data, and storing, by the logical root in the current position in the result buffer, results of a bitwise OR operation of all the contribution data by all compute nodes of the operational group for the current position, the results received through the global combining network.

  9. Cloud Computing Platform for an Online Model Library System

    Directory of Open Access Journals (Sweden)

    Mingang Chen

    2013-01-01

    Full Text Available The rapid developing of digital content industry calls for online model libraries. For the efficiency, user experience, and reliability merits of the model library, this paper designs a Web 3D model library system based on a cloud computing platform. Taking into account complex models, which cause difficulties in real-time 3D interaction, we adopt the model simplification and size adaptive adjustment methods to make the system with more efficient interaction. Meanwhile, a cloud-based architecture is developed to ensure the reliability and scalability of the system. The 3D model library system is intended to be accessible by online users with good interactive experiences. The feasibility of the solution has been tested by experiments.

  10. Fast Evaluation of Segmentation Quality with Parallel Computing

    Directory of Open Access Journals (Sweden)

    Henry Cruz

    2017-01-01

    Full Text Available In digital image processing and computer vision, a fairly frequent task is the performance comparison of different algorithms on enormous image databases. This task is usually time-consuming and tedious, such that any kind of tool to simplify this work is welcome. To achieve an efficient and more practical handling of a normally tedious evaluation, we implemented the automatic detection system, with the help of MATLAB®’s Parallel Computing Toolbox™. The key parts of the system have been parallelized to achieve simultaneous execution and analysis of segmentation algorithms on the one hand and the evaluation of detection accuracy for the nonforested regions, such as a study case, on the other hand. As a positive side effect, CPU usage was reduced and processing time was significantly decreased by 68.54% compared to sequential processing (i.e., executing the system with each algorithm one by one.

  11. Final Report: Center for Programming Models for Scalable Parallel Computing

    Energy Technology Data Exchange (ETDEWEB)

    Mellor-Crummey, John [William Marsh Rice University

    2011-09-13

    As part of the Center for Programming Models for Scalable Parallel Computing, Rice University collaborated with project partners in the design, development and deployment of language, compiler, and runtime support for parallel programming models to support application development for the “leadership-class” computer systems at DOE national laboratories. Work over the course of this project has focused on the design, implementation, and evaluation of a second-generation version of Coarray Fortran. Research and development efforts of the project have focused on the CAF 2.0 language, compiler, runtime system, and supporting infrastructure. This has involved working with the teams that provide infrastructure for CAF that we rely on, implementing new language and runtime features, producing an open source compiler that enabled us to evaluate our ideas, and evaluating our design and implementation through the use of benchmarks. The report details the research, development, findings, and conclusions from this work.

  12. Performing a local reduction operation on a parallel computer

    Science.gov (United States)

    Blocksome, Michael A.; Faraj, Daniel A.

    2012-12-11

    A parallel computer including compute nodes, each including two reduction processing cores, a network write processing core, and a network read processing core, each processing core assigned an input buffer. Copying, in interleaved chunks by the reduction processing cores, contents of the reduction processing cores' input buffers to an interleaved buffer in shared memory; copying, by one of the reduction processing cores, contents of the network write processing core's input buffer to shared memory; copying, by another of the reduction processing cores, contents of the network read processing core's input buffer to shared memory; and locally reducing in parallel by the reduction processing cores: the contents of the reduction processing core's input buffer; every other interleaved chunk of the interleaved buffer; the copied contents of the network write processing core's input buffer; and the copied contents of the network read processing core's input buffer.

  13. Establishing a group of endpoints in a parallel computer

    Science.gov (United States)

    Archer, Charles J.; Blocksome, Michael A.; Ratterman, Joseph D.; Smith, Brian E.; Xue, Hanhong

    2016-02-02

    A parallel computer executes a number of tasks, each task includes a number of endpoints and the endpoints are configured to support collective operations. In such a parallel computer, establishing a group of endpoints receiving a user specification of a set of endpoints included in a global collection of endpoints, where the user specification defines the set in accordance with a predefined virtual representation of the endpoints, the predefined virtual representation is a data structure setting forth an organization of tasks and endpoints included in the global collection of endpoints and the user specification defines the set of endpoints without a user specification of a particular endpoint; and defining a group of endpoints in dependence upon the predefined virtual representation of the endpoints and the user specification.

  14. Mechatronic Model Based Computed Torque Control of a Parallel Manipulator

    Directory of Open Access Journals (Sweden)

    Zhiyong Yang

    2008-11-01

    Full Text Available With high speed and accuracy the parallel manipulators have wide application in the industry, but there still exist many difficulties in the actual control process because of the time-varying and coupling. Unfortunately, the present-day commercial controlles cannot provide satisfying performance for its single axis linear control only. Therefore, aimed at a novel 2-DOF (Degree of Freedom parallel manipulator called Diamond 600, a motor-mechanism coupling dynamic model based control scheme employing the computed torque control algorithm are presented in this paper. First, the integrated dynamic coupling model is deduced, according to equivalent torques between the mechanical structure and the PM (Permanent Magnetism servomotor. Second, computed torque controller is described in detail for the above proposed model. At last, a series of numerical simulations and experiments are carried out to test the effectiveness of the system, and the results verify the favourable tracking ability and robustness.

  15. Mechatronic Model Based Computed Torque Control of a Parallel Manipulator

    Directory of Open Access Journals (Sweden)

    Zhiyong Yang

    2008-03-01

    Full Text Available With high speed and accuracy the parallel manipulators have wide application in the industry, but there still exist many difficulties in the actual control process because of the time-varying and coupling. Unfortunately, the present-day commercial controlles cannot provide satisfying performance for its single axis linear control only. Therefore, aimed at a novel 2-DOF (Degree of Freedom parallel manipulator called Diamond 600, a motor-mechanism coupling dynamic model based control scheme employing the computed torque control algorithm are presented in this paper. First, the integrated dynamic coupling model is deduced, according to equivalent torques between the mechanical structure and the PM (Permanent Magnetism servomotor. Second, computed torque controller is described in detail for the above proposed model. At last, a series of numerical simulations and experiments are carried out to test the effectiveness of the system, and the results verify the favourable tracking ability and robustness.

  16. A scalable PC-based parallel computer for lattice QCD

    International Nuclear Information System (INIS)

    Fodor, Z.; Katz, S.D.; Pappa, G.

    2003-01-01

    A PC-based parallel computer for medium/large scale lattice QCD simulations is suggested. The Eoetvoes Univ., Inst. Theor. Phys. cluster consists of 137 Intel P4-1.7GHz nodes. Gigabit Ethernet cards are used for nearest neighbor communication in a two-dimensional mesh. The sustained performance for dynamical staggered (wilson) quarks on large lattices is around 70(110) GFlops. The exceptional price/performance ratio is below $1/Mflop

  17. A scalable PC-based parallel computer for lattice QCD

    International Nuclear Information System (INIS)

    Fodor, Z.; Papp, G.

    2002-09-01

    A PC-based parallel computer for medium/large scale lattice QCD simulations is suggested. The Eoetvoes Univ., Inst. Theor. Phys. cluster consists of 137 Intel P4-1.7 GHz nodes. Gigabit Ethernet cards are used for nearest neighbor communication in a two-dimensional mesh. The sustained performance for dynamical staggered(wilson) quarks on large lattices is around 70(110) GFlops. The exceptional price/performance ratio is below $1/Mflop. (orig.)

  18. Domain Decomposition: A Bridge between Nature and Parallel Computers

    Science.gov (United States)

    1992-09-01

    B., "Domain Decomposition Algorithms for Indefinite Elliptic Problems," S"IAM Journal of S; cientific and Statistical (’omputing, Vol. 13, 1992, pp...AD-A256 575 NASA Contractor Report 189709 ICASE Report No. 92-44 ICASE DOMAIN DECOMPOSITION: A BRIDGE BETWEEN NATURE AND PARALLEL COMPUTERS DTIC dE...effectively implemented on dis- tributed memory multiprocessors. In 1990 (as reported in Ref. 38 using the tile algo- rithm), a 103,201-unknown 2D elliptic

  19. Noise simulation in cone beam CT imaging with parallel computing

    International Nuclear Information System (INIS)

    Tu, S.-J.; Shaw, Chris C; Chen, Lingyun

    2006-01-01

    We developed a computer noise simulation model for cone beam computed tomography imaging using a general purpose PC cluster. This model uses a mono-energetic x-ray approximation and allows us to investigate three primary performance components, specifically quantum noise, detector blurring and additive system noise. A parallel random number generator based on the Weyl sequence was implemented in the noise simulation and a visualization technique was accordingly developed to validate the quality of the parallel random number generator. In our computer simulation model, three-dimensional (3D) phantoms were mathematically modelled and used to create 450 analytical projections, which were then sampled into digital image data. Quantum noise was simulated and added to the analytical projection image data, which were then filtered to incorporate flat panel detector blurring. Additive system noise was generated and added to form the final projection images. The Feldkamp algorithm was implemented and used to reconstruct the 3D images of the phantoms. A 24 dual-Xeon PC cluster was used to compute the projections and reconstructed images in parallel with each CPU processing 10 projection views for a total of 450 views. Based on this computer simulation system, simulated cone beam CT images were generated for various phantoms and technique settings. Noise power spectra for the flat panel x-ray detector and reconstructed images were then computed to characterize the noise properties. As an example among the potential applications of our noise simulation model, we showed that images of low contrast objects can be produced and used for image quality evaluation

  20. Local rollback for fault-tolerance in parallel computing systems

    Science.gov (United States)

    Blumrich, Matthias A [Yorktown Heights, NY; Chen, Dong [Yorktown Heights, NY; Gara, Alan [Yorktown Heights, NY; Giampapa, Mark E [Yorktown Heights, NY; Heidelberger, Philip [Yorktown Heights, NY; Ohmacht, Martin [Yorktown Heights, NY; Steinmacher-Burow, Burkhard [Boeblingen, DE; Sugavanam, Krishnan [Yorktown Heights, NY

    2012-01-24

    A control logic device performs a local rollback in a parallel super computing system. The super computing system includes at least one cache memory device. The control logic device determines a local rollback interval. The control logic device runs at least one instruction in the local rollback interval. The control logic device evaluates whether an unrecoverable condition occurs while running the at least one instruction during the local rollback interval. The control logic device checks whether an error occurs during the local rollback. The control logic device restarts the local rollback interval if the error occurs and the unrecoverable condition does not occur during the local rollback interval.

  1. An Alternative Algorithm for Computing Watersheds on Shared Memory Parallel Computers

    NARCIS (Netherlands)

    Meijster, A.; Roerdink, J.B.T.M.

    1995-01-01

    In this paper a parallel implementation of a watershed algorithm is proposed. The algorithm can easily be implemented on shared memory parallel computers. The watershed transform is generally considered to be inherently sequential since the discrete watershed of an image is defined using recursion.

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

    International Nuclear Information System (INIS)

    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

  3. Fencing direct memory access data transfers in a parallel active messaging interface of a parallel computer

    Science.gov (United States)

    Blocksome, Michael A.; Mamidala, Amith R.

    2013-09-03

    Fencing direct memory access (`DMA`) data transfers in a parallel active messaging interface (`PAMI`) of a parallel computer, the PAMI including data communications endpoints, each endpoint including specifications of a client, a context, and a task, the endpoints coupled for data communications through the PAMI and through DMA controllers operatively coupled to segments of shared random access memory through which the DMA controllers deliver data communications deterministically, including initiating execution through the PAMI of an ordered sequence of active DMA instructions for DMA data transfers between two endpoints, effecting deterministic DMA data transfers through a DMA controller and a segment of shared memory; and executing through the PAMI, with no FENCE accounting for DMA data transfers, an active FENCE instruction, the FENCE instruction completing execution only after completion of all DMA instructions initiated prior to execution of the FENCE instruction for DMA data transfers between the two endpoints.

  4. Data communications for a collective operation in a parallel active messaging interface of a parallel computer

    Science.gov (United States)

    Faraj, Daniel A

    2013-07-16

    Algorithm selection for data communications in a parallel active messaging interface (`PAMI`) of a parallel computer, the PAMI composed of data communications endpoints, each endpoint including specifications of a client, a context, and a task, endpoints coupled for data communications through the PAMI, including associating in the PAMI data communications algorithms and bit masks; receiving in an origin endpoint of the PAMI a collective instruction, the instruction specifying transmission of a data communications message from the origin endpoint to a target endpoint; constructing a bit mask for the received collective instruction; selecting, from among the associated algorithms and bit masks, a data communications algorithm in dependence upon the constructed bit mask; and executing the collective instruction, transmitting, according to the selected data communications algorithm from the origin endpoint to the target endpoint, the data communications message.

  5. Data communications in a parallel active messaging interface of a parallel computer

    Science.gov (United States)

    Davis, Kristan D; Faraj, Daniel A

    2013-07-09

    Algorithm selection for data communications in a parallel active messaging interface (`PAMI`) of a parallel computer, the PAMI composed of data communications endpoints, each endpoint including specifications of a client, a context, and a task, endpoints coupled for data communications through the PAMI, including associating in the PAMI data communications algorithms and ranges of message sizes so that each algorithm is associated with a separate range of message sizes; receiving in an origin endpoint of the PAMI a data communications instruction, the instruction specifying transmission of a data communications message from the origin endpoint to a target endpoint, the data communications message characterized by a message size; selecting, from among the associated algorithms and ranges, a data communications algorithm in dependence upon the message size; and transmitting, according to the selected data communications algorithm from the origin endpoint to the target endpoint, the data communications message.

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

    International Nuclear Information System (INIS)

    Nash, T.

    1989-01-01

    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. (orig.)

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

    Science.gov (United States)

    Nash, Thomas

    1989-12-01

    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 system, 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.

  8. Performing an allreduce operation on a plurality of compute nodes of a parallel computer

    Science.gov (United States)

    Faraj, Ahmad [Rochester, MN

    2012-04-17

    Methods, apparatus, and products are disclosed for performing an allreduce operation on a plurality of compute nodes of a parallel computer. Each compute node includes at least two processing cores. Each processing core has contribution data for the allreduce operation. Performing an allreduce operation on a plurality of compute nodes of a parallel computer includes: establishing one or more logical rings among the compute nodes, each logical ring including at least one processing core from each compute node; performing, for each logical ring, a global allreduce operation using the contribution data for the processing cores included in that logical ring, yielding a global allreduce result for each processing core included in that logical ring; and performing, for each compute node, a local allreduce operation using the global allreduce results for each processing core on that compute node.

  9. Computational hybrid anthropometric paediatric phantom library for internal radiation dosimetry

    DEFF Research Database (Denmark)

    Xie, Tianwu; Kuster, Niels; Zaidi, Habib

    2017-01-01

    for children demonstrated that they follow the same trend when correlated with age. The constructed hybrid computational phantom library opens up the prospect of comprehensive radiation dosimetry calculations and risk assessment for the paediatric population of different age groups and diverse anthropometric...

  10. Computer Simulation of the Circulation Subsystem of a Library

    Science.gov (United States)

    Shaw, W. M., Jr.

    1975-01-01

    When circulation data are used as input parameters for a computer simulation of a library's circulation subsystem, the results of the simulation provide information on book availability and delays. The model may be used to simulate alternative loan policies. (Author/LS)

  11. Centaure: an heterogeneous parallel architecture for computer vision

    International Nuclear Information System (INIS)

    Peythieux, Marc

    1997-01-01

    This dissertation deals with the architecture of parallel computers dedicated to computer vision. In the first chapter, the problem to be solved is presented, as well as the architecture of the Sympati and Symphonie computers, on which this work is based. The second chapter is about the state of the art of computers and integrated processors that can execute computer vision and image processing codes. The third chapter contains a description of the architecture of Centaure. It has an heterogeneous structure: it is composed of a multiprocessor system based on Analog Devices ADSP21060 Sharc digital signal processor, and of a set of Symphonie computers working in a multi-SIMD fashion. Centaure also has a modular structure. Its basic node is composed of one Symphonie computer, tightly coupled to a Sharc thanks to a dual ported memory. The nodes of Centaure are linked together by the Sharc communication links. The last chapter deals with a performance validation of Centaure. The execution times on Symphonie and on Centaure of a benchmark which is typical of industrial vision, are presented and compared. In the first place, these results show that the basic node of Centaure allows a faster execution than Symphonie, and that increasing the size of the tested computer leads to a better speed-up with Centaure than with Symphonie. In the second place, these results validate the choice of running the low level structure of Centaure in a multi- SIMD fashion. (author) [fr

  12. Development of real-time visualization system for Computational Fluid Dynamics on parallel computers

    International Nuclear Information System (INIS)

    Muramatsu, Kazuhiro; Otani, Takayuki; Matsumoto, Hideki; Takei, Toshifumi; Doi, Shun

    1998-03-01

    A real-time visualization system for computational fluid dynamics in a network connecting between a parallel computing server and the client terminal was developed. Using the system, a user can visualize the results of a CFD (Computational Fluid Dynamics) simulation on the parallel computer as a client terminal during the actual computation on a server. Using GUI (Graphical User Interface) on the client terminal, to user is also able to change parameters of the analysis and visualization during the real-time of the calculation. The system carries out both of CFD simulation and generation of a pixel image data on the parallel computer, and compresses the data. Therefore, the amount of data from the parallel computer to the client is so small in comparison with no compression that the user can enjoy the swift image appearance comfortably. Parallelization of image data generation is based on Owner Computation Rule. GUI on the client is built on Java applet. A real-time visualization is thus possible on the client PC only if Web browser is implemented on it. (author)

  13. Semi-coarsening multigrid methods for parallel computing

    Energy Technology Data Exchange (ETDEWEB)

    Jones, J.E.

    1996-12-31

    Standard multigrid methods are not well suited for problems with anisotropic coefficients which can occur, for example, on grids that are stretched to resolve a boundary layer. There are several different modifications of the standard multigrid algorithm that yield efficient methods for anisotropic problems. In the paper, we investigate the parallel performance of these multigrid algorithms. Multigrid algorithms which work well for anisotropic problems are based on line relaxation and/or semi-coarsening. In semi-coarsening multigrid algorithms a grid is coarsened in only one of the coordinate directions unlike standard or full-coarsening multigrid algorithms where a grid is coarsened in each of the coordinate directions. When both semi-coarsening and line relaxation are used, the resulting multigrid algorithm is robust and automatic in that it requires no knowledge of the nature of the anisotropy. This is the basic multigrid algorithm whose parallel performance we investigate in the paper. The algorithm is currently being implemented on an IBM SP2 and its performance is being analyzed. In addition to looking at the parallel performance of the basic semi-coarsening algorithm, we present algorithmic modifications with potentially better parallel efficiency. One modification reduces the amount of computational work done in relaxation at the expense of using multiple coarse grids. This modification is also being implemented with the aim of comparing its performance to that of the basic semi-coarsening algorithm.

  14. Dynamic stability calculations for power grids employing a parallel computer

    Energy Technology Data Exchange (ETDEWEB)

    Schmidt, K

    1982-06-01

    The aim of dynamic contingency calculations in power systems is to estimate the effects of assumed disturbances, such as loss of generation. Due to the large dimensions of the problem these simulations require considerable computing time and costs, to the effect that they are at present only used in a planning state but not for routine checks in power control stations. In view of the homogeneity of the problem, where a multitude of equal generator models, having different parameters, are to be integrated simultaneously, the use of a parallel computer looks very attractive. The results of this study employing a prototype parallel computer (SMS 201) are presented. It consists of up to 128 equal microcomputers bus-connected to a control computer. Each of the modules is programmed to simulate a node of the power grid. Generators with their associated control are represented by models of 13 states each. Passive nodes are complemented by 'phantom'-generators, so that the whole power grid is homogenous, thus removing the need for load-flow-iterations. Programming of microcomputers is essentially performed in FORTRAN.

  15. Fast electrostatic force calculation on parallel computer clusters

    International Nuclear Information System (INIS)

    Kia, Amirali; Kim, Daejoong; Darve, Eric

    2008-01-01

    The fast multipole method (FMM) and smooth particle mesh Ewald (SPME) are well known fast algorithms to evaluate long range electrostatic interactions in molecular dynamics and other fields. FMM is a multi-scale method which reduces the computation cost by approximating the potential due to a group of particles at a large distance using few multipole functions. This algorithm scales like O(N) for N particles. SPME algorithm is an O(NlnN) method which is based on an interpolation of the Fourier space part of the Ewald sum and evaluating the resulting convolutions using fast Fourier transform (FFT). Those algorithms suffer from relatively poor efficiency on large parallel machines especially for mid-size problems around hundreds of thousands of atoms. A variation of the FMM, called PWA, based on plane wave expansions is presented in this paper. A new parallelization strategy for PWA, which takes advantage of the specific form of this expansion, is described. Its parallel efficiency is compared with SPME through detail time measurements on two different computer clusters

  16. Performance evaluation for compressible flow calculations on five parallel computers of different architectures

    International Nuclear Information System (INIS)

    Kimura, Toshiya.

    1997-03-01

    A two-dimensional explicit Euler solver has been implemented for five MIMD parallel computers of different machine architectures in Center for Promotion of Computational Science and Engineering of Japan Atomic Energy Research Institute. These parallel computers are Fujitsu VPP300, NEC SX-4, CRAY T94, IBM SP2, and Hitachi SR2201. The code was parallelized by several parallelization methods, and a typical compressible flow problem has been calculated for different grid sizes changing the number of processors. Their effective performances for parallel calculations, such as calculation speed, speed-up ratio and parallel efficiency, have been investigated and evaluated. The communication time among processors has been also measured and evaluated. As a result, the differences on the performance and the characteristics between vector-parallel and scalar-parallel computers can be pointed, and it will present the basic data for efficient use of parallel computers and for large scale CFD simulations on parallel computers. (author)

  17. Methods and apparatus for capture and storage of semantic information with sub-files in a parallel computing system

    Science.gov (United States)

    Faibish, Sorin; Bent, John M; Tzelnic, Percy; Grider, Gary; Torres, Aaron

    2015-02-03

    Techniques are provided for storing files in a parallel computing system using sub-files with semantically meaningful boundaries. A method is provided for storing at least one file generated by a distributed application in a parallel computing system. The file comprises one or more of a complete file and a plurality of sub-files. The method comprises the steps of obtaining a user specification of semantic information related to the file; providing the semantic information as a data structure description to a data formatting library write function; and storing the semantic information related to the file with one or more of the sub-files in one or more storage nodes of the parallel computing system. The semantic information provides a description of data in the file. The sub-files can be replicated based on semantically meaningful boundaries.

  18. An Introduction to Parallel Cluster Computing Using PVM for Computer Modeling and Simulation of Engineering Problems

    International Nuclear Information System (INIS)

    Spencer, VN

    2001-01-01

    An investigation has been conducted regarding the ability of clustered personal computers to improve the performance of executing software simulations for solving engineering problems. The power and utility of personal computers continues to grow exponentially through advances in computing capabilities such as newer microprocessors, advances in microchip technologies, electronic packaging, and cost effective gigabyte-size hard drive capacity. Many engineering problems require significant computing power. Therefore, the computation has to be done by high-performance computer systems that cost millions of dollars and need gigabytes of memory to complete the task. Alternately, it is feasible to provide adequate computing in the form of clustered personal computers. This method cuts the cost and size by linking (clustering) personal computers together across a network. Clusters also have the advantage that they can be used as stand-alone computers when they are not operating as a parallel computer. Parallel computing software to exploit clusters is available for computer operating systems like Unix, Windows NT, or Linux. This project concentrates on the use of Windows NT, and the Parallel Virtual Machine (PVM) system to solve an engineering dynamics problem in Fortran

  19. Computers, Education and the Library at The Bronx High School of Science.

    Science.gov (United States)

    Nachbar, Sondra; Sussman, Valerie

    1988-01-01

    Describes the services and programs offered by the library at The Bronx High School of Science. Topics discussed include the library collection; a basic library skills mini-course for freshmen and incoming sophomores; current uses of the library's computer system; and plans to automate the library's card catalog and circulation records.…

  20. Parallel computation of automatic differentiation applied to magnetic field calculations

    International Nuclear Information System (INIS)

    Hinkins, R.L.; Lawrence Berkeley Lab., CA

    1994-09-01

    The author presents a parallelization of an accelerator physics application to simulate magnetic field in three dimensions. The problem involves the evaluation of high order derivatives with respect to two variables of a multivariate function. Automatic differentiation software had been used with some success, but the computation time was prohibitive. The implementation runs on several platforms, including a network of workstations using PVM, a MasPar using MPFortran, and a CM-5 using CMFortran. A careful examination of the code led to several optimizations that improved its serial performance by a factor of 8.7. The parallelization produced further improvements, especially on the MasPar with a speedup factor of 620. As a result a problem that took six days on a SPARC 10/41 now runs in minutes on the MasPar, making it feasible for physicists at Lawrence Berkeley Laboratory to simulate larger magnets

  1. A finite element solution method for quadrics parallel computer

    International Nuclear Information System (INIS)

    Zucchini, A.

    1996-08-01

    A distributed preconditioned conjugate gradient method for finite element analysis has been developed and implemented on a parallel SIMD Quadrics computer. The main characteristic of the method is that it does not require any actual assembling of all element equations in a global system. The physical domain of the problem is partitioned in cells of n p finite elements and each cell element is assigned to a different node of an n p -processors machine. Element stiffness matrices are stored in the data memory of the assigned processing node and the solution process is completely executed in parallel at element level. Inter-element and therefore inter-processor communications are required once per iteration to perform local sums of vector quantities between neighbouring elements. A prototype implementation has been tested on an 8-nodes Quadrics machine in a simple 2D benchmark problem

  2. Parallel computation of transverse wakes in linear colliders

    International Nuclear Information System (INIS)

    Zhan, Xiaowei; Ko, Kwok.

    1996-11-01

    SLAC has proposed the detuned structure (DS) as one possible design to control the emittance growth of long bunch trains due to transverse wakefields in the Next Linear Collider (NLC). The DS consists of 206 cells with tapering from cell to cell of the order of few microns to provide Gaussian detuning of the dipole modes. The decoherence of these modes leads to two orders of magnitude reduction in wakefield experienced by the trailing bunch. To model such a large heterogeneous structure realistically is impractical with finite-difference codes using structured grids. The authors have calculated the wakefield in the DS on a parallel computer with a finite-element code using an unstructured grid. The parallel implementation issues are presented along with simulation results that include contributions from higher dipole bands and wall dissipation

  3. A scalable implementation of RI-SCF on parallel computers

    International Nuclear Information System (INIS)

    Fruechtl, H.A.; Kendall, R.A.; Harrison, R.J.

    1996-01-01

    In order to avoid the integral bottleneck of conventional SCF calculations, the Resolution of the Identity (RI) method is used to obtain an approximate solution to the Hartree-Fock equations. In this approximation only three-center integrals are needed to build the Fock matrix. It has been implemented as part of the NWChem package of portable and scalable ab initio programs for parallel computers. Utilizing the V-approximation, both the Coulomb and exchange contribution to the Fock matrix can be calculated from a transformed set of three-center integrals which have to be precalculated and stored. A distributed in-core method as well as a disk based implementation have been programmed. Details of the implementation as well as the parallel programming tools used are described. We also give results and timings from benchmark calculations

  4. High performance parallel computers for science: New developments at the Fermilab advanced computer program

    International Nuclear Information System (INIS)

    Nash, T.; Areti, H.; Atac, R.

    1988-08-01

    Fermilab's Advanced Computer Program (ACP) has been developing highly cost effective, yet practical, parallel computers for high energy physics since 1984. The ACP's latest developments are proceeding in two directions. A Second Generation ACP Multiprocessor System for experiments will include $3500 RISC processors each with performance over 15 VAX MIPS. To support such high performance, the new system allows parallel I/O, parallel interprocess communication, and parallel host processes. The ACP Multi-Array Processor, has been developed for theoretical physics. Each $4000 node is a FORTRAN or C programmable pipelined 20 MFlops (peak), 10 MByte single board computer. These are plugged into a 16 port crossbar switch crate which handles both inter and intra crate communication. The crates are connected in a hypercube. Site oriented applications like lattice gauge theory are supported by system software called CANOPY, which makes the hardware virtually transparent to users. A 256 node, 5 GFlop, system is under construction. 10 refs., 7 figs

  5. Introduction of library administration system using an office computer in the smallscale library

    Energy Technology Data Exchange (ETDEWEB)

    Itabashi, Keizo; Ishikawa, Masashi

    1984-01-01

    Research Information Center was established in Fusion Research Center at Naka site as a new section of Department of Technical Information of Japan Atomic Energy Research Institute. A library materials management system utilizing an office computer was introduced to provide good services. The system is a total-system centered on services at counter except purchase business and the serviced materials are books, reports, journals and pamphlets. The system has produced good effects on many aspects, e.g. a significantly easy inventory of library materials, and complete removal of user's handwriting for borrowing materials, by using an optical chracter recognition handscanner. Those improvements have resulted in better image of the library.

  6. Simulation of partially coherent light propagation using parallel computing devices

    Science.gov (United States)

    Magalhães, Tiago C.; Rebordão, José M.

    2017-08-01

    Light acquires or loses coherence and coherence is one of the few optical observables. Spectra can be derived from coherence functions and understanding any interferometric experiment is also relying upon coherence functions. Beyond the two limiting cases (full coherence or incoherence) the coherence of light is always partial and it changes with propagation. We have implemented a code to compute the propagation of partially coherent light from the source plane to the observation plane using parallel computing devices (PCDs). In this paper, we restrict the propagation in free space only. To this end, we used the Open Computing Language (OpenCL) and the open-source toolkit PyOpenCL, which gives access to OpenCL parallel computation through Python. To test our code, we chose two coherence source models: an incoherent source and a Gaussian Schell-model source. In the former case, we divided into two different source shapes: circular and rectangular. The results were compared to the theoretical values. Our implemented code allows one to choose between the PyOpenCL implementation and a standard one, i.e using the CPU only. To test the computation time for each implementation (PyOpenCL and standard), we used several computer systems with different CPUs and GPUs. We used powers of two for the dimensions of the cross-spectral density matrix (e.g. 324, 644) and a significant speed increase is observed in the PyOpenCL implementation when compared to the standard one. This can be an important tool for studying new source models.

  7. Cluster implementation for parallel computation within MATLAB software environment

    International Nuclear Information System (INIS)

    Santana, Antonio O. de; Dantas, Carlos C.; Charamba, Luiz G. da R.; Souza Neto, Wilson F. de; Melo, Silvio B. Melo; Lima, Emerson A. de O.

    2013-01-01

    A cluster for parallel computation with MATLAB software the COCGT - Cluster for Optimizing Computing in Gamma ray Transmission methods, is implemented. The implementation correspond to creation of a local net of computers, facilities and configurations of software, as well as the accomplishment of cluster tests for determine and optimizing of performance in the data processing. The COCGT implementation was required by data computation from gamma transmission measurements applied to fluid dynamic and tomography reconstruction in a FCC-Fluid Catalytic Cracking cold pilot unity, and simulation data as well. As an initial test the determination of SVD - Singular Values Decomposition - of random matrix with dimension (n , n), n=1000, using the Girco's law modified, revealed that COCGT was faster in comparison to the literature [1] cluster, which is similar and operates at the same conditions. Solution of a system of linear equations provided a new test for the COCGT performance by processing a square matrix with n=10000, computing time was 27 s and for square matrix with n=12000, computation time was 45 s. For determination of the cluster behavior in relation to 'parfor' (parallel for-loop) and 'spmd' (single program multiple data), two codes were used containing those two commands and the same problem: determination of SVD of a square matrix with n= 1000. The execution of codes by means of COCGT proved: 1) for the code with 'parfor', the performance improved with the labs number from 1 to 8 labs; 2) for the code 'spmd', just 1 lab (core) was enough to process and give results in less than 1 s. In similar situation, with the difference that now the SVD will be determined from square matrix with n1500, for code with 'parfor', and n=7000, for code with 'spmd'. That results take to conclusions: 1) for the code with 'parfor', the behavior was the same already described above; 2) for code with 'spmd', the same besides having produced a larger performance, it supports a

  8. Parallel computation of multigroup reactivity coefficient using iterative method

    Science.gov (United States)

    Susmikanti, Mike; Dewayatna, Winter

    2013-09-01

    One of the research activities to support the commercial radioisotope production program is a safety research target irradiation FPM (Fission Product Molybdenum). FPM targets form a tube made of stainless steel in which the nuclear degrees of superimposed high-enriched uranium. FPM irradiation tube is intended to obtain fission. The fission material widely used in the form of kits in the world of nuclear medicine. Irradiation FPM tube reactor core would interfere with performance. One of the disorders comes from changes in flux or reactivity. It is necessary to study a method for calculating safety terrace ongoing configuration changes during the life of the reactor, making the code faster became an absolute necessity. Neutron safety margin for the research reactor can be reused without modification to the calculation of the reactivity of the reactor, so that is an advantage of using perturbation method. The criticality and flux in multigroup diffusion model was calculate at various irradiation positions in some uranium content. This model has a complex computation. Several parallel algorithms with iterative method have been developed for the sparse and big matrix solution. The Black-Red Gauss Seidel Iteration and the power iteration parallel method can be used to solve multigroup diffusion equation system and calculated the criticality and reactivity coeficient. This research was developed code for reactivity calculation which used one of safety analysis with parallel processing. It can be done more quickly and efficiently by utilizing the parallel processing in the multicore computer. This code was applied for the safety limits calculation of irradiated targets FPM with increment Uranium.

  9. SPINET: A Parallel Computing Approach to Spine Simulations

    Directory of Open Access Journals (Sweden)

    Peter G. Kropf

    1996-01-01

    Full Text Available Research in scientitic programming enables us to realize more and more complex applications, and on the other hand, application-driven demands on computing methods and power are continuously growing. Therefore, interdisciplinary approaches become more widely used. The interdisciplinary SPINET project presented in this article applies modern scientific computing tools to biomechanical simulations: parallel computing and symbolic and modern functional programming. The target application is the human spine. Simulations of the spine help us to investigate and better understand the mechanisms of back pain and spinal injury. Two approaches have been used: the first uses the finite element method for high-performance simulations of static biomechanical models, and the second generates a simulation developmenttool for experimenting with different dynamic models. A finite element program for static analysis has been parallelized for the MUSIC machine. To solve the sparse system of linear equations, a conjugate gradient solver (iterative method and a frontal solver (direct method have been implemented. The preprocessor required for the frontal solver is written in the modern functional programming language SML, the solver itself in C, thus exploiting the characteristic advantages of both functional and imperative programming. The speedup analysis of both solvers show very satisfactory results for this irregular problem. A mixed symbolic-numeric environment for rigid body system simulations is presented. It automatically generates C code from a problem specification expressed by the Lagrange formalism using Maple.

  10. A hybrid method for the parallel computation of Green's functions

    International Nuclear Information System (INIS)

    Petersen, Dan Erik; Li Song; Stokbro, Kurt; Sorensen, Hans Henrik B.; Hansen, Per Christian; Skelboe, Stig; Darve, Eric

    2009-01-01

    Quantum transport models for nanodevices using the non-equilibrium Green's function method require the repeated calculation of the block tridiagonal part of the Green's and lesser Green's function matrices. This problem is related to the calculation of the inverse of a sparse matrix. Because of the large number of times this calculation needs to be performed, this is computationally very expensive even on supercomputers. The classical approach is based on recurrence formulas which cannot be efficiently parallelized. This practically prevents the solution of large problems with hundreds of thousands of atoms. We propose new recurrences for a general class of sparse matrices to calculate Green's and lesser Green's function matrices which extend formulas derived by Takahashi and others. We show that these recurrences may lead to a dramatically reduced computational cost because they only require computing a small number of entries of the inverse matrix. Then, we propose a parallelization strategy for block tridiagonal matrices which involves a combination of Schur complement calculations and cyclic reduction. It achieves good scalability even on problems of modest size.

  11. Large-scale parallel genome assembler over cloud computing environment.

    Science.gov (United States)

    Das, Arghya Kusum; Koppa, Praveen Kumar; Goswami, Sayan; Platania, Richard; Park, Seung-Jong

    2017-06-01

    The size of high throughput DNA sequencing data has already reached the terabyte scale. To manage this huge volume of data, many downstream sequencing applications started using locality-based computing over different cloud infrastructures to take advantage of elastic (pay as you go) resources at a lower cost. However, the locality-based programming model (e.g. MapReduce) is relatively new. Consequently, developing scalable data-intensive bioinformatics applications using this model and understanding the hardware environment that these applications require for good performance, both require further research. In this paper, we present a de Bruijn graph oriented Parallel Giraph-based Genome Assembler (GiGA), as well as the hardware platform required for its optimal performance. GiGA uses the power of Hadoop (MapReduce) and Giraph (large-scale graph analysis) to achieve high scalability over hundreds of compute nodes by collocating the computation and data. GiGA achieves significantly higher scalability with competitive assembly quality compared to contemporary parallel assemblers (e.g. ABySS and Contrail) over traditional HPC cluster. Moreover, we show that the performance of GiGA is significantly improved by using an SSD-based private cloud infrastructure over traditional HPC cluster. We observe that the performance of GiGA on 256 cores of this SSD-based cloud infrastructure closely matches that of 512 cores of traditional HPC cluster.

  12. CX: A Scalable, Robust Network for Parallel Computing

    Directory of Open Access Journals (Sweden)

    Peter Cappello

    2002-01-01

    Full Text Available CX, a network-based computational exchange, is presented. The system's design integrates variations of ideas from other researchers, such as work stealing, non-blocking tasks, eager scheduling, and space-based coordination. The object-oriented API is simple, compact, and cleanly separates application logic from the logic that supports interprocess communication and fault tolerance. Computations, of course, run to completion in the presence of computational hosts that join and leave the ongoing computation. Such hosts, or producers, use task caching and prefetching to overlap computation with interprocessor communication. To break a potential task server bottleneck, a network of task servers is presented. Even though task servers are envisioned as reliable, the self-organizing, scalable network of n- servers, described as a sibling-connected height-balanced fat tree, tolerates a sequence of n-1 server failures. Tasks are distributed throughout the server network via a simple "diffusion" process. CX is intended as a test bed for research on automated silent auctions, reputation services, authentication services, and bonding services. CX also provides a test bed for algorithm research into network-based parallel computation.

  13. Computational design of chimeric protein libraries for directed evolution.

    Science.gov (United States)

    Silberg, Jonathan J; Nguyen, Peter Q; Stevenson, Taylor

    2010-01-01

    The best approach for creating libraries of functional proteins with large numbers of nondisruptive amino acid substitutions is protein recombination, in which structurally related polypeptides are swapped among homologous proteins. Unfortunately, as more distantly related proteins are recombined, the fraction of variants having a disrupted structure increases. One way to enrich the fraction of folded and potentially interesting chimeras in these libraries is to use computational algorithms to anticipate which structural elements can be swapped without disturbing the integrity of a protein's structure. Herein, we describe how the algorithm Schema uses the sequences and structures of the parent proteins recombined to predict the structural disruption of chimeras, and we outline how dynamic programming can be used to find libraries with a range of amino acid substitution levels that are enriched in variants with low Schema disruption.

  14. Pteros 2.0: Evolution of the fast parallel molecular analysis library for C++ and python.

    Science.gov (United States)

    Yesylevskyy, Semen O

    2015-07-15

    Pteros is the high-performance open-source library for molecular modeling and analysis of molecular dynamics trajectories. Starting from version 2.0 Pteros is available for C++ and Python programming languages with very similar interfaces. This makes it suitable for writing complex reusable programs in C++ and simple interactive scripts in Python alike. New version improves the facilities for asynchronous trajectory reading and parallel execution of analysis tasks by introducing analysis plugins which could be written in either C++ or Python in completely uniform way. The high level of abstraction provided by analysis plugins greatly simplifies prototyping and implementation of complex analysis algorithms. Pteros is available for free under Artistic License from http://sourceforge.net/projects/pteros/. © 2015 Wiley Periodicals, Inc.

  15. Routing performance analysis and optimization within a massively parallel computer

    Science.gov (United States)

    Archer, Charles Jens; Peters, Amanda; Pinnow, Kurt Walter; Swartz, Brent Allen

    2013-04-16

    An apparatus, program product and method optimize the operation of a massively parallel computer system by, in part, receiving actual performance data concerning an application executed by the plurality of interconnected nodes, and analyzing the actual performance data to identify an actual performance pattern. A desired performance pattern may be determined for the application, and an algorithm may be selected from among a plurality of algorithms stored within a memory, the algorithm being configured to achieve the desired performance pattern based on the actual performance data.

  16. Particle orbit tracking on a parallel computer: Hypertrack

    International Nuclear Information System (INIS)

    Cole, B.; Bourianoff, G.; Pilat, F.; Talman, R.

    1991-05-01

    A program has been written which performs particle orbit tracking on the Intel iPSC/860 distributed memory parallel computer. The tracking is performed using a thin element approach. A brief description of the structure and performance of the code is presented, along with applications of the code to the analysis of accelerator lattices for the SSC. The concept of ''ensemble tracking'', i.e. the tracking of ensemble averages of noninteracting particles, such as the emittance, is presented. Preliminary results of such studies will be presented. 2 refs., 6 figs

  17. Work-Efficient Parallel Skyline Computation for the GPU

    DEFF Research Database (Denmark)

    Bøgh, Kenneth Sejdenfaden; Chester, Sean; Assent, Ira

    2015-01-01

    offers the potential for parallelizing skyline computation across thousands of cores. However, attempts to port skyline algorithms to the GPU have prioritized throughput and failed to outperform sequential algorithms. In this paper, we introduce a new skyline algorithm, designed for the GPU, that uses...... a global, static partitioning scheme. With the partitioning, we can permit controlled branching to exploit transitive relationships and avoid most point-to-point comparisons. The result is a non-traditional GPU algorithm, SkyAlign, that prioritizes work-effciency and respectable throughput, rather than...

  18. Parameters that affect parallel processing for computational electromagnetic simulation codes on high performance computing clusters

    Science.gov (United States)

    Moon, Hongsik

    What is the impact of multicore and associated advanced technologies on computational software for science? Most researchers and students have multicore laptops or desktops for their research and they need computing power to run computational software packages. Computing power was initially derived from Central Processing Unit (CPU) clock speed. That changed when increases in clock speed became constrained by power requirements. Chip manufacturers turned to multicore CPU architectures and associated technological advancements to create the CPUs for the future. Most software applications benefited by the increased computing power the same way that increases in clock speed helped applications run faster. However, for Computational ElectroMagnetics (CEM) software developers, this change was not an obvious benefit - it appeared to be a detriment. Developers were challenged to find a way to correctly utilize the advancements in hardware so that their codes could benefit. The solution was parallelization and this dissertation details the investigation to address these challenges. Prior to multicore CPUs, advanced computer technologies were compared with the performance using benchmark software and the metric was FLoting-point Operations Per Seconds (FLOPS) which indicates system performance for scientific applications that make heavy use of floating-point calculations. Is FLOPS an effective metric for parallelized CEM simulation tools on new multicore system? Parallel CEM software needs to be benchmarked not only by FLOPS but also by the performance of other parameters related to type and utilization of the hardware, such as CPU, Random Access Memory (RAM), hard disk, network, etc. The codes need to be optimized for more than just FLOPs and new parameters must be included in benchmarking. In this dissertation, the parallel CEM software named High Order Basis Based Integral Equation Solver (HOBBIES) is introduced. This code was developed to address the needs of the

  19. Integrated massively parallel sequencing of 15 autosomal STRs and Amelogenin using a simplified library preparation approach.

    Science.gov (United States)

    Xue, Jian; Wu, Riga; Pan, Yajiao; Wang, Shunxia; Qu, Baowang; Qin, Ying; Shi, Yuequn; Zhang, Chuchu; Li, Ran; Zhang, Liyan; Zhou, Cheng; Sun, Hongyu

    2018-04-02

    Massively parallel sequencing (MPS) technologies, also termed as next-generation sequencing (NGS), are becoming increasingly popular in study of short tandem repeats (STR). However, current library preparation methods are usually based on ligation or two-round PCR that requires more steps, making it time-consuming (about 2 days), laborious and expensive. In this study, a 16-plex STR typing system was designed with fusion primer strategy based on the Ion Torrent S5 XL platform which could effectively resolve the above challenges for forensic DNA database-type samples (bloodstains, saliva stains, etc.). The efficiency of this system was tested in 253 Han Chinese participants. The libraries were prepared without DNA isolation and adapter ligation, and the whole process only required approximately 5 h. The proportion of thoroughly genotyped samples in which all the 16 loci were successfully genotyped was 86% (220/256). Of the samples, 99.7% showed 100% concordance between NGS-based STR typing and capillary electrophoresis (CE)-based STR typing. The inconsistency might have been caused by off-ladder alleles and mutations in primer binding sites. Overall, this panel enabled the large-scale genotyping of the DNA samples with controlled quality and quantity because it is a simple, operation-friendly process flow that saves labor, time and costs. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. Representing and computing regular languages on massively parallel networks

    Energy Technology Data Exchange (ETDEWEB)

    Miller, M.I.; O' Sullivan, J.A. (Electronic Systems and Research Lab., of Electrical Engineering, Washington Univ., St. Louis, MO (US)); Boysam, B. (Dept. of Electrical, Computer and Systems Engineering, Rensselaer Polytechnic Inst., Troy, NY (US)); Smith, K.R. (Dept. of Electrical Engineering, Southern Illinois Univ., Edwardsville, IL (US))

    1991-01-01

    This paper proposes a general method for incorporating rule-based constraints corresponding to regular languages into stochastic inference problems, thereby allowing for a unified representation of stochastic and syntactic pattern constraints. The authors' approach first established the formal connection of rules to Chomsky grammars, and generalizes the original work of Shannon on the encoding of rule-based channel sequences to Markov chains of maximum entropy. This maximum entropy probabilistic view leads to Gibb's representations with potentials which have their number of minima growing at precisely the exponential rate that the language of deterministically constrained sequences grow. These representations are coupled to stochastic diffusion algorithms, which sample the language-constrained sequences by visiting the energy minima according to the underlying Gibbs' probability law. The coupling to stochastic search methods yields the all-important practical result that fully parallel stochastic cellular automata may be derived to generate samples from the rule-based constraint sets. The production rules and neighborhood state structure of the language of sequences directly determines the necessary connection structures of the required parallel computing surface. Representations of this type have been mapped to the DAP-510 massively-parallel processor consisting of 1024 mesh-connected bit-serial processing elements for performing automated segmentation of electron-micrograph images.

  1. Parallel Computer System for 3D Visualization Stereo on GPU

    Science.gov (United States)

    Al-Oraiqat, Anas M.; Zori, Sergii A.

    2018-03-01

    This paper proposes the organization of a parallel computer system based on Graphic Processors Unit (GPU) for 3D stereo image synthesis. The development is based on the modified ray tracing method developed by the authors for fast search of tracing rays intersections with scene objects. The system allows significant increase in the productivity for the 3D stereo synthesis of photorealistic quality. The generalized procedure of 3D stereo image synthesis on the Graphics Processing Unit/Graphics Processing Clusters (GPU/GPC) is proposed. The efficiency of the proposed solutions by GPU implementation is compared with single-threaded and multithreaded implementations on the CPU. The achieved average acceleration in multi-thread implementation on the test GPU and CPU is about 7.5 and 1.6 times, respectively. Studying the influence of choosing the size and configuration of the computational Compute Unified Device Archi-tecture (CUDA) network on the computational speed shows the importance of their correct selection. The obtained experimental estimations can be significantly improved by new GPUs with a large number of processing cores and multiprocessors, as well as optimized configuration of the computing CUDA network.

  2. Parallel computing and molecular dynamics of biological membranes

    International Nuclear Information System (INIS)

    La Penna, G.; Letardi, S.; Minicozzi, V.; Morante, S.; Rossi, G.C.; Salina, G.

    1998-01-01

    In this talk I discuss the general question of the portability of molecular dynamics codes for diffusive systems on parallel computers of the APE family. The intrinsic single precision of the today available platforms does not seem to affect the numerical accuracy of the simulations, while the absence of integer addressing from CPU to individual nodes puts strong constraints on possible programming strategies. Liquids can be satisfactorily simulated using the ''systolic'' method. For more complex systems, like the biological ones at which we are ultimately interested in, the ''domain decomposition'' approach is best suited to beat the quadratic growth of the inter-molecular computational time with the number of atoms of the system. The promising perspectives of using this strategy for extensive simulations of lipid bilayers are briefly reviewed. (orig.)

  3. Parallel computation for distributed parameter system-from vector processors to Adena computer

    Energy Technology Data Exchange (ETDEWEB)

    Nogi, T

    1983-04-01

    Research on advanced parallel hardware and software architectures for very high-speed computation deserves and needs more support and attention to fulfil its promise. Novel architectures for parallel processing are being made ready. Architectures for parallel processing can be roughly divided into two groups. One is a vector processor in which a single central processing unit involves multiple vector-arithmetic registers. The other is a processor array in which slave processors are connected to a host processor to perform parallel computation. In this review, the concept and data structure of the Adena (alternating-direction edition nexus array) architecture, which is conformable to distributed-parameter simulation algorithms, are described. 5 references.

  4. Concurrent computation of attribute filters on shared memory parallel machines

    NARCIS (Netherlands)

    Wilkinson, Michael H.F.; Gao, Hui; Hesselink, Wim H.; Jonker, Jan-Eppo; Meijster, Arnold

    2008-01-01

    Morphological attribute filters have not previously been parallelized mainly because they are both global and nonseparable. We propose a parallel algorithm that achieves efficient parallelism for a large class of attribute filters, including attribute openings, closings, thinnings, and thickenings,

  5. Parallel Computation of Unsteady Flows on a Network of Workstations

    Science.gov (United States)

    1997-01-01

    Parallel computation of unsteady flows requires significant computational resources. The utilization of a network of workstations seems an efficient solution to the problem where large problems can be treated at a reasonable cost. This approach requires the solution of several problems: 1) the partitioning and distribution of the problem over a network of workstation, 2) efficient communication tools, 3) managing the system efficiently for a given problem. Of course, there is the question of the efficiency of any given numerical algorithm to such a computing system. NPARC code was chosen as a sample for the application. For the explicit version of the NPARC code both two- and three-dimensional problems were studied. Again both steady and unsteady problems were investigated. The issues studied as a part of the research program were: 1) how to distribute the data between the workstations, 2) how to compute and how to communicate at each node efficiently, 3) how to balance the load distribution. In the following, a summary of these activities is presented. Details of the work have been presented and published as referenced.

  6. Simple, parallel, high-performance virtual machines for extreme computations

    International Nuclear Information System (INIS)

    Chokoufe Nejad, Bijan; Ohl, Thorsten; Reuter, Jurgen

    2014-11-01

    We introduce a high-performance virtual machine (VM) written in a numerically fast language like Fortran or C to evaluate very large expressions. We discuss the general concept of how to perform computations in terms of a VM and present specifically a VM that is able to compute tree-level cross sections for any number of external legs, given the corresponding byte code from the optimal matrix element generator, O'Mega. Furthermore, this approach allows to formulate the parallel computation of a single phase space point in a simple and obvious way. We analyze hereby the scaling behaviour with multiple threads as well as the benefits and drawbacks that are introduced with this method. Our implementation of a VM can run faster than the corresponding native, compiled code for certain processes and compilers, especially for very high multiplicities, and has in general runtimes in the same order of magnitude. By avoiding the tedious compile and link steps, which may fail for source code files of gigabyte sizes, new processes or complex higher order corrections that are currently out of reach could be evaluated with a VM given enough computing power.

  7. Cloud identification using genetic algorithms and massively parallel computation

    Science.gov (United States)

    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. Parallel processing using an optical delay-based reservoir computer

    Science.gov (United States)

    Van der Sande, Guy; Nguimdo, Romain Modeste; Verschaffelt, Guy

    2016-04-01

    Delay systems subject to delayed optical feedback have recently shown great potential in solving computationally hard tasks. By implementing a neuro-inspired computational scheme relying on the transient response to optical data injection, high processing speeds have been demonstrated. However, reservoir computing systems based on delay dynamics discussed in the literature are designed by coupling many different stand-alone components which lead to bulky, lack of long-term stability, non-monolithic systems. Here we numerically investigate the possibility of implementing reservoir computing schemes based on semiconductor ring lasers. Semiconductor ring lasers are semiconductor lasers where the laser cavity consists of a ring-shaped waveguide. SRLs are highly integrable and scalable, making them ideal candidates for key components in photonic integrated circuits. SRLs can generate light in two counterpropagating directions between which bistability has been demonstrated. We demonstrate that two independent machine learning tasks , even with different nature of inputs with different input data signals can be simultaneously computed using a single photonic nonlinear node relying on the parallelism offered by photonics. We illustrate the performance on simultaneous chaotic time series prediction and a classification of the Nonlinear Channel Equalization. We take advantage of different directional modes to process individual tasks. Each directional mode processes one individual task to mitigate possible crosstalk between the tasks. Our results indicate that prediction/classification with errors comparable to the state-of-the-art performance can be obtained even with noise despite the two tasks being computed simultaneously. We also find that a good performance is obtained for both tasks for a broad range of the parameters. The results are discussed in detail in [Nguimdo et al., IEEE Trans. Neural Netw. Learn. Syst. 26, pp. 3301-3307, 2015

  9. Computational performance of a smoothed particle hydrodynamics simulation for shared-memory parallel computing

    Science.gov (United States)

    Nishiura, Daisuke; Furuichi, Mikito; Sakaguchi, Hide

    2015-09-01

    The computational performance of a smoothed particle hydrodynamics (SPH) simulation is investigated for three types of current shared-memory parallel computer devices: many integrated core (MIC) processors, graphics processing units (GPUs), and multi-core CPUs. We are especially interested in efficient shared-memory allocation methods for each chipset, because the efficient data access patterns differ between compute unified device architecture (CUDA) programming for GPUs and OpenMP programming for MIC processors and multi-core CPUs. We first introduce several parallel implementation techniques for the SPH code, and then examine these on our target computer architectures to determine the most effective algorithms for each processor unit. In addition, we evaluate the effective computing performance and power efficiency of the SPH simulation on each architecture, as these are critical metrics for overall performance in a multi-device environment. In our benchmark test, the GPU is found to produce the best arithmetic performance as a standalone device unit, and gives the most efficient power consumption. The multi-core CPU obtains the most effective computing performance. The computational speed of the MIC processor on Xeon Phi approached that of two Xeon CPUs. This indicates that using MICs is an attractive choice for existing SPH codes on multi-core CPUs parallelized by OpenMP, as it gains computational acceleration without the need for significant changes to the source code.

  10. The Scythe Statistical Library: An Open Source C++ Library for Statistical Computation

    Directory of Open Access Journals (Sweden)

    Daniel Pemstein

    2011-08-01

    Full Text Available The Scythe Statistical Library is an open source C++ library for statistical computation. It includes a suite of matrix manipulation functions, a suite of pseudo-random number generators, and a suite of numerical optimization routines. Programs written using Scythe are generally much faster than those written in commonly used interpreted languages, such as R and proglang{MATLAB}; and can be compiled on any system with the GNU GCC compiler (and perhaps with other C++ compilers. One of the primary design goals of the Scythe developers has been ease of use for non-expert C++ programmers. Ease of use is provided through three primary mechanisms: (1 operator and function over-loading, (2 numerous pre-fabricated utility functions, and (3 clear documentation and example programs. Additionally, Scythe is quite flexible and entirely extensible because the source code is available to all users under the GNU General Public License.

  11. Portable and Transparent Message Compression in MPI Libraries to Improve the Performance and Scalability of Parallel Applications

    Energy Technology Data Exchange (ETDEWEB)

    Albonesi, David; Burtscher, Martin

    2009-04-17

    The goal of this project has been to develop a lossless compression algorithm for message-passing libraries that can accelerate HPC systems by reducing the communication time. Because both compression and decompression have to be performed in software in real time, the algorithm has to be extremely fast while still delivering a good compression ratio. During the first half of this project, they designed a new compression algorithm called FPC for scientific double-precision data, made the source code available on the web, and published two papers describing its operation, the first in the proceedings of the Data Compression Conference and the second in the IEEE Transactions on Computers. At comparable average compression ratios, this algorithm compresses and decompresses 10 to 100 times faster than BZIP2, DFCM, FSD, GZIP, and PLMI on the three architectures tested. With prediction tables that fit into the CPU's L1 data acache, FPC delivers a guaranteed throughput of six gigabits per second on a 1.6 GHz Itanium 2 system. The C source code and documentation of FPC are posted on-line and have already been downloaded hundreds of times. To evaluate FPC, they gathered 13 real-world scientific datasets from around the globe, including satellite data, crash-simulation data, and messages from HPC systems. Based on the large number of requests they received, they also made these datasets available to the community (with permission of the original sources). While FPC represents a great step forward, it soon became clear that its throughput was too slow for the emerging 10 gigabits per second networks. Hence, no speedup can be gained by including this algorithm in an MPI library. They therefore changed the aim of the second half of the project. Instead of implementing FPC in an MPI library, they refocused their efforts to develop a parallel compression algorithm to further boost the throughput. After all, all modern high-end microprocessors contain multiple CPUs on a

  12. Pacing a data transfer operation between compute nodes on a parallel computer

    Science.gov (United States)

    Blocksome, Michael A [Rochester, MN

    2011-09-13

    Methods, systems, and products are disclosed for pacing a data transfer between compute nodes on a parallel computer that include: transferring, by an origin compute node, a chunk of an application message to a target compute node; sending, by the origin compute node, a pacing request to a target direct memory access (`DMA`) engine on the target compute node using a remote get DMA operation; determining, by the origin compute node, whether a pacing response to the pacing request has been received from the target DMA engine; and transferring, by the origin compute node, a next chunk of the application message if the pacing response to the pacing request has been received from the target DMA engine.

  13. Nordic Summer School on Parallel Computing in Optimization

    CERN Document Server

    Pardalos, Panos; Storøy, Sverre

    1997-01-01

    During the last three decades, breakthroughs in computer technology have made a tremendous impact on optimization. In particular, parallel computing has made it possible to solve larger and computationally more difficult prob­ lems. This volume contains mainly lecture notes from a Nordic Summer School held at the Linkoping Institute of Technology, Sweden in August 1995. In order to make the book more complete, a few authors were invited to contribute chapters that were not part of the course on this first occasion. The purpose of this Nordic course in advanced studies was three-fold. One goal was to introduce the students to the new achievements in a new and very active field, bring them close to world leading researchers, and strengthen their competence in an area with internationally explosive rate of growth. A second goal was to strengthen the bonds between students from different Nordic countries, and to encourage collaboration and joint research ventures over the borders. In this respect, the course bui...

  14. Efficient relaxed-Jacobi smoothers for multigrid on parallel computers

    Science.gov (United States)

    Yang, Xiang; Mittal, Rajat

    2017-03-01

    In this Technical Note, we present a family of Jacobi-based multigrid smoothers suitable for the solution of discretized elliptic equations. These smoothers are based on the idea of scheduled-relaxation Jacobi proposed recently by Yang & Mittal (2014) [18] and employ two or three successive relaxed Jacobi iterations with relaxation factors derived so as to maximize the smoothing property of these iterations. The performance of these new smoothers measured in terms of convergence acceleration and computational workload, is assessed for multi-domain implementations typical of parallelized solvers, and compared to the lexicographic point Gauss-Seidel smoother. The tests include the geometric multigrid method on structured grids as well as the algebraic grid method on unstructured grids. The tests demonstrate that unlike Gauss-Seidel, the convergence of these Jacobi-based smoothers is unaffected by domain decomposition, and furthermore, they outperform the lexicographic Gauss-Seidel by factors that increase with domain partition count.

  15. Optimized collectives using a DMA on a parallel computer

    Science.gov (United States)

    Chen, Dong [Croton On Hudson, NY; Gabor, Dozsa [Ardsley, NY; Giampapa, Mark E [Irvington, NY; Heidelberger,; Phillip, [Cortlandt Manor, NY

    2011-02-08

    Optimizing collective operations using direct memory access controller on a parallel computer, in one aspect, may comprise establishing a byte counter associated with a direct memory access controller for each submessage in a message. The byte counter includes at least a base address of memory and a byte count associated with a submessage. A byte counter associated with a submessage is monitored to determine whether at least a block of data of the submessage has been received. The block of data has a predetermined size, for example, a number of bytes. The block is processed when the block has been fully received, for example, when the byte count indicates all bytes of the block have been received. The monitoring and processing may continue for all blocks in all submessages in the message.

  16. The Impact of Information Technology on Library Anxiety: The Role of Computer Attitudes

    Directory of Open Access Journals (Sweden)

    Qun G. Jiao

    2017-09-01

    Full Text Available Over the past two decades, computer-based technologies have become dominant forces to shape and reshape the products and services the academic library has to offer. The applicationo of library technologies has had a profound impact on the way library resources are being used. Although many students continue to experience high levels of library anxiety, it is likely that the new technologies in the library have led to them experiencing other forms of negative affective states that may be, in part, a function of their attitude towards computers. This study investigates whether students' computer attitudes predict levels of library anxiety.

  17. An Accurate liver segmentation method using parallel computing algorithm

    International Nuclear Information System (INIS)

    Elbasher, Eiman Mohammed Khalied

    2014-12-01

    Computed Tomography (CT or CAT scan) is a noninvasive diagnostic imaging procedure that uses a combination of X-rays and computer technology to produce horizontal, or axial, images (often called slices) of the body. A CT scan shows detailed images of any part of the body, including the bones muscles, fat and organs CT scans are more detailed than standard x-rays. CT scans may be done with or without "contrast Contrast refers to a substance taken by mouth and/ or injected into an intravenous (IV) line that causes the particular organ or tissue under study to be seen more clearly. CT scan of the liver and biliary tract are used in the diagnosis of many diseases in the abdomen structures, particularly when another type of examination, such as X-rays, physical examination, and ultra sound is not conclusive. Unfortunately, the presence of noise and artifact in the edges and fine details in the CT images limit the contrast resolution and make diagnostic procedure more difficult. This experimental study was conducted at the College of Medical Radiological Science, Sudan University of Science and Technology and Fidel Specialist Hospital. The sample of study was included 50 patients. The main objective of this research was to study an accurate liver segmentation method using a parallel computing algorithm, and to segment liver and adjacent organs using image processing technique. The main technique of segmentation used in this study was watershed transform. The scope of image processing and analysis applied to medical application is to improve the quality of the acquired image and extract quantitative information from medical image data in an efficient and accurate way. The results of this technique agreed wit the results of Jarritt et al, (2010), Kratchwil et al, (2010), Jover et al, (2011), Yomamoto et al, (1996), Cai et al (1999), Saudha and Jayashree (2010) who used different segmentation filtering based on the methods of enhancing the computed tomography images. Anther

  18. Arc4nix: A cross-platform geospatial analytical library for cluster and cloud computing

    Science.gov (United States)

    Tang, Jingyin; Matyas, Corene J.

    2018-02-01

    Big Data in geospatial technology is a grand challenge for processing capacity. The ability to use a GIS for geospatial analysis on Cloud Computing and High Performance Computing (HPC) clusters has emerged as a new approach to provide feasible solutions. However, users lack the ability to migrate existing research tools to a Cloud Computing or HPC-based environment because of the incompatibility of the market-dominating ArcGIS software stack and Linux operating system. This manuscript details a cross-platform geospatial library "arc4nix" to bridge this gap. Arc4nix provides an application programming interface compatible with ArcGIS and its Python library "arcpy". Arc4nix uses a decoupled client-server architecture that permits geospatial analytical functions to run on the remote server and other functions to run on the native Python environment. It uses functional programming and meta-programming language to dynamically construct Python codes containing actual geospatial calculations, send them to a server and retrieve results. Arc4nix allows users to employ their arcpy-based script in a Cloud Computing and HPC environment with minimal or no modification. It also supports parallelizing tasks using multiple CPU cores and nodes for large-scale analyses. A case study of geospatial processing of a numerical weather model's output shows that arcpy scales linearly in a distributed environment. Arc4nix is open-source software.

  19. Parallelized computation for computer simulation of electrocardiograms using personal computers with multi-core CPU and general-purpose GPU.

    Science.gov (United States)

    Shen, Wenfeng; Wei, Daming; Xu, Weimin; Zhu, Xin; Yuan, Shizhong

    2010-10-01

    Biological computations like electrocardiological modelling and simulation usually require high-performance computing environments. This paper introduces an implementation of parallel computation for computer simulation of electrocardiograms (ECGs) in a personal computer environment with an Intel CPU of Core (TM) 2 Quad Q6600 and a GPU of Geforce 8800GT, with software support by OpenMP and CUDA. It was tested in three parallelization device setups: (a) a four-core CPU without a general-purpose GPU, (b) a general-purpose GPU plus 1 core of CPU, and (c) a four-core CPU plus a general-purpose GPU. To effectively take advantage of a multi-core CPU and a general-purpose GPU, an algorithm based on load-prediction dynamic scheduling was developed and applied to setting (c). In the simulation with 1600 time steps, the speedup of the parallel computation as compared to the serial computation was 3.9 in setting (a), 16.8 in setting (b), and 20.0 in setting (c). This study demonstrates that a current PC with a multi-core CPU and a general-purpose GPU provides a good environment for parallel computations in biological modelling and simulation studies. Copyright 2010 Elsevier Ireland Ltd. All rights reserved.

  20. A Computer Library for Ray Tracing in Analytical Media

    International Nuclear Information System (INIS)

    Miqueles, Eduardo; Coimbra, Tiago A; Figueiredo, J J S de

    2013-01-01

    Ray tracing technique is an important tool not only for forward but also for inverse problems in Geophysics, which most of the seismic processing steps depends on. However, implementing ray tracing codes can be very time consuming. This article presents a computer library to trace rays in 2.5D media composed by stack of layers. The velocity profile inside each layer is such that the eikonal equation can be analitically solved. Therefore, the ray tracing within such profile is made fast and accurately. The great advantage of an analytical ray tracing library is the numerical precision of the quantities computed and the fast execution of the implemented codes. Although ray tracing programs already exist for a long time, for example the seis package by Cervený, with a numerical approach to compute the ray. Regardless of the fact that numerical methods can solve more general problems, the analytical ones could be part of a more sofisticated simulation process, where the ray tracing time is completely relevant. We demonstrate the feasibility of our codes using numerical examples.

  1. Computer Assisted Circulation Control at Health Sciences Library SUNYAB

    Directory of Open Access Journals (Sweden)

    Jean K. Miller

    1972-06-01

    Full Text Available A description of the circulation system which the Health Sciences Library at the State University of New York at Buffalo has been using since October 1970. Features of the system include automatic production of overdue, fine, and billing notices; notices for call-in of requested books; and book availability notices. Remote operation and processing on the IBM 360/40 and CDC 6400 computer are accomplished via the Administrative Terminal System (ATS and Terminal job Entry (T]E. The system provides information for management of the collection and improved service to the user.

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

    Science.gov (United States)

    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.

  3. III - Template Metaprogramming for massively parallel scientific computing - Templates for Iteration; Thread-level Parallelism

    CERN Multimedia

    CERN. Geneva

    2016-01-01

    Large scale scientific computing raises questions on different levels ranging from the fomulation of the problems to the choice of the best algorithms and their implementation for a specific platform. There are similarities in these different topics that can be exploited by modern-style C++ template metaprogramming techniques to produce readable, maintainable and generic code. Traditional low-level code tend to be fast but platform-dependent, and it obfuscates the meaning of the algorithm. On the other hand, object-oriented approach is nice to read, but may come with an inherent performance penalty. These lectures aim to present he basics of the Expression Template (ET) idiom which allows us to keep the object-oriented approach without sacrificing performance. We will in particular show to to enhance ET to include SIMD vectorization. We will then introduce techniques for abstracting iteration, and introduce thread-level parallelism for use in heavy data-centric loads. We will show to to apply these methods i...

  4. An Implementation of Parallel and Networked Computing Schemes for the Real-Time Image Reconstruction Based on Electrical Tomography

    International Nuclear Information System (INIS)

    Park, Sook Hee

    2001-02-01

    This thesis implements and analyzes the parallel and networked computing libraries based on the multiprocessor computer architecture as well as networked computers, aiming at improving the computation speed of ET(Electrical Tomography) system which requires enormous CPU time in reconstructing the unknown internal state of the target object. As an instance of the typical tomography technology, ET partitions the cross-section of the target object into the tiny elements and calculates the resistivity of them with signal values measured at the boundary electrodes surrounding the surface of the object after injecting the predetermined current pattern through the object. The number of elements is determined considering the trade-off between the accuracy of the reconstructed image and the computation time. As the elements become more finer, the number of element increases, and the system can get the better image. However, the reconstruction time increases polynomially with the number of partitioned elements since the procedure consists of a number of time consuming matrix operations such as multiplication, inverse, pseudo inverse, Jacobian and so on. Consequently, the demand for improving computation speed via multiple processor grows indispensably. Moreover, currently released PCs can be stuffed with up to 4 CPUs interconnected to the shared memory while some operating systems enable the application process to benefit from such computer by allocating the threaded job to each CPU, resulting in concurrent processing. In addition, a networked computing or cluster computing environment is commonly available to almost every computer which contains communication protocol and is connected to local or global network. After partitioning the given job(numerical operation), each CPU or computer calculates the partial result independently, and the results are merged via common memory to produce the final result. It is desirable to adopt the commonly used library such as Matlab to

  5. Parallel Computational Fluid Dynamics 2007 : Implementations and Experiences on Large Scale and Grid Computing

    CERN Document Server

    2009-01-01

    At the 19th Annual Conference on Parallel Computational Fluid Dynamics held in Antalya, Turkey, in May 2007, the most recent developments and implementations of large-scale and grid computing were presented. This book, comprised of the invited and selected papers of this conference, details those advances, which are of particular interest to CFD and CFD-related communities. It also offers the results related to applications of various scientific and engineering problems involving flows and flow-related topics. Intended for CFD researchers and graduate students, this book is a state-of-the-art presentation of the relevant methodology and implementation techniques of large-scale computing.

  6. MCBooster: a library for fast Monte Carlo generation of phase-space decays on massively parallel platforms.

    Science.gov (United States)

    Alves Júnior, A. A.; Sokoloff, M. D.

    2017-10-01

    MCBooster is a header-only, C++11-compliant library that provides routines to generate and perform calculations on large samples of phase space Monte Carlo events. To achieve superior performance, MCBooster is capable to perform most of its calculations in parallel using CUDA- and OpenMP-enabled devices. MCBooster is built on top of the Thrust library and runs on Linux systems. This contribution summarizes the main features of MCBooster. A basic description of the user interface and some examples of applications are provided, along with measurements of performance in a variety of environments

  7. Use Of Computer Among Library Staff In Four Universities Of ...

    African Journals Online (AJOL)

    4) selected Universities of Technology Libraries in Northern Nigeria. Survey research was adopted with population of 151 Library staff and a random sample size of 120 staff in four (4) selected Universities of Technology Libraries in Northern ...

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

    Science.gov (United States)

    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.

  9. Parallel In Situ Indexing for Data-intensive Computing

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Jinoh; Abbasi, Hasan; Chacon, Luis; Docan, Ciprian; Klasky, Scott; Liu, Qing; Podhorszki, Norbert; Shoshani, Arie; Wu, Kesheng

    2011-09-09

    As computing power increases exponentially, vast amount of data is created by many scientific re- search activities. However, the bandwidth for storing the data to disks and reading the data from disks has been improving at a much slower pace. These two trends produce an ever-widening data access gap. Our work brings together two distinct technologies to address this data access issue: indexing and in situ processing. From decades of database research literature, we know that indexing is an effective way to address the data access issue, particularly for accessing relatively small fraction of data records. As data sets increase in sizes, more and more analysts need to use selective data access, which makes indexing an even more important for improving data access. The challenge is that most implementations of in- dexing technology are embedded in large database management systems (DBMS), but most scientific datasets are not managed by any DBMS. In this work, we choose to include indexes with the scientific data instead of requiring the data to be loaded into a DBMS. We use compressed bitmap indexes from the FastBit software which are known to be highly effective for query-intensive workloads common to scientific data analysis. To use the indexes, we need to build them first. The index building procedure needs to access the whole data set and may also require a significant amount of compute time. In this work, we adapt the in situ processing technology to generate the indexes, thus removing the need of read- ing data from disks and to build indexes in parallel. The in situ data processing system used is ADIOS, a middleware for high-performance I/O. Our experimental results show that the indexes can improve the data access time up to 200 times depending on the fraction of data selected, and using in situ data processing system can effectively reduce the time needed to create the indexes, up to 10 times with our in situ technique when using identical parallel settings.

  10. Identifying logical planes formed of compute nodes of a subcommunicator in a parallel computer

    Science.gov (United States)

    Davis, Kristan D.; Faraj, Daniel A.

    2016-03-01

    In a parallel computer, a plurality of logical planes formed of compute nodes of a subcommunicator may be identified by: for each compute node of the subcommunicator and for a number of dimensions beginning with a first dimension: establishing, by a plane building node, in a positive direction of the first dimension, all logical planes that include the plane building node and compute nodes of the subcommunicator in a positive direction of a second dimension, where the second dimension is orthogonal to the first dimension; and establishing, by the plane building node, in a negative direction of the first dimension, all logical planes that include the plane building node and compute nodes of the subcommunicator in the positive direction of the second dimension.

  11. I - Template Metaprogramming for Massively Parallel Scientific Computing - Expression Templates

    CERN Multimedia

    CERN. Geneva

    2016-01-01

    Large scale scientific computing raises questions on different levels ranging from the fomulation of the problems to the choice of the best algorithms and their implementation for a specific platform. There are similarities in these different topics that can be exploited by modern-style C++ template metaprogramming techniques to produce readable, maintainable and generic code. Traditional low-level code tend to be fast but platform-dependent, and it obfuscates the meaning of the algorithm. On the other hand, object-oriented approach is nice to read, but may come with an inherent performance penalty. These lectures aim to present he basics of the Expression Template (ET) idiom which allows us to keep the object-oriented approach without sacrificing performance. We will in particular show to to enhance ET to include SIMD vectorization. We will then introduce techniques for abstracting iteration, and introduce thread-level parallelism for use in heavy data-centric loads. We will show to to apply these methods i...

  12. Parallel multiphysics algorithms and software for computational nuclear engineering

    International Nuclear Information System (INIS)

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

    2009-01-01

    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.

  13. Adaptive Dynamic Process Scheduling on Distributed Memory Parallel Computers

    Directory of Open Access Journals (Sweden)

    Wei Shu

    1994-01-01

    Full Text Available One of the challenges in programming distributed memory parallel machines is deciding how to allocate work to processors. This problem is particularly important for computations with unpredictable dynamic behaviors or irregular structures. We present a scheme for dynamic scheduling of medium-grained processes that is useful in this context. The adaptive contracting within neighborhood (ACWN is a dynamic, distributed, load-dependent, and scalable scheme. It deals with dynamic and unpredictable creation of processes and adapts to different systems. The scheme is described and contrasted with two other schemes that have been proposed in this context, namely the randomized allocation and the gradient model. The performance of the three schemes on an Intel iPSC/2 hypercube is presented and analyzed. The experimental results show that even though the ACWN algorithm incurs somewhat larger overhead than the randomized allocation, it achieves better performance in most cases due to its adaptiveness. Its feature of quickly spreading the work helps it outperform the gradient model in performance and scalability.

  14. Numerical studies on the interaction between atmosphere and ocean using different kinds of parallel computers

    International Nuclear Information System (INIS)

    Lee, Soon-Hwan; Chino, Masamichi

    2000-01-01

    The coupling between atmosphere and ocean model has physical and computational difficulties for short-term forecasting of weather and ocean current. In this research, a combination system between high-resolution meso-scale atmospheric model and ocean model has been constructed using a new message-passing library, called Stampi (Seamless Thinking Aid Message Passing Interface), for prediction of particle dispersion at emergency nuclear accident. Stampi, which is based on the MPI (Message Passing Interface) 2 specification, makes us carry out parallel calculations of combination system without parallelization skill to model code. And it realizes dynamic process creation on different machines and communication between spawned one within the scope of MPI semantics. The models included in this combination system are PHYSIC as an atmosphere model, and POM (Princeton Ocean Model) as an ocean model. We applied this combination system to predict sea surface current at Sea of Japan in winter season. Simulation results indicate that the wind stress near the sea surface tends to be a predominant factor to determine surface ocean currents and dispersion of radioactive contamination in the ocean. The surface ocean current is well correspondent with wind direction, induced by high mountains at North Korea. The satellite data of NSCAT (NASA-SCATterometer), which is an image of sea surface current, also agrees well with the results of this system. (author)

  15. Parallel computing of a climate model on the dawn 1000 by domain decomposition method

    Science.gov (United States)

    Bi, Xunqiang

    1997-12-01

    In this paper the parallel computing of a grid-point nine-level atmospheric general circulation model on the Dawn 1000 is introduced. The model was developed by the Institute of Atmospheric Physics (IAP), Chinese Academy of Sciences (CAS). The Dawn 1000 is a MIMD massive parallel computer made by National Research Center for Intelligent Computer (NCIC), CAS. A two-dimensional domain decomposition method is adopted to perform the parallel computing. The potential ways to increase the speed-up ratio and exploit more resources of future massively parallel supercomputation are also discussed.

  16. Parallel computing for data science with examples in R, C++ and CUDA

    CERN Document Server

    Matloff, Norman

    2015-01-01

    Parallel Computing for Data Science: With Examples in R, C++ and CUDA is one of the first parallel computing books to concentrate exclusively on parallel data structures, algorithms, software tools, and applications in data science. It includes examples not only from the classic ""n observations, p variables"" matrix format but also from time series, network graph models, and numerous other structures common in data science. The examples illustrate the range of issues encountered in parallel programming.With the main focus on computation, the book shows how to compute on three types of platfor

  17. Endpoint-based parallel data processing with non-blocking collective instructions in a parallel active messaging interface of a parallel computer

    Science.gov (United States)

    Archer, Charles J; Blocksome, Michael A; Cernohous, Bob R; Ratterman, Joseph D; Smith, Brian E

    2014-11-11

    Endpoint-based parallel data processing with non-blocking collective instructions in a PAMI of a parallel computer is disclosed. The PAMI is composed of data communications endpoints, each including a specification of data communications parameters for a thread of execution on a compute node, including specifications of a client, a context, and a task. The compute nodes are coupled for data communications through the PAMI. The parallel application establishes a data communications geometry specifying a set of endpoints that are used in collective operations of the PAMI by associating with the geometry a list of collective algorithms valid for use with the endpoints of the geometry; registering in each endpoint in the geometry a dispatch callback function for a collective operation; and executing without blocking, through a single one of the endpoints in the geometry, an instruction for the collective operation.

  18. Parallel Synthesis of a Library of Symmetrically- and Dissymmetrically-disubstituted Imidazole-4,5-dicarboxamides Bearing Amino Acid Esters

    Directory of Open Access Journals (Sweden)

    Rosanna Solinas

    2009-01-01

    Full Text Available The imidazole-4,5-dicarboxylic acid scaffold is readily derivatized with amino acid esters to afford symmetrically- and dissymmetrically-disubstituted imidazole-4,5-dicarboxamides with intramolecularly hydrogen bonded conformations that predispose the presentation of amino acid pharmacophores. In this work, a total of 45 imidazole-4,5-dicarboxamides bearing amino acid esters were prepared by parallel synthesis. The library members were purified by column chromatography on silica gel and the purified compounds characterized by LC-MS with LC detection at 214 nm. A selection of the final compounds was also analyzed by 1H-NMR spectroscopy. The analytically pure final products have been submitted to the Molecular Library Small Molecule Repository (MLSMR for screening in the Molecular Library Screening Center Network (MLSCN as part of the NIH Roadmap.

  19. Introduction to massively-parallel computing in high-energy physics

    CERN Document Server

    AUTHOR|(CDS)2083520

    1993-01-01

    Ever since computers were first used for scientific and numerical work, there has existed an "arms race" between the technical development of faster computing hardware, and the desires of scientists to solve larger problems in shorter time-scales. However, the vast leaps in processor performance achieved through advances in semi-conductor science have reached a hiatus as the technology comes up against the physical limits of the speed of light and quantum effects. This has lead all high performance computer manufacturers to turn towards a parallel architecture for their new machines. In these lectures we will introduce the history and concepts behind parallel computing, and review the various parallel architectures and software environments currently available. We will then introduce programming methodologies that allow efficient exploitation of parallel machines, and present case studies of the parallelization of typical High Energy Physics codes for the two main classes of parallel computing architecture (S...

  20. Parallel Computation of the Jacobian Matrix for Nonlinear Equation Solvers Using MATLAB

    Science.gov (United States)

    Rose, Geoffrey K.; Nguyen, Duc T.; Newman, Brett A.

    2017-01-01

    Demonstrating speedup for parallel code on a multicore shared memory PC can be challenging in MATLAB due to underlying parallel operations that are often opaque to the user. This can limit potential for improvement of serial code even for the so-called embarrassingly parallel applications. One such application is the computation of the Jacobian matrix inherent to most nonlinear equation solvers. Computation of this matrix represents the primary bottleneck in nonlinear solver speed such that commercial finite element (FE) and multi-body-dynamic (MBD) codes attempt to minimize computations. A timing study using MATLAB's Parallel Computing Toolbox was performed for numerical computation of the Jacobian. Several approaches for implementing parallel code were investigated while only the single program multiple data (spmd) method using composite objects provided positive results. Parallel code speedup is demonstrated but the goal of linear speedup through the addition of processors was not achieved due to PC architecture.

  1. Kmerind: A Flexible Parallel Library for K-mer Indexing of Biological Sequences on Distributed Memory Systems.

    Science.gov (United States)

    Pan, Tony; Flick, Patrick; Jain, Chirag; Liu, Yongchao; Aluru, Srinivas

    2017-10-09

    Counting and indexing fixed length substrings, or k-mers, in biological sequences is a key step in many bioinformatics tasks including genome alignment and mapping, genome assembly, and error correction. While advances in next generation sequencing technologies have dramatically reduced the cost and improved latency and throughput, few bioinformatics tools can efficiently process the datasets at the current generation rate of 1.8 terabases every 3 days. We present Kmerind, a high performance parallel k-mer indexing library for distributed memory environments. The Kmerind library provides a set of simple and consistent APIs with sequential semantics and parallel implementations that are designed to be flexible and extensible. Kmerind's k-mer counter performs similarly or better than the best existing k-mer counting tools even on shared memory systems. In a distributed memory environment, Kmerind counts k-mers in a 120 GB sequence read dataset in less than 13 seconds on 1024 Xeon CPU cores, and fully indexes their positions in approximately 17 seconds. Querying for 1% of the k-mers in these indices can be completed in 0.23 seconds and 28 seconds, respectively. Kmerind is the first k-mer indexing library for distributed memory environments, and the first extensible library for general k-mer indexing and counting. Kmerind is available at https://github.com/ParBLiSS/kmerind.

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  3. An object-oriented programming paradigm for parallelization of computational fluid dynamics

    International Nuclear Information System (INIS)

    Ohta, Takashi.

    1997-03-01

    We propose an object-oriented programming paradigm for parallelization of scientific computing programs, and show that the approach can be a very useful strategy. Generally, parallelization of scientific programs tends to be complicated and unportable due to the specific requirements of each parallel computer or compiler. In this paper, we show that the object-oriented programming design, which separates the parallel processing parts from the solver of the applications, can achieve the large improvement in the maintenance of the codes, as well as the high portability. We design the program for the two-dimensional Euler equations according to the paradigm, and evaluate the parallel performance on IBM SP2. (author)

  4. Parallelization of MCNP 4, a Monte Carlo neutron and photon transport code system, in highly parallel distributed memory type computer

    International Nuclear Information System (INIS)

    Masukawa, Fumihiro; Takano, Makoto; Naito, Yoshitaka; Yamazaki, Takao; Fujisaki, Masahide; Suzuki, Koichiro; Okuda, Motoi.

    1993-11-01

    In order to improve the accuracy and calculating speed of shielding analyses, MCNP 4, a Monte Carlo neutron and photon transport code system, has been parallelized and measured of its efficiency in the highly parallel distributed memory type computer, AP1000. The code has been analyzed statically and dynamically, then the suitable algorithm for parallelization has been determined for the shielding analysis functions of MCNP 4. This includes a strategy where a new history is assigned to the idling processor element dynamically during the execution. Furthermore, to avoid the congestion of communicative processing, the batch concept, processing multi-histories by a unit, has been introduced. By analyzing a sample cask problem with 2,000,000 histories by the AP1000 with 512 processor elements, the 82 % of parallelization efficiency is achieved, and the calculational speed has been estimated to be around 50 times as fast as that of FACOM M-780. (author)

  5. Evaluation of DEC`s GIGAswitch for distributed parallel computing

    Energy Technology Data Exchange (ETDEWEB)

    Chen, H.; Hutchins, J.; Brandt, J.

    1993-10-01

    One of Sandia`s research efforts is to reduce the end-to-end communication delay in a parallel-distributed computing environment. GIGAswitch is DEC`s implementation of a gigabit local area network based on switched FDDI technology. Using the GIGAswitch, the authors intend to minimize the medium access latency suffered by shared-medium FDDI technology. Experimental results show that the GIGAswitch adds 16.5 microseconds of switching and bridging delay to an end-to-end communication. Although the added latency causes a 1.8% throughput degradation and a 5% line efficiency degradation, the availability of dedicated bandwidth is much more than what is available to a workstation on a shared medium. For example, ten directly connected workstations each would have a dedicated bandwidth of 95 Mbps, but if they were sharing the FDDI bandwidth, each would have 10% of the total bandwidth, i.e., less than 10 Mbps. In addition, they have found that when there is no output port contention, the switch`s aggregate bandwidth will scale up to multiples of its port bandwidth. However, with output port contention, the throughput and latency performance suffered significantly. Their mathematical and simulation models indicate that the GIGAswitch line efficiency could be as low as 63% when there are nine input ports contending for the same output port. The data indicate that the delay introduced by contention at the server workstation is 50 times that introduced by the GIGAswitch. The authors conclude that the GIGAswitch meets the performance requirements of today`s high-end workstations and that the switched FDDI technology provides an alternative that utilizes existing workstation interfaces while increasing the aggregate bandwidth. However, because the speed of workstations is increasing by a factor of 2 every 1.5 years, the switched FDDI technology is only good as an interim solution.

  6. Parallel Sequencing of Expressed Sequence Tags from Two Complementary DNA Libraries for High and Low Phosphorus Adaptation in Common Beans

    Directory of Open Access Journals (Sweden)

    Matthew W. Blair

    2011-11-01

    Full Text Available Expressed sequence tags (ESTs have proven useful for gene discovery in many crops. In this work, our objective was to construct complementary DNA (cDNA libraries from root tissues of common beans ( L. grown under low and high P hydroponic conditions and to conduct EST sequencing and comparative analyses of the libraries. Expressed sequence tag analysis of 3648 clones identified 2372 unigenes, of which 1591 were annotated as known genes while a total of 465 unigenes were not associated with any known gene. Unigenes with hits were categorized according to biological processes, molecular function, and cellular compartmentalization. Given the young tissue used to make the root libraries, genes for catalytic activity and binding were highly expressed. Comparisons with previous root EST sequencing and between the two libraries made here resulted in a set of genes to study further for differential gene expression and adaptation to low P, such as a 14 kDa praline-rich protein, a metallopeptidase, tonoplast intrinsic protein, adenosine triphosphate (ATP citrate synthase, and cell proliferation genes expressed in the low P treated plants. Given that common beans are often grown on acid soils of the tropics and subtropics that are usually low in P these genes and the two parallel libraries will be useful for selection for better uptake of this essential macronutrient. The importance of EST generation for common bean root tissues under low P and other abiotic soil stresses is also discussed.

  7. Issues in developing parallel iterative algorithms for solving partial differential equations on a (transputer-based) distributed parallel computing system

    International Nuclear Information System (INIS)

    Rajagopalan, S.; Jethra, A.; Khare, A.N.; Ghodgaonkar, M.D.; Srivenkateshan, R.; Menon, S.V.G.

    1990-01-01

    Issues relating to implementing iterative procedures, for numerical solution of elliptic partial differential equations, on a distributed parallel computing system are discussed. Preliminary investigations show that a speed-up of about 3.85 is achievable on a four transputer pipeline network. (author). 2 figs., 3 a ppendixes., 7 refs

  8. Simulating Hydrologic Flow and Reactive Transport with PFLOTRAN and PETSc on Emerging Fine-Grained Parallel Computer Architectures

    Science.gov (United States)

    Mills, R. T.; Rupp, K.; Smith, B. F.; Brown, J.; Knepley, M.; Zhang, H.; Adams, M.; Hammond, G. E.

    2017-12-01

    As the high-performance computing community pushes towards the exascale horizon, power and heat considerations have driven the increasing importance and prevalence of fine-grained parallelism in new computer architectures. High-performance computing centers have become increasingly reliant on GPGPU accelerators and "manycore" processors such as the Intel Xeon Phi line, and 512-bit SIMD registers have even been introduced in the latest generation of Intel's mainstream Xeon server processors. The high degree of fine-grained parallelism and more complicated memory hierarchy considerations of such "manycore" processors present several challenges to existing scientific software. Here, we consider how the massively parallel, open-source hydrologic flow and reactive transport code PFLOTRAN - and the underlying Portable, Extensible Toolkit for Scientific Computation (PETSc) library on which it is built - can best take advantage of such architectures. We will discuss some key features of these novel architectures and our code optimizations and algorithmic developments targeted at them, and present experiences drawn from working with a wide range of PFLOTRAN benchmark problems on these architectures.

  9. Engineering Computer Games: A Parallel Learning Opportunity for Undergraduate Engineering and Primary (K-5 Students

    Directory of Open Access Journals (Sweden)

    Mark Michael Budnik

    2011-04-01

    Full Text Available In this paper, we present how our College of Engineering is developing a growing portfolio of engineering computer games as a parallel learning opportunity for undergraduate engineering and primary (grade K-5 students. Around the world, many schools provide secondary students (grade 6-12 with opportunities to pursue pre-engineering classes. However, by the time students reach this age, many of them have already determined their educational goals and preferred careers. Our College of Engineering is developing resources to provide primary students, still in their educational formative years, with opportunities to learn more about engineering. One of these resources is a library of engineering games targeted to the primary student population. The games are designed by sophomore students in our College of Engineering. During their Introduction to Computational Techniques course, the students use the LabVIEW environment to develop the games. This software provides a wealth of design resources for the novice programmer; using it to develop the games strengthens the undergraduates

  10. 3D streamers simulation in a pin to plane configuration using massively parallel computing

    Science.gov (United States)

    Plewa, J.-M.; Eichwald, O.; Ducasse, O.; Dessante, P.; Jacobs, C.; Renon, N.; Yousfi, M.

    2018-03-01

    This paper concerns the 3D simulation of corona discharge using high performance computing (HPC) managed with the message passing interface (MPI) library. In the field of finite volume methods applied on non-adaptive mesh grids and in the case of a specific 3D dynamic benchmark test devoted to streamer studies, the great efficiency of the iterative R&B SOR and BiCGSTAB methods versus the direct MUMPS method was clearly demonstrated in solving the Poisson equation using HPC resources. The optimization of the parallelization and the resulting scalability was undertaken as a function of the HPC architecture for a number of mesh cells ranging from 8 to 512 million and a number of cores ranging from 20 to 1600. The R&B SOR method remains at least about four times faster than the BiCGSTAB method and requires significantly less memory for all tested situations. The R&B SOR method was then implemented in a 3D MPI parallelized code that solves the classical first order model of an atmospheric pressure corona discharge in air. The 3D code capabilities were tested by following the development of one, two and four coplanar streamers generated by initial plasma spots for 6 ns. The preliminary results obtained allowed us to follow in detail the formation of the tree structure of a corona discharge and the effects of the mutual interactions between the streamers in terms of streamer velocity, trajectory and diameter. The computing time for 64 million of mesh cells distributed over 1000 cores using the MPI procedures is about 30 min ns-1, regardless of the number of streamers.

  11. ALOHA: Automatic libraries of helicity amplitudes for Feynman diagram computations

    Science.gov (United States)

    de Aquino, Priscila; Link, William; Maltoni, Fabio; Mattelaer, Olivier; Stelzer, Tim

    2012-10-01

    We present an application that automatically writes the HELAS (HELicity Amplitude Subroutines) library corresponding to the Feynman rules of any quantum field theory Lagrangian. The code is written in Python and takes the Universal FeynRules Output (UFO) as an input. From this input it produces the complete set of routines, wave-functions and amplitudes, that are needed for the computation of Feynman diagrams at leading as well as at higher orders. The representation is language independent and currently it can output routines in Fortran, C++, and Python. A few sample applications implemented in the MADGRAPH 5 framework are presented. Program summary Program title: ALOHA Catalogue identifier: AEMS_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEMS_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: http://www.opensource.org/licenses/UoI-NCSA.php No. of lines in distributed program, including test data, etc.: 6094320 No. of bytes in distributed program, including test data, etc.: 7479819 Distribution format: tar.gz Programming language: Python2.6 Computer: 32/64 bit Operating system: Linux/Mac/Windows RAM: 512 Mbytes Classification: 4.4, 11.6 Nature of problem: An effcient numerical evaluation of a squared matrix element can be done with the help of the helicity routines implemented in the HELAS library [1]. This static library contains a limited number of helicity functions and is therefore not always able to provide the needed routine in the presence of an arbitrary interaction. This program provides a way to automatically create the corresponding routines for any given model. Solution method: ALOHA takes the Feynman rules associated to the vertex obtained from the model information (in the UFO format [2]), and multiplies it by the different wavefunctions or propagators. As a result the analytical expression of the helicity routines is obtained. Subsequently, this expression is

  12. DIMACS Workshop on Interconnection Networks and Mapping, and Scheduling Parallel Computations

    CERN Document Server

    Rosenberg, Arnold L; Sotteau, Dominique; NSF Science and Technology Center in Discrete Mathematics and Theoretical Computer Science; Interconnection networks and mapping and scheduling parallel computations

    1995-01-01

    The interconnection network is one of the most basic components of a massively parallel computer system. Such systems consist of hundreds or thousands of processors interconnected to work cooperatively on computations. One of the central problems in parallel computing is the task of mapping a collection of processes onto the processors and routing network of a parallel machine. Once this mapping is done, it is critical to schedule computations within and communication among processor from universities and laboratories, as well as practitioners involved in the design, implementation, and application of massively parallel systems. Focusing on interconnection networks of parallel architectures of today and of the near future , the book includes topics such as network topologies,network properties, message routing, network embeddings, network emulation, mappings, and efficient scheduling. inputs for a process are available where and when the process is scheduled to be computed. This book contains the refereed pro...

  13. A platform independent communication library for distributed computing

    NARCIS (Netherlands)

    Groen, D.; Rieder, S.; Grosso, P.; de Laat, C.; Portegies Zwart, S.

    2010-01-01

    We present MPWide, a platform independent communication library for performing message passing between supercomputers. Our library couples several local MPI applications through a long distance network using, for example, optical links. The implementation is deliberately kept light-weight, platform

  14. A method of paralleling computer calculation for two-dimensional kinetic plasma model

    International Nuclear Information System (INIS)

    Brazhnik, V.A.; Demchenko, V.V.; Dem'yanov, V.G.; D'yakov, V.E.; Ol'shanskij, V.V.; Panchenko, V.I.

    1987-01-01

    A method for parallel computer calculation and OSIRIS program complex realizing it and designed for numerical plasma simulation by the macroparticle method are described. The calculation can be carried out either with one or simultaneously with two computers BESM-6, that is provided by some package of interacting programs functioning in every computer. Program interaction in every computer is based on event techniques realized in OS DISPAK. Parallel computer calculation with two BESM-6 computers allows to accelerate the computation 1.5 times

  15. Cooperative storage of shared files in a parallel computing system with dynamic block size

    Science.gov (United States)

    Bent, John M.; Faibish, Sorin; Grider, Gary

    2015-11-10

    Improved techniques are provided for parallel writing of data to a shared object in a parallel computing system. A method is provided for storing data generated by a plurality of parallel processes to a shared object in a parallel computing system. The method is performed by at least one of the processes and comprises: dynamically determining a block size for storing the data; exchanging a determined amount of the data with at least one additional process to achieve a block of the data having the dynamically determined block size; and writing the block of the data having the dynamically determined block size to a file system. The determined block size comprises, e.g., a total amount of the data to be stored divided by the number of parallel processes. The file system comprises, for example, a log structured virtual parallel file system, such as a Parallel Log-Structured File System (PLFS).

  16. TerraFERMA: Harnessing Advanced Computational Libraries in Earth Science

    Science.gov (United States)

    Wilson, C. R.; Spiegelman, M.; van Keken, P.

    2012-12-01

    Many important problems in Earth sciences can be described by non-linear coupled systems of partial differential equations. These "multi-physics" problems include thermo-chemical convection in Earth and planetary interiors, interactions of fluids and magmas with the Earth's mantle and crust and coupled flow of water and ice. These problems are of interest to a large community of researchers but are complicated to model and understand. Much of this complexity stems from the nature of multi-physics where small changes in the coupling between variables or constitutive relations can lead to radical changes in behavior, which in turn affect critical computational choices such as discretizations, solvers and preconditioners. To make progress in understanding such coupled systems requires a computational framework where multi-physics problems can be described at a high-level while maintaining the flexibility to easily modify the solution algorithm. Fortunately, recent advances in computational science provide a basis for implementing such a framework. Here we present the Transparent Finite Element Rapid Model Assembler (TerraFERMA), which leverages several advanced open-source libraries for core functionality. FEniCS (fenicsproject.org) provides a high level language for describing the weak forms of coupled systems of equations, and an automatic code generator that produces finite element assembly code. PETSc (www.mcs.anl.gov/petsc) provides a wide range of scalable linear and non-linear solvers that can be composed into effective multi-physics preconditioners. SPuD (amcg.ese.ic.ac.uk/Spud) is an application neutral options system that provides both human and machine-readable interfaces based on a single xml schema. Our software integrates these libraries and provides the user with a framework for exploring multi-physics problems. A single options file fully describes the problem, including all equations, coefficients and solver options. Custom compiled applications are

  17. libmpdata++ 1.0: a library of parallel MPDATA solvers for systems of generalised transport equations

    Science.gov (United States)

    Jaruga, A.; Arabas, S.; Jarecka, D.; Pawlowska, H.; Smolarkiewicz, P. K.; Waruszewski, M.

    2015-04-01

    This paper accompanies the first release of libmpdata++, a C++ library implementing the multi-dimensional positive-definite advection transport algorithm (MPDATA) on regular structured grid. The library offers basic numerical solvers for systems of generalised transport equations. The solvers are forward-in-time, conservative and non-linearly stable. The libmpdata++ library covers the basic second-order-accurate formulation of MPDATA, its third-order variant, the infinite-gauge option for variable-sign fields and a flux-corrected transport extension to guarantee non-oscillatory solutions. The library is equipped with a non-symmetric variational elliptic solver for implicit evaluation of pressure gradient terms. All solvers offer parallelisation through domain decomposition using shared-memory parallelisation. The paper describes the library programming interface, and serves as a user guide. Supported options are illustrated with benchmarks discussed in the MPDATA literature. Benchmark descriptions include code snippets as well as quantitative representations of simulation results. Examples of applications include homogeneous transport in one, two and three dimensions in Cartesian and spherical domains; a shallow-water system compared with analytical solution (originally derived for a 2-D case); and a buoyant convection problem in an incompressible Boussinesq fluid with interfacial instability. All the examples are implemented out of the library tree. Regardless of the differences in the problem dimensionality, right-hand-side terms, boundary conditions and parallelisation approach, all the examples use the same unmodified library, which is a key goal of libmpdata++ design. The design, based on the principle of separation of concerns, prioritises the user and developer productivity. The libmpdata++ library is implemented in C++, making use of the Blitz++ multi-dimensional array containers, and is released as free/libre and open-source software.

  18. libmpdata++ 0.1: a library of parallel MPDATA solvers for systems of generalised transport equations

    Science.gov (United States)

    Jaruga, A.; Arabas, S.; Jarecka, D.; Pawlowska, H.; Smolarkiewicz, P. K.; Waruszewski, M.

    2014-11-01

    This paper accompanies first release of libmpdata++, a C++ library implementing the Multidimensional Positive-Definite Advection Transport Algorithm (MPDATA). The library offers basic numerical solvers for systems of generalised transport equations. The solvers are forward-in-time, conservative and non-linearly stable. The libmpdata++ library covers the basic second-order-accurate formulation of MPDATA, its third-order variant, the infinite-gauge option for variable-sign fields and a flux-corrected transport extension to guarantee non-oscillatory solutions. The library is equipped with a non-symmetric variational elliptic solver for implicit evaluation of pressure gradient terms. All solvers offer parallelisation through domain decomposition using shared-memory parallelisation. The paper describes the library programming interface, and serves as a user guide. Supported options are illustrated with benchmarks discussed in the MPDATA literature. Benchmark descriptions include code snippets as well as quantitative representations of simulation results. Examples of applications include: homogeneous transport in one, two and three dimensions in Cartesian and spherical domains; shallow-water system compared with analytical solution (originally derived for a 2-D case); and a buoyant convection problem in an incompressible Boussinesq fluid with interfacial instability. All the examples are implemented out of the library tree. Regardless of the differences in the problem dimensionality, right-hand-side terms, boundary conditions and parallelisation approach, all the examples use the same unmodified library, which is a key goal of libmpdata++ design. The design, based on the principle of separation of concerns, prioritises the user and developer productivity. The libmpdata++ library is implemented in C++, making use of the Blitz++ multi-dimensional array containers, and is released as free/libre and open-source software.

  19. CARP: a computer code and albedo data library for use by BREESE, the MORSE albedo package

    International Nuclear Information System (INIS)

    Emmett, M.B.; Rhoades, W.A.

    1978-10-01

    The CARP computer code was written to allow processing of DOT angular flux tapes to produce albedo data for use in the MORSE computer code. An albedo data library was produced containing several materials. 3 tables

  20. Experiences Using an Open Source Software Library to Teach Computer Vision Subjects

    Science.gov (United States)

    Cazorla, Miguel; Viejo, Diego

    2015-01-01

    Machine vision is an important subject in computer science and engineering degrees. For laboratory experimentation, it is desirable to have a complete and easy-to-use tool. In this work we present a Java library, oriented to teaching computer vision. We have designed and built the library from the scratch with emphasis on readability and…

  1. Computer Software: Copyright and Licensing Considerations for Schools and Libraries. ERIC Digest.

    Science.gov (United States)

    Reed, Mary Hutchings

    This digest notes that the terms and conditions of computer software package license agreements control the use of software in schools and libraries, and examines the implications of computer software license agreements for classroom use and for library lending policies. Guidelines are provided for interpreting the Copyright Act, and insuring the…

  2. Computational hybrid anthropometric paediatric phantom library for internal radiation dosimetry

    Science.gov (United States)

    Xie, Tianwu; Kuster, Niels; Zaidi, Habib

    2017-04-01

    Hybrid computational phantoms combine voxel-based and simplified equation-based modelling approaches to provide unique advantages and more realism for the construction of anthropomorphic models. In this work, a methodology and C++ code are developed to generate hybrid computational phantoms covering statistical distributions of body morphometry in the paediatric population. The paediatric phantoms of the Virtual Population Series (IT’IS Foundation, Switzerland) were modified to match target anthropometric parameters, including body mass, body length, standing height and sitting height/stature ratio, determined from reference databases of the National Centre for Health Statistics and the National Health and Nutrition Examination Survey. The phantoms were selected as representative anchor phantoms for the newborn, 1, 2, 5, 10 and 15 years-old children, and were subsequently remodelled to create 1100 female and male phantoms with 10th, 25th, 50th, 75th and 90th body morphometries. Evaluation was performed qualitatively using 3D visualization and quantitatively by analysing internal organ masses. Overall, the newly generated phantoms appear very reasonable and representative of the main characteristics of the paediatric population at various ages and for different genders, body sizes and sitting stature ratios. The mass of internal organs increases with height and body mass. The comparison of organ masses of the heart, kidney, liver, lung and spleen with published autopsy and ICRP reference data for children demonstrated that they follow the same trend when correlated with age. The constructed hybrid computational phantom library opens up the prospect of comprehensive radiation dosimetry calculations and risk assessment for the paediatric population of different age groups and diverse anthropometric parameters.

  3. Event Based Simulator for Parallel Computing over the Wide Area Network for Real Time Visualization

    Science.gov (United States)

    Sundararajan, Elankovan; Harwood, Aaron; Kotagiri, Ramamohanarao; Satria Prabuwono, Anton

    As the computational requirement of applications in computational science continues to grow tremendously, the use of computational resources distributed across the Wide Area Network (WAN) becomes advantageous. However, not all applications can be executed over the WAN due to communication overhead that can drastically slowdown the computation. In this paper, we introduce an event based simulator to investigate the performance of parallel algorithms executed over the WAN. The event based simulator known as SIMPAR (SIMulator for PARallel computation), simulates the actual computations and communications involved in parallel computation over the WAN using time stamps. Visualization of real time applications require steady stream of processed data flow for visualization purposes. Hence, SIMPAR may prove to be a valuable tool to investigate types of applications and computing resource requirements to provide uninterrupted flow of processed data for real time visualization purposes. The results obtained from the simulation show concurrence with the expected performance using the L-BSP model.

  4. A Parallel and Distributed Surrogate Model Implementation for Computational Steering

    KAUST Repository

    Butnaru, Daniel; Buse, Gerrit; Pfluger, Dirk

    2012-01-01

    of the input parameters. Such an exploration process is however not possible if the simulation is computationally too expensive. For these cases we present in this paper a scalable computational steering approach utilizing a fast surrogate model as substitute

  5. Using parallel computing in modeling and optimization of mineral ...

    African Journals Online (AJOL)

    Then to solve ultimate pit limit problem it is required to find such a sub graph in a graph whose sum of weights will be maximal. One of the possible solutions of this problem is using genetic algorithms. We use a ... Details of implementation parallel genetic algorithm for searching open pit limits are provided. Comparison with ...

  6. Computation of watersheds based on parallel graph algorithms

    NARCIS (Netherlands)

    Meijster, A.; Roerdink, J.B.T.M.; Maragos, P; Schafer, RW; Butt, MA

    1996-01-01

    In this paper the implementation of a parallel watershed algorithm is described. The algorithm has been implemented on a Cray J932, which is a shared memory architecture with 32 processors. The watershed transform has generally been considered to be inherently sequential, but recently a few research

  7. Locating hardware faults in a data communications network of a parallel computer

    Science.gov (United States)

    Archer, Charles J.; Megerian, Mark G.; Ratterman, Joseph D.; Smith, Brian E.

    2010-01-12

    Hardware faults location in a data communications network of a parallel computer. Such a parallel computer includes a plurality of compute nodes and a data communications network that couples the compute nodes for data communications and organizes the compute node as a tree. Locating hardware faults includes identifying a next compute node as a parent node and a root of a parent test tree, identifying for each child compute node of the parent node a child test tree having the child compute node as root, running a same test suite on the parent test tree and each child test tree, and identifying the parent compute node as having a defective link connected from the parent compute node to a child compute node if the test suite fails on the parent test tree and succeeds on all the child test trees.

  8. UMPHE: A Library for Effective Computing On Encrypted Data

    Directory of Open Access Journals (Sweden)

    Philipp Borisovich Burtyka

    2016-03-01

    Full Text Available The paper describes the design and implementation of a new software library that implements fully homomorphic encryption schemes based on unilateral matrix polynomials. The library is written in C++ using the NTL mathematical library and has multilayer structure. The main focus is on optimizations and batching techniques. The paper presents novel encryption and key generation algorithms for matrix polynomial based cryptosystems and techniques for data movement between the slots of the ciphertext.

  9. Parallel Algorithms for Monte Carlo Particle Transport Simulation on Exascale Computing Architectures

    Science.gov (United States)

    Romano, Paul Kollath

    measured data from simulations in OpenMC on a full-core benchmark problem. Finally, a novel algorithm for decomposing large tally data was proposed, analyzed, and implemented/tested in OpenMC. The algorithm relies on disjoint sets of compute processes and tally servers. The analysis showed that for a range of parameters relevant to LWR analysis, the tally server algorithm should perform with minimal overhead. Tests were performed on Intrepid and Titan and demonstrated that the algorithm did indeed perform well over a wide range of parameters. (Copies available exclusively from MIT Libraries, libraries.mit.edu/docs - docs mit.edu)

  10. HONEI: A collection of libraries for numerical computations targeting multiple processor architectures

    Science.gov (United States)

    van Dyk, Danny; Geveler, Markus; Mallach, Sven; Ribbrock, Dirk; Göddeke, Dominik; Gutwenger, Carsten

    2009-12-01

    We present HONEI, an open-source collection of libraries offering a hardware oriented approach to numerical calculations. HONEI abstracts the hardware, and applications written on top of HONEI can be executed on a wide range of computer architectures such as CPUs, GPUs and the Cell processor. We demonstrate the flexibility and performance of our approach with two test applications, a Finite Element multigrid solver for the Poisson problem and a robust and fast simulation of shallow water waves. By linking against HONEI's libraries, we achieve a two-fold speedup over straight forward C++ code using HONEI's SSE backend, and additional 3-4 and 4-16 times faster execution on the Cell and a GPU. A second important aspect of our approach is that the full performance capabilities of the hardware under consideration can be exploited by adding optimised application-specific operations to the HONEI libraries. HONEI provides all necessary infrastructure for development and evaluation of such kernels, significantly simplifying their development. Program summaryProgram title: HONEI Catalogue identifier: AEDW_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEDW_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GPLv2 No. of lines in distributed program, including test data, etc.: 216 180 No. of bytes in distributed program, including test data, etc.: 1 270 140 Distribution format: tar.gz Programming language: C++ Computer: x86, x86_64, NVIDIA CUDA GPUs, Cell blades and PlayStation 3 Operating system: Linux RAM: at least 500 MB free Classification: 4.8, 4.3, 6.1 External routines: SSE: none; [1] for GPU, [2] for Cell backend Nature of problem: Computational science in general and numerical simulation in particular have reached a turning point. The revolution developers are facing is not primarily driven by a change in (problem-specific) methodology, but rather by the fundamental paradigm shift of the

  11. Data Sets, Ensemble Cloud Computing, and the University Library (Invited)

    Science.gov (United States)

    Plale, B. A.

    2013-12-01

    The environmental researcher at the public university has new resources at their disposal to aid in research and publishing. Cloud computing provides compute cycles on demand for analysis and modeling scenarios. Cloud computing is attractive for e-Science because of the ease with which cores can be accessed on demand, and because the virtual machine implementation that underlies cloud computing reduces the cost of porting a numeric or analysis code to a new platform. At the university, many libraries at larger universities are developing the e-Science skills to serve as repositories of record for publishable data sets. But these are confusing times for the publication of data sets from environmental research. The large publishers of scientific literature are advocating a process whereby data sets are tightly tied to a publication. In other words, a paper published in the scientific literature that gives results based on data, must have an associated data set accessible that backs up the results. This approach supports reproducibility of results in that publishers maintain a repository for the papers they publish, and the data sets that the papers used. Does such a solution that maps one data set (or subset) to one paper fit the needs of the environmental researcher who among other things uses complex models, mines longitudinal data bases, and generates observational results? The second school of thought has emerged out of NSF, NOAA, and NASA funded efforts over time: data sets exist coherent at a location, such as occurs at National Snow and Ice Data Center (NSIDC). But when a collection is coherent, reproducibility of individual results is more challenging. We argue for a third complementary option: the university repository as a location for data sets produced as a result of university-based research. This location for a repository relies on the expertise developing in the university libraries across the country, and leverages tools, such as are being developed

  12. Wing-Body Aeroelasticity Using Finite-Difference Fluid/Finite-Element Structural Equations on Parallel Computers

    Science.gov (United States)

    Byun, Chansup; Guruswamy, Guru P.; Kutler, Paul (Technical Monitor)

    1994-01-01

    In recent years significant advances have been made for parallel computers in both hardware and software. Now parallel computers have become viable tools in computational mechanics. Many application codes developed on conventional computers have been modified to benefit from parallel computers. Significant speedups in some areas have been achieved by parallel computations. For single-discipline use of both fluid dynamics and structural dynamics, computations have been made on wing-body configurations using parallel computers. However, only a limited amount of work has been completed in combining these two disciplines for multidisciplinary applications. The prime reason is the increased level of complication associated with a multidisciplinary approach. In this work, procedures to compute aeroelasticity on parallel computers using direct coupling of fluid and structural equations will be investigated for wing-body configurations. The parallel computer selected for computations is an Intel iPSC/860 computer which is a distributed-memory, multiple-instruction, multiple data (MIMD) computer with 128 processors. In this study, the computational efficiency issues of parallel integration of both fluid and structural equations will be investigated in detail. The fluid and structural domains will be modeled using finite-difference and finite-element approaches, respectively. Results from the parallel computer will be compared with those from the conventional computers using a single processor. This study will provide an efficient computational tool for the aeroelastic analysis of wing-body structures on MIMD type parallel computers.

  13. What makes computational open source software libraries successful?

    Science.gov (United States)

    Bangerth, Wolfgang; Heister, Timo

    2013-01-01

    Software is the backbone of scientific computing. Yet, while we regularly publish detailed accounts about the results of scientific software, and while there is a general sense of which numerical methods work well, our community is largely unaware of best practices in writing the large-scale, open source scientific software upon which our discipline rests. This is particularly apparent in the commonly held view that writing successful software packages is largely the result of simply ‘being a good programmer’ when in fact there are many other factors involved, for example the social skill of community building. In this paper, we consider what we have found to be the necessary ingredients for successful scientific software projects and, in particular, for software libraries upon which the vast majority of scientific codes are built today. In particular, we discuss the roles of code, documentation, communities, project management and licenses. We also briefly comment on the impact on academic careers of engaging in software projects.

  14. What makes computational open source software libraries successful?

    International Nuclear Information System (INIS)

    Bangerth, Wolfgang; Heister, Timo

    2013-01-01

    Software is the backbone of scientific computing. Yet, while we regularly publish detailed accounts about the results of scientific software, and while there is a general sense of which numerical methods work well, our community is largely unaware of best practices in writing the large-scale, open source scientific software upon which our discipline rests. This is particularly apparent in the commonly held view that writing successful software packages is largely the result of simply ‘being a good programmer’ when in fact there are many other factors involved, for example the social skill of community building. In this paper, we consider what we have found to be the necessary ingredients for successful scientific software projects and, in particular, for software libraries upon which the vast majority of scientific codes are built today. In particular, we discuss the roles of code, documentation, communities, project management and licenses. We also briefly comment on the impact on academic careers of engaging in software projects. (paper)

  15. A parallel finite-difference method for computational aerodynamics

    International Nuclear Information System (INIS)

    Swisshelm, J.M.

    1989-01-01

    A finite-difference scheme for solving complex three-dimensional aerodynamic flow on parallel-processing supercomputers is presented. The method consists of a basic flow solver with multigrid convergence acceleration, embedded grid refinements, and a zonal equation scheme. Multitasking and vectorization have been incorporated into the algorithm. Results obtained include multiprocessed flow simulations from the Cray X-MP and Cray-2. Speedups as high as 3.3 for the two-dimensional case and 3.5 for segments of the three-dimensional case have been achieved on the Cray-2. The entire solver attained a factor of 2.7 improvement over its unitasked version on the Cray-2. The performance of the parallel algorithm on each machine is analyzed. 14 refs

  16. Parallel Computational Intelligence-Based Multi-Camera Surveillance System

    OpenAIRE

    Orts-Escolano, Sergio; Garcia-Rodriguez, Jose; Morell, Vicente; Cazorla, Miguel; Azorin-Lopez, Jorge; García-Chamizo, Juan Manuel

    2014-01-01

    In this work, we present a multi-camera surveillance system based on the use of self-organizing neural networks to represent events on video. The system processes several tasks in parallel using GPUs (graphic processor units). It addresses multiple vision tasks at various levels, such as segmentation, representation or characterization, analysis and monitoring of the movement. These features allow the construction of a robust representation of the environment and interpret the behavior of mob...

  17. Depth-Averaged Non-Hydrostatic Hydrodynamic Model Using a New Multithreading Parallel Computing Method

    Directory of Open Access Journals (Sweden)

    Ling Kang

    2017-03-01

    Full Text Available Compared to the hydrostatic hydrodynamic model, the non-hydrostatic hydrodynamic model can accurately simulate flows that feature vertical accelerations. The model’s low computational efficiency severely restricts its wider application. This paper proposes a non-hydrostatic hydrodynamic model based on a multithreading parallel computing method. The horizontal momentum equation is obtained by integrating the Navier–Stokes equations from the bottom to the free surface. The vertical momentum equation is approximated by the Keller-box scheme. A two-step method is used to solve the model equations. A parallel strategy based on block decomposition computation is utilized. The original computational domain is subdivided into two subdomains that are physically connected via a virtual boundary technique. Two sub-threads are created and tasked with the computation of the two subdomains. The producer–consumer model and the thread lock technique are used to achieve synchronous communication between sub-threads. The validity of the model was verified by solitary wave propagation experiments over a flat bottom and slope, followed by two sinusoidal wave propagation experiments over submerged breakwater. The parallel computing method proposed here was found to effectively enhance computational efficiency and save 20%–40% computation time compared to serial computing. The parallel acceleration rate and acceleration efficiency are approximately 1.45% and 72%, respectively. The parallel computing method makes a contribution to the popularization of non-hydrostatic models.

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

    Science.gov (United States)

    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

  19. MEDUSA - An overset grid flow solver for network-based parallel computer systems

    Science.gov (United States)

    Smith, Merritt H.; Pallis, Jani M.

    1993-01-01

    Continuing improvement in processing speed has made it feasible to solve the Reynolds-Averaged Navier-Stokes equations for simple three-dimensional flows on advanced workstations. Combining multiple workstations into a network-based heterogeneous parallel computer allows the application of programming principles learned on MIMD (Multiple Instruction Multiple Data) distributed memory parallel computers to the solution of larger problems. An overset-grid flow solution code has been developed which uses a cluster of workstations as a network-based parallel computer. Inter-process communication is provided by the Parallel Virtual Machine (PVM) software. Solution speed equivalent to one-third of a Cray-YMP processor has been achieved from a cluster of nine commonly used engineering workstation processors. Load imbalance and communication overhead are the principal impediments to parallel efficiency in this application.

  20. Parallel computation of Euler and Navier-Stokes flows

    International Nuclear Information System (INIS)

    Swisshelm, J.M.; Johnson, G.M.; Kumar, S.P.

    1986-01-01

    A multigrid technique useful for accelerating the convergence of Euler and Navier-Stokes flow computations has been restructured to improve its performance on both SIMD and MIMD computers. The new algorithm allows both the construction of longer coarse-grid vectors and the multitasking of entire grids. Computational results are presented for the CDC Cyber 205, Cray X-MP, and Denelcor HEP I. 15 references

  1. COMPSs-Mobile: parallel programming for mobile-cloud computing

    OpenAIRE

    Lordan Gomis, Francesc-Josep; Badia Sala, Rosa Maria

    2016-01-01

    The advent of Cloud and the popularization of mobile devices have led us to a shift in computing access. Computing users will have an interaction display while the real computation will be performed remotely, in the Cloud. COMPSs-Mobile is a framework that aims to ease the development of energy-efficient and high-performing applications for this environment. The framework provides an infrastructure-unaware programming model that allows developers to code regular Android applications that, ...

  2. From experiment to design -- Fault characterization and detection in parallel computer systems using computational accelerators

    Science.gov (United States)

    Yim, Keun Soo

    This dissertation summarizes experimental validation and co-design studies conducted to optimize the fault detection capabilities and overheads in hybrid computer systems (e.g., using CPUs and Graphics Processing Units, or GPUs), and consequently to improve the scalability of parallel computer systems using computational accelerators. The experimental validation studies were conducted to help us understand the failure characteristics of CPU-GPU hybrid computer systems under various types of hardware faults. The main characterization targets were faults that are difficult to detect and/or recover from, e.g., faults that cause long latency failures (Ch. 3), faults in dynamically allocated resources (Ch. 4), faults in GPUs (Ch. 5), faults in MPI programs (Ch. 6), and microarchitecture-level faults with specific timing features (Ch. 7). The co-design studies were based on the characterization results. One of the co-designed systems has a set of source-to-source translators that customize and strategically place error detectors in the source code of target GPU programs (Ch. 5). Another co-designed system uses an extension card to learn the normal behavioral and semantic execution patterns of message-passing processes executing on CPUs, and to detect abnormal behaviors of those parallel processes (Ch. 6). The third co-designed system is a co-processor that has a set of new instructions in order to support software-implemented fault detection techniques (Ch. 7). The work described in this dissertation gains more importance because heterogeneous processors have become an essential component of state-of-the-art supercomputers. GPUs were used in three of the five fastest supercomputers that were operating in 2011. Our work included comprehensive fault characterization studies in CPU-GPU hybrid computers. In CPUs, we monitored the target systems for a long period of time after injecting faults (a temporally comprehensive experiment), and injected faults into various types of

  3. Parallel computer calculation of quantum spin lattices; Calcul de chaines de spins quantiques sur ordinateur parallele

    Energy Technology Data Exchange (ETDEWEB)

    Lamarcq, J. [Service de Physique Theorique, CEA Centre d`Etudes de Saclay, 91 - Gif-sur-Yvette (France)

    1998-07-10

    Numerical simulation allows the theorists to convince themselves about the validity of the models they use. Particularly by simulating the spin lattices one can judge about the validity of a conjecture. Simulating a system defined by a large number of degrees of freedom requires highly sophisticated machines. This study deals with modelling the magnetic interactions between the ions of a crystal. Many exact results have been found for spin 1/2 systems but not for systems of other spins for which many simulation have been carried out. The interest for simulations has been renewed by the Haldane`s conjecture stipulating the existence of a energy gap between the ground state and the first excited states of a spin 1 lattice. The existence of this gap has been experimentally demonstrated. This report contains the following four chapters: 1. Spin systems; 2. Calculation of eigenvalues; 3. Programming; 4. Parallel calculation 14 refs., 6 figs.

  4. A kind of video image digitizing circuit based on computer parallel port

    International Nuclear Information System (INIS)

    Wang Yi; Tang Le; Cheng Jianping; Li Yuanjing; Zhang Binquan

    2003-01-01

    A kind of video images digitizing circuit based on parallel port was developed to digitize the flash x ray images in our Multi-Channel Digital Flash X ray Imaging System. The circuit can digitize the video images and store in static memory. The digital images can be transferred to computer through parallel port and can be displayed, processed and stored. (authors)

  5. Mathematical Methods and Algorithms of Mobile Parallel Computing on the Base of Multi-core Processors

    Directory of Open Access Journals (Sweden)

    Alexander B. Bakulev

    2012-11-01

    Full Text Available This article deals with mathematical models and algorithms, providing mobility of sequential programs parallel representation on the high-level language, presents formal model of operation environment processes management, based on the proposed model of programs parallel representation, presenting computation process on the base of multi-core processors.

  6. Performance of a Sequential and Parallel Computational Fluid Dynamic (CFD) Solver on a Missile Body Configuration

    National Research Council Canada - National Science Library

    Hisley, Dixie

    1999-01-01

    .... The goals of this report are: (1) to investigate the performance of message passing and loop level parallelization techniques, as they were implemented in the computational fluid dynamics (CFD...

  7. Massively Parallel Computing at Sandia and Its Application to National Defense

    National Research Council Canada - National Science Library

    Dosanjh, Sudip

    1991-01-01

    Two years ago, researchers at Sandia National Laboratories showed that a massively parallel computer with 1024 processors could solve scientific problems more than 1000 times faster than a single processor...

  8. Computational cost of isogeometric multi-frontal solvers on parallel distributed memory machines

    KAUST Repository

    Woźniak, Maciej; Paszyński, Maciej R.; Pardo, D.; Dalcin, Lisandro; Calo, Victor M.

    2015-01-01

    This paper derives theoretical estimates of the computational cost for isogeometric multi-frontal direct solver executed on parallel distributed memory machines. We show theoretically that for the Cp-1 global continuity of the isogeometric solution

  9. Computer model of a reverberant and parallel circuit coupling

    Science.gov (United States)

    Kalil, Camila de Andrade; de Castro, Maria Clícia Stelling; Cortez, Célia Martins

    2017-11-01

    The objective of the present study was to deepen the knowledge about the functioning of the neural circuits by implementing a signal transmission model using the Graph Theory in a small network of neurons composed of an interconnected reverberant and parallel circuit, in order to investigate the processing of the signals in each of them and the effects on the output of the network. For this, a program was developed in C language and simulations were done using neurophysiological data obtained in the literature.

  10. Paging memory from random access memory to backing storage in a parallel computer

    Science.gov (United States)

    Archer, Charles J; Blocksome, Michael A; Inglett, Todd A; Ratterman, Joseph D; Smith, Brian E

    2013-05-21

    Paging memory from random access memory (`RAM`) to backing storage in a parallel computer that includes a plurality of compute nodes, including: executing a data processing application on a virtual machine operating system in a virtual machine on a first compute node; providing, by a second compute node, backing storage for the contents of RAM on the first compute node; and swapping, by the virtual machine operating system in the virtual machine on the first compute node, a page of memory from RAM on the first compute node to the backing storage on the second compute node.

  11. Applications of parallel computer architectures to the real-time simulation of nuclear power systems

    International Nuclear Information System (INIS)

    Doster, J.M.; Sills, E.D.

    1988-01-01

    In this paper the authors report on efforts to utilize parallel computer architectures for the thermal-hydraulic simulation of nuclear power systems and current research efforts toward the development of advanced reactor operator aids and control systems based on this new technology. Many aspects of reactor thermal-hydraulic calculations are inherently parallel, and the computationally intensive portions of these calculations can be effectively implemented on modern computers. Timing studies indicate faster-than-real-time, high-fidelity physics models can be developed when the computational algorithms are designed to take advantage of the computer's architecture. These capabilities allow for the development of novel control systems and advanced reactor operator aids. Coupled with an integral real-time data acquisition system, evolving parallel computer architectures can provide operators and control room designers improved control and protection capabilities. Current research efforts are currently under way in this area

  12. TME (Task Mapping Editor): tool for executing distributed parallel computing. TME user's manual

    International Nuclear Information System (INIS)

    Takemiya, Hiroshi; Yamagishi, Nobuhiro; Imamura, Toshiyuki

    2000-03-01

    At the Center for Promotion of Computational Science and Engineering, a software environment PPExe has been developed to support scientific computing on a parallel computer cluster (distributed parallel scientific computing). TME (Task Mapping Editor) is one of components of the PPExe and provides a visual programming environment for distributed parallel scientific computing. Users can specify data dependence among tasks (programs) visually as a data flow diagram and map these tasks onto computers interactively through GUI of TME. The specified tasks are processed by other components of PPExe such as Meta-scheduler, RIM (Resource Information Monitor), and EMS (Execution Management System) according to the execution order of these tasks determined by TME. In this report, we describe the usage of TME. (author)

  13. T-cell libraries allow simple parallel generation of multiple peptide-specific human T-cell clones.

    Science.gov (United States)

    Theaker, Sarah M; Rius, Cristina; Greenshields-Watson, Alexander; Lloyd, Angharad; Trimby, Andrew; Fuller, Anna; Miles, John J; Cole, David K; Peakman, Mark; Sewell, Andrew K; Dolton, Garry

    2016-03-01

    Isolation of peptide-specific T-cell clones is highly desirable for determining the role of T-cells in human disease, as well as for the development of therapies and diagnostics. However, generation of monoclonal T-cells with the required specificity is challenging and time-consuming. Here we describe a library-based strategy for the simple parallel detection and isolation of multiple peptide-specific human T-cell clones from CD8(+) or CD4(+) polyclonal T-cell populations. T-cells were first amplified by CD3/CD28 microbeads in a 96U-well library format, prior to screening for desired peptide recognition. T-cells from peptide-reactive wells were then subjected to cytokine-mediated enrichment followed by single-cell cloning, with the entire process from sample to validated clone taking as little as 6 weeks. Overall, T-cell libraries represent an efficient and relatively rapid tool for the generation of peptide-specific T-cell clones, with applications shown here in infectious disease (Epstein-Barr virus, influenza A, and Ebola virus), autoimmunity (type 1 diabetes) and cancer. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

  14. Reducing power consumption while synchronizing a plurality of compute nodes during execution of a parallel application

    Science.gov (United States)

    Archer, Charles J [Rochester, MN; Blocksome, Michael A [Rochester, MN; Peters, Amanda E [Cambridge, MA; Ratterman, Joseph D [Rochester, MN; Smith, Brian E [Rochester, MN

    2012-04-17

    Methods, apparatus, and products are disclosed for reducing power consumption while synchronizing a plurality of compute nodes during execution of a parallel application that include: beginning, by each compute node, performance of a blocking operation specified by the parallel application, each compute node beginning the blocking operation asynchronously with respect to the other compute nodes; reducing, for each compute node, power to one or more hardware components of that compute node in response to that compute node beginning the performance of the blocking operation; and restoring, for each compute node, the power to the hardware components having power reduced in response to all of the compute nodes beginning the performance of the blocking operation.

  15. Reducing power consumption while synchronizing a plurality of compute nodes during execution of a parallel application

    Science.gov (United States)

    Archer, Charles J [Rochester, MN; Blocksome, Michael A [Rochester, MN; Peters, Amanda A [Rochester, MN; Ratterman, Joseph D [Rochester, MN; Smith, Brian E [Rochester, MN

    2012-01-10

    Methods, apparatus, and products are disclosed for reducing power consumption while synchronizing a plurality of compute nodes during execution of a parallel application that include: beginning, by each compute node, performance of a blocking operation specified by the parallel application, each compute node beginning the blocking operation asynchronously with respect to the other compute nodes; reducing, for each compute node, power to one or more hardware components of that compute node in response to that compute node beginning the performance of the blocking operation; and restoring, for each compute node, the power to the hardware components having power reduced in response to all of the compute nodes beginning the performance of the blocking operation.

  16. Line-plane broadcasting in a data communications network of a parallel computer

    Science.gov (United States)

    Archer, Charles J.; Berg, Jeremy E.; Blocksome, Michael A.; Smith, Brian E.

    2010-06-08

    Methods, apparatus, and products are disclosed for line-plane broadcasting in a data communications network of a parallel computer, the parallel computer comprising a plurality of compute nodes connected together through the network, the network optimized for point to point data communications and characterized by at least a first dimension, a second dimension, and a third dimension, that include: initiating, by a broadcasting compute node, a broadcast operation, including sending a message to all of the compute nodes along an axis of the first dimension for the network; sending, by each compute node along the axis of the first dimension, the message to all of the compute nodes along an axis of the second dimension for the network; and sending, by each compute node along the axis of the second dimension, the message to all of the compute nodes along an axis of the third dimension for the network.

  17. Ocean Modeling and Visualization on Massively Parallel Computer

    Science.gov (United States)

    Chao, Yi; Li, P. Peggy; Wang, Ping; Katz, Daniel S.; Cheng, Benny N.

    1997-01-01

    Climate modeling is one of the grand challenges of computational science, and ocean modeling plays an important role in both understanding the current climatic conditions and predicting future climate change.

  18. Parallel Computational Intelligence-Based Multi-Camera Surveillance System

    Directory of Open Access Journals (Sweden)

    Sergio Orts-Escolano

    2014-04-01

    Full Text Available In this work, we present a multi-camera surveillance system based on the use of self-organizing neural networks to represent events on video. The system processes several tasks in parallel using GPUs (graphic processor units. It addresses multiple vision tasks at various levels, such as segmentation, representation or characterization, analysis and monitoring of the movement. These features allow the construction of a robust representation of the environment and interpret the behavior of mobile agents in the scene. It is also necessary to integrate the vision module into a global system that operates in a complex environment by receiving images from multiple acquisition devices at video frequency. Offering relevant information to higher level systems, monitoring and making decisions in real time, it must accomplish a set of requirements, such as: time constraints, high availability, robustness, high processing speed and re-configurability. We have built a system able to represent and analyze the motion in video acquired by a multi-camera network and to process multi-source data in parallel on a multi-GPU architecture.

  19. On efficiency of fire simulation realization: parallelization with greater number of computational meshes

    Science.gov (United States)

    Valasek, Lukas; Glasa, Jan

    2017-12-01

    Current fire simulation systems are capable to utilize advantages of high-performance computer (HPC) platforms available and to model fires efficiently in parallel. In this paper, efficiency of a corridor fire simulation on a HPC computer cluster is discussed. The parallel MPI version of Fire Dynamics Simulator is used for testing efficiency of selected strategies of allocation of computational resources of the cluster using a greater number of computational cores. Simulation results indicate that if the number of cores used is not equal to a multiple of the total number of cluster node cores there are allocation strategies which provide more efficient calculations.

  20. Parallel diffusion calculation for the PHAETON on-line multiprocessor computer

    International Nuclear Information System (INIS)

    Collart, J.M.; Fedon-Magnaud, C.; Lautard, J.J.

    1987-04-01

    The aim of the PHAETON project is the design of an on-line computer in order to increase the immediate knowledge of the main operating and safety parameters in power plants. A significant stage is the computation of the three dimensional flux distribution. For cost and safety reason a computer based on a parallel microprocessor architecture has been studied. This paper presents a first approach to parallelized three dimensional diffusion calculation. A computing software has been written and built in a four processors demonstrator. We present the realization in progress, concerning the final equipment. 8 refs

  1. Fencing network direct memory access data transfers in a parallel active messaging interface of a parallel computer

    Science.gov (United States)

    Blocksome, Michael A.; Mamidala, Amith R.

    2015-07-07

    Fencing direct memory access (`DMA`) data transfers in a parallel active messaging interface (`PAMI`) of a parallel computer, the PAMI including data communications endpoints, each endpoint including specifications of a client, a context, and a task, the endpoints coupled for data communications through the PAMI and through DMA controllers operatively coupled to a deterministic data communications network through which the DMA controllers deliver data communications deterministically, including initiating execution through the PAMI of an ordered sequence of active DMA instructions for DMA data transfers between two endpoints, effecting deterministic DMA data transfers through a DMA controller and the deterministic data communications network; and executing through the PAMI, with no FENCE accounting for DMA data transfers, an active FENCE instruction, the FENCE instruction completing execution only after completion of all DMA instructions initiated prior to execution of the FENCE instruction for DMA data transfers between the two endpoints.

  2. Digital tomosynthesis parallel imaging computational analysis with shift and add and back projection reconstruction algorithms.

    Science.gov (United States)

    Chen, Ying; Balla, Apuroop; Rayford II, Cleveland E; Zhou, Weihua; Fang, Jian; Cong, Linlin

    2010-01-01

    Digital tomosynthesis is a novel technology that has been developed for various clinical applications. Parallel imaging configuration is utilised in a few tomosynthesis imaging areas such as digital chest tomosynthesis. Recently, parallel imaging configuration for breast tomosynthesis began to appear too. In this paper, we present the investigation on computational analysis of impulse response characterisation as the start point of our important research efforts to optimise the parallel imaging configurations. Results suggest that impulse response computational analysis is an effective method to compare and optimise imaging configurations.

  3. A homotopy method for solving Riccati equations on a shared memory parallel computer

    International Nuclear Information System (INIS)

    Zigic, D.; Watson, L.T.; Collins, E.G. Jr.; Davis, L.D.

    1993-01-01

    Although there are numerous algorithms for solving Riccati equations, there still remains a need for algorithms which can operate efficiently on large problems and on parallel machines. This paper gives a new homotopy-based algorithm for solving Riccati equations on a shared memory parallel computer. The central part of the algorithm is the computation of the kernel of the Jacobian matrix, which is essential for the corrector iterations along the homotopy zero curve. Using a Schur decomposition the tensor product structure of various matrices can be efficiently exploited. The algorithm allows for efficient parallelization on shared memory machines

  4. Parallel computation for blood cell classification in medical hyperspectral imagery

    International Nuclear Information System (INIS)

    Li, Wei; Wu, Lucheng; Qiu, Xianbo; Ran, Qiong; Xie, Xiaoming

    2016-01-01

    With the advantage of fine spectral resolution, hyperspectral imagery provides great potential for cell classification. This paper provides a promising classification system including the following three stages: (1) band selection for a subset of spectral bands with distinctive and informative features, (2) spectral-spatial feature extraction, such as local binary patterns (LBP), and (3) followed by an effective classifier. Moreover, these three steps are further implemented on graphics processing units (GPU) respectively, which makes the system real-time and more practical. The GPU parallel implementation is compared with the serial implementation on central processing units (CPU). Experimental results based on real medical hyperspectral data demonstrate that the proposed system is able to offer high accuracy and fast speed, which are appealing for cell classification in medical hyperspectral imagery. (paper)

  5. Vector and parallel processors in computational science. Proceedings

    Energy Technology Data Exchange (ETDEWEB)

    Duff, I S; Reid, J K

    1985-01-01

    This volume contains papers from most of the invited talks and from several of the contributed talks and poster sessions presented at VAPP II. The contents present an extensive coverage of all important aspects of vector and parallel processors, including hardware, languages, numerical algorithms and applications. The topics covered include descriptions of new machines (both research and commercial machines), languages and software aids, and general discussions of whole classes of machines and their uses. Numerical methods papers include Monte Carlo algorithms, iterative and direct methods for solving large systems, finite elements, optimization, random number generation and mathematical software. The specific applications covered include neutron diffusion calculations, molecular dynamics, weather forecasting, lattice gauge calculations, fluid dynamics, flight simulation, cartography, image processing and cryptography. Most machines and architecture types are being used for these applications. many refs.

  6. A Parallel and Distributed Surrogate Model Implementation for Computational Steering

    KAUST Repository

    Butnaru, Daniel

    2012-06-01

    Understanding the influence of multiple parameters in a complex simulation setting is a difficult task. In the ideal case, the scientist can freely steer such a simulation and is immediately presented with the results for a certain configuration of the input parameters. Such an exploration process is however not possible if the simulation is computationally too expensive. For these cases we present in this paper a scalable computational steering approach utilizing a fast surrogate model as substitute for the time-consuming simulation. The surrogate model we propose is based on the sparse grid technique, and we identify the main computational tasks associated with its evaluation and its extension. We further show how distributed data management combined with the specific use of accelerators allows us to approximate and deliver simulation results to a high-resolution visualization system in real-time. This significantly enhances the steering workflow and facilitates the interactive exploration of large datasets. © 2012 IEEE.

  7. Managing internode data communications for an uninitialized process in a parallel computer

    Science.gov (United States)

    Archer, Charles J; Blocksome, Michael A; Miller, Douglas R; Parker, Jeffrey J; Ratterman, Joseph D; Smith, Brian E

    2014-05-20

    A parallel computer includes nodes, each having main memory and a messaging unit (MU). Each MU includes computer memory, which in turn includes, MU message buffers. Each MU message buffer is associated with an uninitialized process on the compute node. In the parallel computer, managing internode data communications for an uninitialized process includes: receiving, by an MU of a compute node, one or more data communications messages in an MU message buffer associated with an uninitialized process on the compute node; determining, by an application agent, that the MU message buffer associated with the uninitialized process is full prior to initialization of the uninitialized process; establishing, by the application agent, a temporary message buffer for the uninitialized process in main computer memory; and moving, by the application agent, data communications messages from the MU message buffer associated with the uninitialized process to the temporary message buffer in main computer memory.

  8. Multiscale Methods, Parallel Computation, and Neural Networks for Real-Time Computer Vision.

    Science.gov (United States)

    Battiti, Roberto

    1990-01-01

    This thesis presents new algorithms for low and intermediate level computer vision. The guiding ideas in the presented approach are those of hierarchical and adaptive processing, concurrent computation, and supervised learning. Processing of the visual data at different resolutions is used not only to reduce the amount of computation necessary to reach the fixed point, but also to produce a more accurate estimation of the desired parameters. The presented adaptive multiple scale technique is applied to the problem of motion field estimation. Different parts of the image are analyzed at a resolution that is chosen in order to minimize the error in the coefficients of the differential equations to be solved. Tests with video-acquired images show that velocity estimation is more accurate over a wide range of motion with respect to the homogeneous scheme. In some cases introduction of explicit discontinuities coupled to the continuous variables can be used to avoid propagation of visual information from areas corresponding to objects with different physical and/or kinematic properties. The human visual system uses concurrent computation in order to process the vast amount of visual data in "real -time." Although with different technological constraints, parallel computation can be used efficiently for computer vision. All the presented algorithms have been implemented on medium grain distributed memory multicomputers with a speed-up approximately proportional to the number of processors used. A simple two-dimensional domain decomposition assigns regions of the multiresolution pyramid to the different processors. The inter-processor communication needed during the solution process is proportional to the linear dimension of the assigned domain, so that efficiency is close to 100% if a large region is assigned to each processor. Finally, learning algorithms are shown to be a viable technique to engineer computer vision systems for different applications starting from

  9. Scalable Parallelization of Skyline Computation for Multi-core Processors

    DEFF Research Database (Denmark)

    Chester, Sean; Sidlauskas, Darius; Assent, Ira

    2015-01-01

    The skyline is an important query operator for multi-criteria decision making. It reduces a dataset to only those points that offer optimal trade-offs of dimensions. In general, it is very expensive to compute. Recently, multi-core CPU algorithms have been proposed to accelerate the computation...... of the skyline. However, they do not sufficiently minimize dominance tests and so are not competitive with state-of-the-art sequential algorithms. In this paper, we introduce a novel multi-core skyline algorithm, Hybrid, which processes points in blocks. It maintains a shared, global skyline among all threads...

  10. Software for the computized neutron data library of the SOKRATOR system

    International Nuclear Information System (INIS)

    Kolesov, V.E.; Krivtsov, A.S.; Solov'ev, N.A.

    1976-01-01

    When preparing data for nuclear reactors and shield computations using the evaluated nuclear data library it is necessary to have a set of special service programs to maintain the library itself. In this paper the structure of this set is discussed and a brief description of some programs is presented

  11. In-House Automation of a Small Library Using a Mainframe Computer.

    Science.gov (United States)

    Waranius, Frances B.; Tellier, Stephen H.

    1986-01-01

    An automated library routine management system was developed in-house to create system unique to the Library and Information Center, Lunar and Planetary Institute, Houston, Texas. A modular approach was used to allow continuity in operations and services as system was implemented. Acronyms and computer accounts and file names are appended.…

  12. Computer tape library for collective dose assessments in the European Community

    International Nuclear Information System (INIS)

    Jones, J.A.; Kelly, G.N.

    1981-01-01

    A computer tape library has been established which can readily be applied to enable calculations to be made of the collective dose to the population of the European Community from radioactive effluent discharges within the EC. The background to the development of the tape library and details of its contents, method of application and availability are summarised in this note. (author)

  13. Parallel distributed computing in modeling of the nanomaterials production technologies

    NARCIS (Netherlands)

    Krzhizhanovskaya, V.V.; Korkhov, V.V.; Zatevakhin, M.A.; Gorbachev, Y.E.

    2008-01-01

    Simulation of physical and chemical processes occurring in the nanomaterial production technologies is a computationally challenging problem, due to the great number of coupled processes, time and length scales to be taken into account. To solve such complex problems with a good level of detail in a

  14. Monte Carlo calculations on a parallel computer using MORSE-C.G

    International Nuclear Information System (INIS)

    Wood, J.

    1995-01-01

    The general purpose particle transport Monte Carlo code, MORSE-C.G., is implemented on a parallel computing transputer-based system having MIMD architecture. Example problems are solved which are representative of the 3-principal types of problem that can be solved by the original serial code, namely, fixed source, eigenvalue (k-eff) and time-dependent. The results from the parallelized version of the code are compared in tables with the serial code run on a mainframe serial computer, and with an independent, deterministic transport code. The performance of the parallel computer as the number of processors is varied is shown graphically. For the parallel strategy used, the loss of efficiency as the number of processors is increased, is investigated. (author)

  15. Preliminary Study on the Enhancement of Reconstruction Speed for Emission Computed Tomography Using Parallel Processing

    International Nuclear Information System (INIS)

    Park, Min Jae; Lee, Jae Sung; Kim, Soo Mee; Kang, Ji Yeon; Lee, Dong Soo; Park, Kwang Suk

    2009-01-01

    Conventional image reconstruction uses simplified physical models of projection. However, real physics, for example 3D reconstruction, takes too long time to process all the data in clinic and is unable in a common reconstruction machine because of the large memory for complex physical models. We suggest the realistic distributed memory model of fast-reconstruction using parallel processing on personal computers to enable large-scale technologies. The preliminary tests for the possibility on virtual machines and various performance test on commercial super computer, Tachyon were performed. Expectation maximization algorithm with common 2D projection and realistic 3D line of response were tested. Since the process time was getting slower (max 6 times) after a certain iteration, optimization for compiler was performed to maximize the efficiency of parallelization. Parallel processing of a program on multiple computers was available on Linux with MPICH and NFS. We verified that differences between parallel processed image and single processed image at the same iterations were under the significant digits of floating point number, about 6 bit. Double processors showed good efficiency (1.96 times) of parallel computing. Delay phenomenon was solved by vectorization method using SSE. Through the study, realistic parallel computing system in clinic was established to be able to reconstruct by plenty of memory using the realistic physical models which was impossible to simplify

  16. Parallel processing algorithms for hydrocodes on a computer with MIMD architecture (DENELCOR's HEP)

    International Nuclear Information System (INIS)

    Hicks, D.L.

    1983-11-01

    In real time simulation/prediction of complex systems such as water-cooled nuclear reactors, if reactor operators had fast simulator/predictors to check the consequences of their operations before implementing them, events such as the incident at Three Mile Island might be avoided. However, existing simulator/predictors such as RELAP run slower than real time on serial computers. It appears that the only way to overcome the barrier to higher computing rates is to use computers with architectures that allow concurrent computations or parallel processing. The computer architecture with the greatest degree of parallelism is labeled Multiple Instruction Stream, Multiple Data Stream (MIMD). An example of a machine of this type is the HEP computer by DENELCOR. It appears that hydrocodes are very well suited for parallelization on the HEP. It is a straightforward exercise to parallelize explicit, one-dimensional Lagrangean hydrocodes in a zone-by-zone parallelization. Similarly, implicit schemes can be parallelized in a zone-by-zone fashion via an a priori, symbolic inversion of the tridiagonal matrix that arises in an implicit scheme. These techniques are extended to Eulerian hydrocodes by using Harlow's rezone technique. The extension from single-phase Eulerian to two-phase Eulerian is straightforward. This step-by-step extension leads to hydrocodes with zone-by-zone parallelization that are capable of two-phase flow simulation. Extensions to two and three spatial dimensions can be achieved by operator splitting. It appears that a zone-by-zone parallelization is the best way to utilize the capabilities of an MIMD machine. 40 references

  17. Parallel performances of three 3D reconstruction methods on MIMD computers: Feldkamp, block ART and SIRT algorithms

    International Nuclear Information System (INIS)

    Laurent, C.; Chassery, J.M.; Peyrin, F.; Girerd, C.

    1996-01-01

    This paper deals with the parallel implementations of reconstruction methods in 3D tomography. 3D tomography requires voluminous data and long computation times. Parallel computing, on MIMD computers, seems to be a good approach to manage this problem. In this study, we present the different steps of the parallelization on an abstract parallel computer. Depending on the method, we use two main approaches to parallelize the algorithms: the local approach and the global approach. Experimental results on MIMD computers are presented. Two 3D images reconstructed from realistic data are showed

  18. QuBiLS-MIDAS: a parallel free-software for molecular descriptors computation based on multilinear algebraic maps.

    Science.gov (United States)

    García-Jacas, César R; Marrero-Ponce, Yovani; Acevedo-Martínez, Liesner; Barigye, Stephen J; Valdés-Martiní, José R; Contreras-Torres, Ernesto

    2014-07-05

    The present report introduces the QuBiLS-MIDAS software belonging to the ToMoCoMD-CARDD suite for the calculation of three-dimensional molecular descriptors (MDs) based on the two-linear (bilinear), three-linear, and four-linear (multilinear or N-linear) algebraic forms. Thus, it is unique software that computes these tensor-based indices. These descriptors, establish relations for two, three, and four atoms by using several (dis-)similarity metrics or multimetrics, matrix transformations, cutoffs, local calculations and aggregation operators. The theoretical background of these N-linear indices is also presented. The QuBiLS-MIDAS software was developed in the Java programming language and employs the Chemical Development Kit library for the manipulation of the chemical structures and the calculation of the atomic properties. This software is composed by a desktop user-friendly interface and an Abstract Programming Interface library. The former was created to simplify the configuration of the different options of the MDs, whereas the library was designed to allow its easy integration to other software for chemoinformatics applications. This program provides functionalities for data cleaning tasks and for batch processing of the molecular indices. In addition, it offers parallel calculation of the MDs through the use of all available processors in current computers. The studies of complexity of the main algorithms demonstrate that these were efficiently implemented with respect to their trivial implementation. Lastly, the performance tests reveal that this software has a suitable behavior when the amount of processors is increased. Therefore, the QuBiLS-MIDAS software constitutes a useful application for the computation of the molecular indices based on N-linear algebraic maps and it can be used freely to perform chemoinformatics studies. Copyright © 2014 Wiley Periodicals, Inc.

  19. Architecture and Initial Development of a Digital Library Platform for Computable Knowledge Objects for Health.

    Science.gov (United States)

    Flynn, Allen J; Bahulekar, Namita; Boisvert, Peter; Lagoze, Carl; Meng, George; Rampton, James; Friedman, Charles P

    2017-01-01

    Throughout the world, biomedical knowledge is routinely generated and shared through primary and secondary scientific publications. However, there is too much latency between publication of knowledge and its routine use in practice. To address this latency, what is actionable in scientific publications can be encoded to make it computable. We have created a purpose-built digital library platform to hold, manage, and share actionable, computable knowledge for health called the Knowledge Grid Library. Here we present it with its system architecture.

  20. Availability and Overlap of Quality Computer Science Journal Holdings in Selected University Libraries in Malaysia

    OpenAIRE

    Zainab, A.N.; Ng, S.L.

    2003-01-01

    The study reveals the availability status of quality journals in the field of computer science held in the libraries of the University of Malaya, (UM), University of Science Malaysia (USM), University of Technology Malaysia (UTM), National University of Malaysia (UKM) and University Putra Malaysia (UPM). These universities are selected since they offer degree programmes in computer science. The study also investigates the degree of overlaps and unique titles in the five libraries. The Univers...

  1. Implementation of QR up- and downdating on a massively parallel |computer

    DEFF Research Database (Denmark)

    Bendtsen, Claus; Hansen, Per Christian; Madsen, Kaj

    1995-01-01

    We describe an implementation of QR up- and downdating on a massively parallel computer (the Connection Machine CM-200) and show that the algorithm maps well onto the computer. In particular, we show how the use of corrected semi-normal equations for downdating can be efficiently implemented. We...... also illustrate the use of our algorithms in a new LP algorithm....

  2. Software Alchemy: Turning Complex Statistical Computations into Embarrassingly-Parallel Ones

    Directory of Open Access Journals (Sweden)

    Norman Matloff

    2016-07-01

    Full Text Available The growth in the use of computationally intensive statistical procedures, especially with big data, has necessitated the usage of parallel computation on diverse platforms such as multicore, GPUs, clusters and clouds. However, slowdown due to interprocess communication costs typically limits such methods to "embarrassingly parallel" (EP algorithms, especially on non-shared memory platforms. This paper develops a broadlyapplicable method for converting many non-EP algorithms into statistically equivalent EP ones. The method is shown to yield excellent levels of speedup for a variety of statistical computations. It also overcomes certain problems of memory limitations.

  3. Parallel synthesis of libraries of anodic and cathodic functionalized electrodeposition paints as immobilization matrix for amperometric biosensors.

    Science.gov (United States)

    Ngounou, Bertrand; Aliyev, Elchin H; Guschin, Dmitrii A; Sultanov, Yusif M; Efendiev, Ayaz A; Schuhmann, Wolfgang

    2007-09-01

    The integration of flexible anchoring groups bearing imidazolyl or pyridyl substituents into the structure of electrodeposition paints (EDP) is the basis for the parallel synthesis of a library containing 107 members of different cathodic and anodic EDPs with a high variation in polymer properties. The obtained EDPs were used as immobilization matrix for biosensor fabrication using glucose oxidase as a model enzyme. Amperometric glucose sensors based on the different EDPs showed a wide variation in their sensor characteristics with respect to the apparent Michaelis-Menten constant (KM(app)) representing the linear measuring range and the maximum current (Imax(app)). Based on these results first assumptions concerning the impact of different side chains in the EDP on the expected biosensor properties could be obtained allowing for an improved rational optimization of EDPs used as immobilization matrix in amperometric biosensors.

  4. Accelerating Neuroimage Registration through Parallel Computation of Similarity Metric.

    Directory of Open Access Journals (Sweden)

    Yun-Gang Luo

    Full Text Available Neuroimage registration is crucial for brain morphometric analysis and treatment efficacy evaluation. However, existing advanced registration algorithms such as FLIRT and ANTs are not efficient enough for clinical use. In this paper, a GPU implementation of FLIRT with the correlation ratio (CR as the similarity metric and a GPU accelerated correlation coefficient (CC calculation for the symmetric diffeomorphic registration of ANTs have been developed. The comparison with their corresponding original tools shows that our accelerated algorithms can greatly outperform the original algorithm in terms of computational efficiency. This paper demonstrates the great potential of applying these registration tools in clinical applications.

  5. Computer Generation of Fourier Transform Libraries for Distributed Memory Architectures

    Science.gov (United States)

    2010-12-01

    tractions used in quantum chemistry . It too performs algebraic transformations tominimize the operations count, and then optimizes code based on...existing parallel DFT algorithms, including their strengths and weaknesses. Four-stepFFT.The four-step algorithm [Hegland, 1994;Norton and Silberger , 1987...Sadayappan, and Alexander Sibiryakov. Synthesis of high-performance parallel programs for a class of ab initio quan- tum chemistry models. Proc. of

  6. Expert Systems for Libraries at SCIL [Small Computers in Libraries]'88.

    Science.gov (United States)

    Kochtanek, Thomas R.; And Others

    1988-01-01

    Six brief papers on expert systems for libraries cover (1) a knowledge-based approach to database design; (2) getting started in expert systems; (3) using public domain software to develop a business reference system; (4) a music cataloging inquiry system; (5) linguistic analysis of reference transactions; and (6) a model of a reference librarian.…

  7. Programming a massively parallel, computation universal system: static behavior

    Energy Technology Data Exchange (ETDEWEB)

    Lapedes, A.; Farber, R.

    1986-01-01

    In previous work by the authors, the ''optimum finding'' properties of Hopfield neural nets were applied to the nets themselves to create a ''neural compiler.'' This was done in such a way that the problem of programming the attractors of one neural net (called the Slave net) was expressed as an optimization problem that was in turn solved by a second neural net (the Master net). In this series of papers that approach is extended to programming nets that contain interneurons (sometimes called ''hidden neurons''), and thus deals with nets capable of universal computation. 22 refs.

  8. Weighted Local Active Pixel Pattern (WLAPP for Face Recognition in Parallel Computation Environment

    Directory of Open Access Journals (Sweden)

    Gundavarapu Mallikarjuna Rao

    2013-10-01

    Full Text Available Abstract  - The availability of multi-core technology resulted totally new computational era. Researchers are keen to explore available potential in state of art-machines for breaking the bearer imposed by serial computation. Face Recognition is one of the challenging applications on so ever computational environment. The main difficulty of traditional Face Recognition algorithms is lack of the scalability. In this paper Weighted Local Active Pixel Pattern (WLAPP, a new scalable Face Recognition Algorithm suitable for parallel environment is proposed.  Local Active Pixel Pattern (LAPP is found to be simple and computational inexpensive compare to Local Binary Patterns (LBP. WLAPP is developed based on concept of LAPP. The experimentation is performed on FG-Net Aging Database with deliberately introduced 20% distortion and the results are encouraging. Keywords — Active pixels, Face Recognition, Local Binary Pattern (LBP, Local Active Pixel Pattern (LAPP, Pattern computing, parallel workers, template, weight computation.  

  9. 10th International Workshop on Parallel Tools for High Performance Computing

    CERN Document Server

    Gracia, José; Hilbrich, Tobias; Knüpfer, Andreas; Resch, Michael; Nagel, Wolfgang

    2017-01-01

    This book presents the proceedings of the 10th International Parallel Tools Workshop, held October 4-5, 2016 in Stuttgart, Germany – a forum to discuss the latest advances in parallel tools. High-performance computing plays an increasingly important role for numerical simulation and modelling in academic and industrial research. At the same time, using large-scale parallel systems efficiently is becoming more difficult. A number of tools addressing parallel program development and analysis have emerged from the high-performance computing community over the last decade, and what may have started as collection of small helper script has now matured to production-grade frameworks. Powerful user interfaces and an extensive body of documentation allow easy usage by non-specialists.

  10. Parallel computation with molecular-motor-propelled agents in nanofabricated networks.

    Science.gov (United States)

    Nicolau, Dan V; Lard, Mercy; Korten, Till; van Delft, Falco C M J M; Persson, Malin; Bengtsson, Elina; Månsson, Alf; Diez, Stefan; Linke, Heiner; Nicolau, Dan V

    2016-03-08

    The combinatorial nature of many important mathematical problems, including nondeterministic-polynomial-time (NP)-complete problems, places a severe limitation on the problem size that can be solved with conventional, sequentially operating electronic computers. There have been significant efforts in conceiving parallel-computation approaches in the past, for example: DNA computation, quantum computation, and microfluidics-based computation. However, these approaches have not proven, so far, to be scalable and practical from a fabrication and operational perspective. Here, we report the foundations of an alternative parallel-computation system in which a given combinatorial problem is encoded into a graphical, modular network that is embedded in a nanofabricated planar device. Exploring the network in a parallel fashion using a large number of independent, molecular-motor-propelled agents then solves the mathematical problem. This approach uses orders of magnitude less energy than conventional computers, thus addressing issues related to power consumption and heat dissipation. We provide a proof-of-concept demonstration of such a device by solving, in a parallel fashion, the small instance {2, 5, 9} of the subset sum problem, which is a benchmark NP-complete problem. Finally, we discuss the technical advances necessary to make our system scalable with presently available technology.

  11. Teaching Scientific Computing: A Model-Centered Approach to Pipeline and Parallel Programming with C

    Directory of Open Access Journals (Sweden)

    Vladimiras Dolgopolovas

    2015-01-01

    Full Text Available The aim of this study is to present an approach to the introduction into pipeline and parallel computing, using a model of the multiphase queueing system. Pipeline computing, including software pipelines, is among the key concepts in modern computing and electronics engineering. The modern computer science and engineering education requires a comprehensive curriculum, so the introduction to pipeline and parallel computing is the essential topic to be included in the curriculum. At the same time, the topic is among the most motivating tasks due to the comprehensive multidisciplinary and technical requirements. To enhance the educational process, the paper proposes a novel model-centered framework and develops the relevant learning objects. It allows implementing an educational platform of constructivist learning process, thus enabling learners’ experimentation with the provided programming models, obtaining learners’ competences of the modern scientific research and computational thinking, and capturing the relevant technical knowledge. It also provides an integral platform that allows a simultaneous and comparative introduction to pipelining and parallel computing. The programming language C for developing programming models and message passing interface (MPI and OpenMP parallelization tools have been chosen for implementation.

  12. Vector and parallel computing on the IBM ES/3090, a powerful approach to solving problems in the utility industry

    International Nuclear Information System (INIS)

    Bellucci, V.J.

    1990-01-01

    This paper describes IBM's approach to parallel computing using the IBM ES/3090 computer. Parallel processing concepts were discussed including its advantages, potential performance improvements and limitations. Particular applications and capabilities for the IBM ES/3090 were presented along with preliminary results from some utilities in the application of parallel processing to simulation of system reliability, air pollution models, and power network dynamics

  13. Multiscale Computing with the Multiscale Modeling Library and Runtime Environment

    NARCIS (Netherlands)

    Borgdorff, J.; Mamonski, M.; Bosak, B.; Groen, D.; Ben Belgacem, M.; Kurowski, K.; Hoekstra, A.G.

    2013-01-01

    We introduce a software tool to simulate multiscale models: the Multiscale Coupling Library and Environment 2 (MUSCLE 2). MUSCLE 2 is a component-based modeling tool inspired by the multiscale modeling and simulation framework, with an easy-to-use API which supports Java, C++, C, and Fortran. We

  14. Linux Adventures on a Laptop. Computers in Small Libraries

    Science.gov (United States)

    Roberts, Gary

    2005-01-01

    This article discusses the pros and cons of open source software, such as Linux. It asserts that despite the technical difficulties of installing and maintaining this type of software, ultimately it is helpful in terms of knowledge acquisition and as a beneficial investment librarians can make in themselves, their libraries, and their patrons.…

  15. Computers behind bars : Information technology in Canadian prison libraries

    DEFF Research Database (Denmark)

    Prange, Laurie

    of information can have upon Canadian prison libraries. Gathered information is compared with the results of Canadian policy regarding the provision of information to inmates. The analysis of the collected facts can provide insight to help prison librarians deal with the increasing popularity of electronic...

  16. CUDA/GPU Technology : Parallel Programming For High Performance Scientific Computing

    OpenAIRE

    YUHENDRA; KUZE, Hiroaki; JOSAPHAT, Tetuko Sri Sumantyo

    2009-01-01

    [ABSTRACT]Graphics processing units (GP Us) originally designed for computer video cards have emerged as the most powerful chip in a high-performance workstation. In the high performance computation capabilities, graphic processing units (GPU) lead to much more powerful performance than conventional CPUs by means of parallel processing. In 2007, the birth of Compute Unified Device Architecture (CUDA) and CUDA-enabled GPUs by NVIDIA Corporation brought a revolution in the general purpose GPU a...

  17. An approach to computing discrete adjoints for MPI-parallelized models applied to Ice Sheet System Model 4.11

    Directory of Open Access Journals (Sweden)

    E. Larour

    2016-11-01

    Full Text Available Within the framework of sea-level rise projections, there is a strong need for hindcast validation of the evolution of polar ice sheets in a way that tightly matches observational records (from radar, gravity, and altimetry observations mainly. However, the computational requirements for making hindcast reconstructions possible are severe and rely mainly on the evaluation of the adjoint state of transient ice-flow models. Here, we look at the computation of adjoints in the context of the NASA/JPL/UCI Ice Sheet System Model (ISSM, written in C++ and designed for parallel execution with MPI. We present the adaptations required in the way the software is designed and written, but also generic adaptations in the tools facilitating the adjoint computations. We concentrate on the use of operator overloading coupled with the AdjoinableMPI library to achieve the adjoint computation of the ISSM. We present a comprehensive approach to (1 carry out type changing through the ISSM, hence facilitating operator overloading, (2 bind to external solvers such as MUMPS and GSL-LU, and (3 handle MPI-based parallelism to scale the capability. We demonstrate the success of the approach by computing sensitivities of hindcast metrics such as the misfit to observed records of surface altimetry on the northeastern Greenland Ice Stream, or the misfit to observed records of surface velocities on Upernavik Glacier, central West Greenland. We also provide metrics for the scalability of the approach, and the expected performance. This approach has the potential to enable a new generation of hindcast-validated projections that make full use of the wealth of datasets currently being collected, or already collected, in Greenland and Antarctica.

  18. Massively parallel computation of PARASOL code on the Origin 3800 system

    International Nuclear Information System (INIS)

    Hosokawa, Masanari; Takizuka, Tomonori

    2001-10-01

    The divertor particle simulation code named PARASOL simulates open-field plasmas between divertor walls self-consistently by using an electrostatic PIC method and a binary collision Monte Carlo model. The PARASOL parallelized with MPI-1.1 for scalar parallel computer worked on Intel Paragon XP/S system. A system SGI Origin 3800 was newly installed (May, 2001). The parallel programming was improved at this switchover. As a result of the high-performance new hardware and this improvement, the PARASOL is speeded up by about 60 times with the same number of processors. (author)

  19. Efficiency Analysis of the Parallel Implementation of the SIMPLE Algorithm on Multiprocessor Computers

    Science.gov (United States)

    Lashkin, S. V.; Kozelkov, A. S.; Yalozo, A. V.; Gerasimov, V. Yu.; Zelensky, D. K.

    2017-12-01

    This paper describes the details of the parallel implementation of the SIMPLE algorithm for numerical solution of the Navier-Stokes system of equations on arbitrary unstructured grids. The iteration schemes for the serial and parallel versions of the SIMPLE algorithm are implemented. In the description of the parallel implementation, special attention is paid to computational data exchange among processors under the condition of the grid model decomposition using fictitious cells. We discuss the specific features for the storage of distributed matrices and implementation of vector-matrix operations in parallel mode. It is shown that the proposed way of matrix storage reduces the number of interprocessor exchanges. A series of numerical experiments illustrates the effect of the multigrid SLAE solver tuning on the general efficiency of the algorithm; the tuning involves the types of the cycles used (V, W, and F), the number of iterations of a smoothing operator, and the number of cells for coarsening. Two ways (direct and indirect) of efficiency evaluation for parallelization of the numerical algorithm are demonstrated. The paper presents the results of solving some internal and external flow problems with the evaluation of parallelization efficiency by two algorithms. It is shown that the proposed parallel implementation enables efficient computations for the problems on a thousand processors. Based on the results obtained, some general recommendations are made for the optimal tuning of the multigrid solver, as well as for selecting the optimal number of cells per processor.

  20. Modeling the Fracture of Ice Sheets on Parallel Computers

    Energy Technology Data Exchange (ETDEWEB)

    Waisman, Haim [Columbia Univ., New York, NY (United States); Tuminaro, Ray [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

    2013-10-10

    The objective of this project was to investigate the complex fracture of ice and understand its role within larger ice sheet simulations and global climate change. This objective was achieved by developing novel physics based models for ice, novel numerical tools to enable the modeling of the physics and by collaboration with the ice community experts. At the present time, ice fracture is not explicitly considered within ice sheet models due in part to large computational costs associated with the accurate modeling of this complex phenomena. However, fracture not only plays an extremely important role in regional behavior but also influences ice dynamics over much larger zones in ways that are currently not well understood. To this end, our research findings through this project offers significant advancement to the field and closes a large gap of knowledge in understanding and modeling the fracture of ice sheets in the polar regions. Thus, we believe that our objective has been achieved and our research accomplishments are significant. This is corroborated through a set of published papers, posters and presentations at technical conferences in the field. In particular significant progress has been made in the mechanics of ice, fracture of ice sheets and ice shelves in polar regions and sophisticated numerical methods that enable the solution of the physics in an efficient way.

  1. Parallel Object-Oriented Computation Applied to a Finite Element Problem

    Directory of Open Access Journals (Sweden)

    Jon B. Weissman

    1993-01-01

    Full Text Available The conventional wisdom in the scientific computing community is that the best way to solve large-scale numerically intensive scientific problems on today's parallel MIMD computers is to use Fortran or C programmed in a data-parallel style using low-level message-passing primitives. This approach inevitably leads to nonportable codes and extensive development time, and restricts parallel programming to the domain of the expert programmer. We believe that these problems are not inherent to parallel computing but are the result of the programming tools used. We will show that comparable performance can be achieved with little effort if better tools that present higher level abstractions are used. The vehicle for our demonstration is a 2D electromagnetic finite element scattering code we have implemented in Mentat, an object-oriented parallel processing system. We briefly describe the application. Mentat, the implementation, and present performance results for both a Mentat and a hand-coded parallel Fortran version.

  2. A language for data-parallel and task parallel programming dedicated to multi-SIMD computers. Contributions to hydrodynamic simulation with lattice gases

    International Nuclear Information System (INIS)

    Pic, Marc Michel

    1995-01-01

    Parallel programming covers task-parallelism and data-parallelism. Many problems need both parallelisms. Multi-SIMD computers allow hierarchical approach of these parallelisms. The T++ language, based on C++, is dedicated to exploit Multi-SIMD computers using a programming paradigm which is an extension of array-programming to tasks managing. Our language introduced array of independent tasks to achieve separately (MIMD), on subsets of processors of identical behaviour (SIMD), in order to translate the hierarchical inclusion of data-parallelism in task-parallelism. To manipulate in a symmetrical way tasks and data we propose meta-operations which have the same behaviour on tasks arrays and on data arrays. We explain how to implement this language on our parallel computer SYMPHONIE in order to profit by the locally-shared memory, by the hardware virtualization, and by the multiplicity of communications networks. We analyse simultaneously a typical application of such architecture. Finite elements scheme for Fluid mechanic needs powerful parallel computers and requires large floating points abilities. Lattice gases is an alternative to such simulations. Boolean lattice bases are simple, stable, modular, need to floating point computation, but include numerical noise. Boltzmann lattice gases present large precision of computation, but needs floating points and are only locally stable. We propose a new scheme, called multi-bit, who keeps the advantages of each boolean model to which it is applied, with large numerical precision and reduced noise. Experiments on viscosity, physical behaviour, noise reduction and spurious invariants are shown and implementation techniques for parallel Multi-SIMD computers detailed. (author) [fr

  3. Parallel Computing Characteristics of Two-Phase Thermal-Hydraulics code, CUPID

    International Nuclear Information System (INIS)

    Lee, Jae Ryong; Yoon, Han Young

    2013-01-01

    Parallelized CUPID code has proved to be able to reproduce multi-dimensional thermal hydraulic analysis by validating with various conceptual problems and experimental data. In this paper, the characteristics of the parallelized CUPID code were investigated. Both single- and two phase simulation are taken into account. Since the scalability of a parallel simulation is known to be better for fine mesh system, two types of mesh system are considered. In addition, the dependency of the preconditioner for matrix solver was also compared. The scalability for the single-phase flow is better than that for two-phase flow due to the less numbers of iterations for solving pressure matrix. The CUPID code was investigated the parallel performance in terms of scalability. The CUPID code was parallelized with domain decomposition method. The MPI library was adopted to communicate the information at the interface cells. As increasing the number of mesh, the scalability is improved. For a given mesh, single-phase flow simulation with diagonal preconditioner shows the best speedup. However, for the two-phase flow simulation, the ILU preconditioner is recommended since it reduces the overall simulation time

  4. Storing files in a parallel computing system based on user-specified parser function

    Science.gov (United States)

    Faibish, Sorin; Bent, John M; Tzelnic, Percy; Grider, Gary; Manzanares, Adam; Torres, Aaron

    2014-10-21

    Techniques are provided for storing files in a parallel computing system based on a user-specified parser function. A plurality of files generated by a distributed application in a parallel computing system are stored by obtaining a parser from the distributed application for processing the plurality of files prior to storage; and storing one or more of the plurality of files in one or more storage nodes of the parallel computing system based on the processing by the parser. The plurality of files comprise one or more of a plurality of complete files and a plurality of sub-files. The parser can optionally store only those files that satisfy one or more semantic requirements of the parser. The parser can also extract metadata from one or more of the files and the extracted metadata can be stored with one or more of the plurality of files and used for searching for files.

  5. Parallel computing simulation of fluid flow in the unsaturated zone of Yucca Mountain, Nevada

    International Nuclear Information System (INIS)

    Zhang, Keni; Wu, Yu-Shu; Bodvarsson, G.S.

    2001-01-01

    This paper presents the application of parallel computing techniques to large-scale modeling of fluid flow in the unsaturated zone (UZ) at Yucca Mountain, Nevada. In this study, parallel computing techniques, as implemented into the TOUGH2 code, are applied in large-scale numerical simulations on a distributed-memory parallel computer. The modeling study has been conducted using an over-one-million-cell three-dimensional numerical model, which incorporates a wide variety of field data for the highly heterogeneous fractured formation at Yucca Mountain. The objective of this study is to analyze the impact of various surface infiltration scenarios (under current and possible future climates) on flow through the UZ system, using various hydrogeological conceptual models with refined grids. The results indicate that the one-million-cell models produce better resolution results and reveal some flow patterns that cannot be obtained using coarse-grid modeling models

  6. Breast Cancer Image Segmentation Using K-Means Clustering Based on GPU Cuda Parallel Computing

    Directory of Open Access Journals (Sweden)

    Andika Elok Amalia

    2018-02-01

    Full Text Available Image processing technology is now widely used in the health area, one example is to help the radiologist to analyze the result of MRI (Magnetic Resonance Imaging, CT Scan and Mammography. Image segmentation is a process which is intended to obtain the objects contained in the image by dividing the image into several areas that have similarity attributes on an object with the aim of facilitating the analysis process. The increasing amount  of patient data and larger image size are new challenges in segmentation process to use time efficiently while still keeping the process quality. Research on the segmentation of medical images have been done but still few that combine with parallel computing. In this research, K-Means clustering on the image of mammography result is implemented using two-way computation which are serial and parallel. The result shows that parallel computing  gives faster average performance execution up to twofold.

  7. 8th International Workshop on Parallel Tools for High Performance Computing

    CERN Document Server

    Gracia, José; Knüpfer, Andreas; Resch, Michael; Nagel, Wolfgang

    2015-01-01

    Numerical simulation and modelling using High Performance Computing has evolved into an established technique in academic and industrial research. At the same time, the High Performance Computing infrastructure is becoming ever more complex. For instance, most of the current top systems around the world use thousands of nodes in which classical CPUs are combined with accelerator cards in order to enhance their compute power and energy efficiency. This complexity can only be mastered with adequate development and optimization tools. Key topics addressed by these tools include parallelization on heterogeneous systems, performance optimization for CPUs and accelerators, debugging of increasingly complex scientific applications, and optimization of energy usage in the spirit of green IT. This book represents the proceedings of the 8th International Parallel Tools Workshop, held October 1-2, 2014 in Stuttgart, Germany – which is a forum to discuss the latest advancements in the parallel tools.

  8. Fluid/Structure Interaction Studies of Aircraft Using High Fidelity Equations on Parallel Computers

    Science.gov (United States)

    Guruswamy, Guru; VanDalsem, William (Technical Monitor)

    1994-01-01

    Abstract Aeroelasticity which involves strong coupling of fluids, structures and controls is an important element in designing an aircraft. Computational aeroelasticity using low fidelity methods such as the linear aerodynamic flow equations coupled with the modal structural equations are well advanced. Though these low fidelity approaches are computationally less intensive, they are not adequate for the analysis of modern aircraft such as High Speed Civil Transport (HSCT) and Advanced Subsonic Transport (AST) which can experience complex flow/structure interactions. HSCT can experience vortex induced aeroelastic oscillations whereas AST can experience transonic buffet associated structural oscillations. Both aircraft may experience a dip in the flutter speed at the transonic regime. For accurate aeroelastic computations at these complex fluid/structure interaction situations, high fidelity equations such as the Navier-Stokes for fluids and the finite-elements for structures are needed. Computations using these high fidelity equations require large computational resources both in memory and speed. Current conventional super computers have reached their limitations both in memory and speed. As a result, parallel computers have evolved to overcome the limitations of conventional computers. This paper will address the transition that is taking place in computational aeroelasticity from conventional computers to parallel computers. The paper will address special techniques needed to take advantage of the architecture of new parallel computers. Results will be illustrated from computations made on iPSC/860 and IBM SP2 computer by using ENSAERO code that directly couples the Euler/Navier-Stokes flow equations with high resolution finite-element structural equations.

  9. Parallel, distributed and GPU computing technologies in single-particle electron microscopy.

    Science.gov (United States)

    Schmeisser, Martin; Heisen, Burkhard C; Luettich, Mario; Busche, Boris; Hauer, Florian; Koske, Tobias; Knauber, Karl-Heinz; Stark, Holger

    2009-07-01

    Most known methods for the determination of the structure of macromolecular complexes are limited or at least restricted at some point by their computational demands. Recent developments in information technology such as multicore, parallel and GPU processing can be used to overcome these limitations. In particular, graphics processing units (GPUs), which were originally developed for rendering real-time effects in computer games, are now ubiquitous and provide unprecedented computational power for scientific applications. Each parallel-processing paradigm alone can improve overall performance; the increased computational performance obtained by combining all paradigms, unleashing the full power of today's technology, makes certain applications feasible that were previously virtually impossible. In this article, state-of-the-art paradigms are introduced, the tools and infrastructure needed to apply these paradigms are presented and a state-of-the-art infrastructure and solution strategy for moving scientific applications to the next generation of computer hardware is outlined.

  10. Scalable and massively parallel Monte Carlo photon transport simulations for heterogeneous computing platforms.

    Science.gov (United States)

    Yu, Leiming; Nina-Paravecino, Fanny; Kaeli, David; Fang, Qianqian

    2018-01-01

    We present a highly scalable Monte Carlo (MC) three-dimensional photon transport simulation platform designed for heterogeneous computing systems. Through the development of a massively parallel MC algorithm using the Open Computing Language framework, this research extends our existing graphics processing unit (GPU)-accelerated MC technique to a highly scalable vendor-independent heterogeneous computing environment, achieving significantly improved performance and software portability. A number of parallel computing techniques are investigated to achieve portable performance over a wide range of computing hardware. Furthermore, multiple thread-level and device-level load-balancing strategies are developed to obtain efficient simulations using multiple central processing units and GPUs. (2018) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE).

  11. Generalized Portable SHMEM Library for High Performance Computing

    Energy Technology Data Exchange (ETDEWEB)

    Parzyszek, Krzysztof [Iowa State Univ., Ames, IA (United States)

    2003-01-01

    This dissertation describes the efforts to design and implement the Generalized Portable SHMEM library, GPSHMEM, as well as supplementary tools. There are two major components of the GPSHMEM project: the GPSHMEM library itself and the Fortran 77 source-to-source translator. The rest of this thesis is divided into two parts. Part I introduces the shared memory model and the distributed shared memory model. It explains the motivation behind GPSHMEM and presents its functionality and performance results. Part II is entirely devoted to the Fortran 77 translator call fgpp. The need for such a tool is demonstrated, functionality goals are stated, and the design issues are presented along with the development of the solutions.

  12. Computer program user's manual for FIREFINDER digital topographic data verification library dubbing system

    Science.gov (United States)

    Ceres, M.; Heselton, L. R., III

    1981-11-01

    This manual describes the computer programs for the FIREFINDER Digital Topographic Data Verification-Library-Dubbing System (FFDTDVLDS), and will assist in the maintenance of these programs. The manual contains detailed flow diagrams and associated descriptions for each computer program routine and subroutine. Complete computer program listings are also included. This information should be used when changes are made in the computer programs. The operating system has been designed to minimize operator intervention.

  13. Heterogeneous Hardware Parallelism Review of the IN2P3 2016 Computing School

    Science.gov (United States)

    Lafage, Vincent

    2017-11-01

    Parallel and hybrid Monte Carlo computation. The Monte Carlo method is the main workhorse for computation of particle physics observables. This paper provides an overview of various HPC technologies that can be used today: multicore (OpenMP, HPX), manycore (OpenCL). The rewrite of a twenty years old Fortran 77 Monte Carlo will illustrate the various programming paradigms in use beyond language implementation. The problem of parallel random number generator will be addressed. We will give a short report of the one week school dedicated to these recent approaches, that took place in École Polytechnique in May 2016.

  14. DVS-SOFTWARE: An Effective Tool for Applying Highly Parallelized Hardware To Computational Geophysics

    Science.gov (United States)

    Herrera, I.; Herrera, G. S.

    2015-12-01

    Most geophysical systems are macroscopic physical systems. The behavior prediction of such systems is carried out by means of computational models whose basic models are partial differential equations (PDEs) [1]. Due to the enormous size of the discretized version of such PDEs it is necessary to apply highly parallelized super-computers. For them, at present, the most efficient software is based on non-overlapping domain decomposition methods (DDM). However, a limiting feature of the present state-of-the-art techniques is due to the kind of discretizations used in them. Recently, I. Herrera and co-workers using 'non-overlapping discretizations' have produced the DVS-Software which overcomes this limitation [2]. The DVS-software can be applied to a great variety of geophysical problems and achieves very high parallel efficiencies (90%, or so [3]). It is therefore very suitable for effectively applying the most advanced parallel supercomputers available at present. In a parallel talk, in this AGU Fall Meeting, Graciela Herrera Z. will present how this software is being applied to advance MOD-FLOW. Key Words: Parallel Software for Geophysics, High Performance Computing, HPC, Parallel Computing, Domain Decomposition Methods (DDM)REFERENCES [1]. Herrera Ismael and George F. Pinder, Mathematical Modelling in Science and Engineering: An axiomatic approach", John Wiley, 243p., 2012. [2]. Herrera, I., de la Cruz L.M. and Rosas-Medina A. "Non Overlapping Discretization Methods for Partial, Differential Equations". NUMER METH PART D E, 30: 1427-1454, 2014, DOI 10.1002/num 21852. (Open source) [3]. Herrera, I., & Contreras Iván "An Innovative Tool for Effectively Applying Highly Parallelized Software To Problems of Elasticity". Geofísica Internacional, 2015 (In press)

  15. Utilization of KENO-IV computer code with HANSEN-ROACH library

    International Nuclear Information System (INIS)

    Lima Barros, M. de; Vellozo, S.O.

    1982-01-01

    Several analysis with KENO-IV computer code, which is based in the Monte Carlo method, and the cross section library HANSEN-ROACH, were done, aiming to present the more convenient form to execute criticality calculations with this computer code and this cross sections. (E.G.) [pt

  16. Close the Gate, Lock the Windows, Bolt the Doors: Securing Library Computers. Online Treasures

    Science.gov (United States)

    Balas, Janet

    2005-01-01

    This article, written by a systems librarian at the Monroeville Public Library, discusses a major issue affecting all computer users, security. It indicates that while, staying up-to-date on the latest security issues has become essential for all computer users, it's more critical for network managers who are responsible for securing computer…

  17. Abstracts of computer programs and data libraries pertaining to photon production data

    International Nuclear Information System (INIS)

    White, J.E.; Manneschmidt, J.B.; Finch, S.Y.; Dickens, J.K.

    1998-01-01

    Abstracts, or descriptions, of computer programs and data libraries pertaining to Photon Production Data (Measurements, Evaluations and Calculations) maintained in the collections of the Radiation Safety Information Computational Center, Oak Ridge, Tennessee USA and at the OECD/NEA Data Bank, Paris, are collected in this document

  18. Abstracts of computer programs and data libraries pertaining to photon production data

    Energy Technology Data Exchange (ETDEWEB)

    White, J.E.; Manneschmidt, J.B.; Finch, S.Y.; Dickens, J.K.

    1998-06-01

    Abstracts, or descriptions, of computer programs and data libraries pertaining to Photon Production Data (Measurements, Evaluations and Calculations) maintained in the collections of the Radiation Safety Information Computational Center, Oak Ridge, Tennessee USA and at the OECD/NEA Data Bank, Paris, are collected in this document.

  19. PAPIRUS, a parallel computing framework for sensitivity analysis, uncertainty propagation, and estimation of parameter distribution

    International Nuclear Information System (INIS)

    Heo, Jaeseok; Kim, Kyung Doo

    2015-01-01

    Highlights: • We developed an interface between an engineering simulation code and statistical analysis software. • Multiple packages of the sensitivity analysis, uncertainty quantification, and parameter estimation algorithms are implemented in the framework. • Parallel computing algorithms are also implemented in the framework to solve multiple computational problems simultaneously. - Abstract: This paper introduces a statistical data analysis toolkit, PAPIRUS, designed to perform the model calibration, uncertainty propagation, Chi-square linearity test, and sensitivity analysis for both linear and nonlinear problems. The PAPIRUS was developed by implementing multiple packages of methodologies, and building an interface between an engineering simulation code and the statistical analysis algorithms. A parallel computing framework is implemented in the PAPIRUS with multiple computing resources and proper communications between the server and the clients of each processor. It was shown that even though a large amount of data is considered for the engineering calculation, the distributions of the model parameters and the calculation results can be quantified accurately with significant reductions in computational effort. A general description about the PAPIRUS with a graphical user interface is presented in Section 2. Sections 2.1–2.5 present the methodologies of data assimilation, uncertainty propagation, Chi-square linearity test, and sensitivity analysis implemented in the toolkit with some results obtained by each module of the software. Parallel computing algorithms adopted in the framework to solve multiple computational problems simultaneously are also summarized in the paper

  20. PAPIRUS, a parallel computing framework for sensitivity analysis, uncertainty propagation, and estimation of parameter distribution

    Energy Technology Data Exchange (ETDEWEB)

    Heo, Jaeseok, E-mail: jheo@kaeri.re.kr; Kim, Kyung Doo, E-mail: kdkim@kaeri.re.kr

    2015-10-15

    Highlights: • We developed an interface between an engineering simulation code and statistical analysis software. • Multiple packages of the sensitivity analysis, uncertainty quantification, and parameter estimation algorithms are implemented in the framework. • Parallel computing algorithms are also implemented in the framework to solve multiple computational problems simultaneously. - Abstract: This paper introduces a statistical data analysis toolkit, PAPIRUS, designed to perform the model calibration, uncertainty propagation, Chi-square linearity test, and sensitivity analysis for both linear and nonlinear problems. The PAPIRUS was developed by implementing multiple packages of methodologies, and building an interface between an engineering simulation code and the statistical analysis algorithms. A parallel computing framework is implemented in the PAPIRUS with multiple computing resources and proper communications between the server and the clients of each processor. It was shown that even though a large amount of data is considered for the engineering calculation, the distributions of the model parameters and the calculation results can be quantified accurately with significant reductions in computational effort. A general description about the PAPIRUS with a graphical user interface is presented in Section 2. Sections 2.1–2.5 present the methodologies of data assimilation, uncertainty propagation, Chi-square linearity test, and sensitivity analysis implemented in the toolkit with some results obtained by each module of the software. Parallel computing algorithms adopted in the framework to solve multiple computational problems simultaneously are also summarized in the paper.

  1. Parallel computing in cluster of GPU applied to a problem of nuclear engineering

    International Nuclear Information System (INIS)

    Moraes, Sergio Ricardo S.; Heimlich, Adino; Resende, Pedro

    2013-01-01

    Cluster computing has been widely used as a low cost alternative for parallel processing in scientific applications. With the use of Message-Passing Interface (MPI) protocol development became even more accessible and widespread in the scientific community. A more recent trend is the use of Graphic Processing Unit (GPU), which is a powerful co-processor able to perform hundreds of instructions in parallel, reaching a capacity of hundreds of times the processing of a CPU. However, a standard PC does not allow, in general, more than two GPUs. Hence, it is proposed in this work development and evaluation of a hybrid low cost parallel approach to the solution to a nuclear engineering typical problem. The idea is to use clusters parallelism technology (MPI) together with GPU programming techniques (CUDA - Compute Unified Device Architecture) to simulate neutron transport through a slab using Monte Carlo method. By using a cluster comprised by four quad-core computers with 2 GPU each, it has been developed programs using MPI and CUDA technologies. Experiments, applying different configurations, from 1 to 8 GPUs has been performed and results were compared with the sequential (non-parallel) version. A speed up of about 2.000 times has been observed when comparing the 8-GPU with the sequential version. Results here presented are discussed and analyzed with the objective of outlining gains and possible limitations of the proposed approach. (author)

  2. Speed up of MCACE, a Monte Carlo code for evaluation of shielding safety, by parallel computer, (3)

    International Nuclear Information System (INIS)

    Takano, Makoto; Masukawa, Fumihiro; Naito, Yoshitaka; Onodera, Emi; Imawaka, Tsuneyuki; Yoda, Yoshihisa.

    1993-07-01

    The parallel computing of the MCACE code has been studied on two platforms; 1) Shared Memory Type Vector-Parallel Computer Monte-4 and 2) Networked Several Workstations. On the Monte-4, a disk-file has been allocated to collect all results computed by 4 CPUs in parallel, executing the copy of the MCACE code on each CPU. On the workstations under network environment, two parallel models have been evaluated; 1) a host-node model and 2) the model used on the Monte-4 where no software for parallelization has been employed but only standard FORTRAN language. The measurement of computing times has showed that speed up of about 3 times has been achieved by using 4 CPUs of the Monte-4. Further, connecting 4 workstations by network, the computing speed by parallelization has achieved faster than our scalar main frame computer, FACOM M-780. (author)

  3. Efficient multi-objective calibration of a computationally intensive hydrologic model with parallel computing software in Python

    Science.gov (United States)

    With enhanced data availability, distributed watershed models for large areas with high spatial and temporal resolution are increasingly used to understand water budgets and examine effects of human activities and climate change/variability on water resources. Developing parallel computing software...

  4. On the Performance of the Python Programming Language for Serial and Parallel Scientific Computations

    Directory of Open Access Journals (Sweden)

    Xing Cai

    2005-01-01

    Full Text Available This article addresses the performance of scientific applications that use the Python programming language. First, we investigate several techniques for improving the computational efficiency of serial Python codes. Then, we discuss the basic programming techniques in Python for parallelizing serial scientific applications. It is shown that an efficient implementation of the array-related operations is essential for achieving good parallel performance, as for the serial case. Once the array-related operations are efficiently implemented, probably using a mixed-language implementation, good serial and parallel performance become achievable. This is confirmed by a set of numerical experiments. Python is also shown to be well suited for writing high-level parallel programs.

  5. Fast parallel algorithms that compute transitive closure of a fuzzy relation

    Science.gov (United States)

    Kreinovich, Vladik YA.

    1993-01-01

    The notion of a transitive closure of a fuzzy relation is very useful for clustering in pattern recognition, for fuzzy databases, etc. The original algorithm proposed by L. Zadeh (1971) requires the computation time O(n(sup 4)), where n is the number of elements in the relation. In 1974, J. C. Dunn proposed a O(n(sup 2)) algorithm. Since we must compute n(n-1)/2 different values s(a, b) (a not equal to b) that represent the fuzzy relation, and we need at least one computational step to compute each of these values, we cannot compute all of them in less than O(n(sup 2)) steps. So, Dunn's algorithm is in this sense optimal. For small n, it is ok. However, for big n (e.g., for big databases), it is still a lot, so it would be desirable to decrease the computation time (this problem was formulated by J. Bezdek). Since this decrease cannot be done on a sequential computer, the only way to do it is to use a computer with several processors working in parallel. We show that on a parallel computer, transitive closure can be computed in time O((log(sub 2)(n))2).

  6. Effecting a broadcast with an allreduce operation on a parallel computer

    Science.gov (United States)

    Almasi, Gheorghe; Archer, Charles J.; Ratterman, Joseph D.; Smith, Brian E.

    2010-11-02

    A parallel computer comprises a plurality of compute nodes organized into at least one operational group for collective parallel operations. Each compute node is assigned a unique rank and is coupled for data communications through a global combining network. One compute node is assigned to be a logical root. A send buffer and a receive buffer is configured. Each element of a contribution of the logical root in the send buffer is contributed. One or more zeros corresponding to a size of the element are injected. An allreduce operation with a bitwise OR using the element and the injected zeros is performed. And the result for the allreduce operation is determined and stored in each receive buffer.

  7. Approaches for introducing high molecular diversity in scaffolds: fast parallel synthesis of highly substituted 1H-quinolin-4-one libraries.

    Science.gov (United States)

    Kuznetsov, Vladimir; Gorohovsky, Sofia; Levy, Amalia; Meir, Simcha; Shkoulev, Vladimir; Menashe, Naim; Greenwald, Moshe; Aizikovich, Alexander; Ofer, Dror; Byk, Gerardo; Gellerman, Garry

    2004-01-01

    We have developed a two steps strategy for the parallel synthesis of highly diversified quinolin-ones. In the first step we have combined and improved different synthetic methods for generating quinolin-4-ones bearing four different substitutions at specific positions using round bottomed flasks. The synthesis was assessed for a large number of substituted quinolin-4-ones. In the second step, the improved method was adapted to a parallel array synthesis using a 12 positions carrousel as demonstrated for the synthesis of 42-variable quinolin-4-ones. The first combinatorial library set 14(a-x) was obtained with a chemical purity of more than 95% without purification, the second library set 15(a-r), which included two synthetic steps, needed combinatorial purification using an innovative parallel purifier. The proposed approach contributes to a more extensive diversification of molecular scaffolds in general and provides access to highly substituted quinolinones in particular.

  8. Parallelization of the preconditioned IDR solver for modern multicore computer systems

    Science.gov (United States)

    Bessonov, O. A.; Fedoseyev, A. I.

    2012-10-01

    This paper present the analysis, parallelization and optimization approach for the large sparse matrix solver CNSPACK for modern multicore microprocessors. CNSPACK is an advanced solver successfully used for coupled solution of stiff problems arising in multiphysics applications such as CFD, semiconductor transport, kinetic and quantum problems. It employs iterative IDR algorithm with ILU preconditioning (user chosen ILU preconditioning order). CNSPACK has been successfully used during last decade for solving problems in several application areas, including fluid dynamics and semiconductor device simulation. However, there was a dramatic change in processor architectures and computer system organization in recent years. Due to this, performance criteria and methods have been revisited, together with involving the parallelization of the solver and preconditioner using Open MP environment. Results of the successful implementation for efficient parallelization are presented for the most advances computer system (Intel Core i7-9xx or two-processor Xeon 55xx/56xx).

  9. Fast parallel molecular algorithms for DNA-based computation: factoring integers.

    Science.gov (United States)

    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.

  10. A review of parallel computing for large-scale remote sensing image mosaicking

    OpenAIRE

    Chen, Lajiao; Ma, Yan; Liu, Peng; Wei, Jingbo; Jie, Wei; He, Jijun

    2015-01-01

    Interest in image mosaicking has been spurred by a wide variety of research and management needs. However, for large-scale applications, remote sensing image mosaicking usually requires significant computational capabilities. Several studies have attempted to apply parallel computing to improve image mosaicking algorithms and to speed up calculation process. The state of the art of this field has not yet been summarized, which is, however, essential for a better understanding and for further ...

  11. DendroPy: a Python library for phylogenetic computing.

    Science.gov (United States)

    Sukumaran, Jeet; Holder, Mark T

    2010-06-15

    DendroPy is a cross-platform library for the Python programming language that provides for object-oriented reading, writing, simulation and manipulation of phylogenetic data, with an emphasis on phylogenetic tree operations. DendroPy uses a splits-hash mapping to perform rapid calculations of tree distances, similarities and shape under various metrics. It contains rich simulation routines to generate trees under a number of different phylogenetic and coalescent models. DendroPy's data simulation and manipulation facilities, in conjunction with its support of a broad range of phylogenetic data formats (NEXUS, Newick, PHYLIP, FASTA, NeXML, etc.), allow it to serve a useful role in various phyloinformatics and phylogeographic pipelines. The stable release of the library is available for download and automated installation through the Python Package Index site (http://pypi.python.org/pypi/DendroPy), while the active development source code repository is available to the public from GitHub (http://github.com/jeetsukumaran/DendroPy).

  12. GPU-based parallel computing in real-time modeling of atmospheric transport and diffusion of radioactive material

    International Nuclear Information System (INIS)

    Santos, Marcelo C. dos; Pereira, Claudio M.N.A.; Schirru, Roberto; Pinheiro, André; Coordenacao de Pos-Graduacao e Pesquisa de Engenharia

    2017-01-01

    Atmospheric radionuclide dispersion systems (ARDS) are essential mechanisms to predict the consequences of unexpected radioactive releases from nuclear power plants. Considering, that during an eventuality of an accident with a radioactive material release, an accurate forecast is vital to guide the evacuation plan of the possible affected areas. However, in order to predict the dispersion of the radioactive material and its impact on the environment, the model must process information about source term (radioactive materials released, activities and location), weather condition (wind, humidity and precipitation) and geographical characteristics (topography). Furthermore, ARDS is basically composed of 4 main modules: Source Term, Wind Field, Plume Dispersion and Doses Calculations. The Wind Field and Plume Dispersion modules are the ones that require a high computational performance to achieve accurate results within an acceptable time. Taking this into account, this work focuses on the development of a GPU-based parallel Plume Dispersion module, focusing on the radionuclide transport and diffusion calculations, which use a given wind field and a released source term as parameters. The program is being developed using the C ++ programming language, allied with CUDA libraries. In comparative case study between a parallel and sequential version of the slower function of the Plume Dispersion module, a speedup of 11.63 times could be observed. (author)

  13. GPU-based parallel computing in real-time modeling of atmospheric transport and diffusion of radioactive material

    Energy Technology Data Exchange (ETDEWEB)

    Santos, Marcelo C. dos; Pereira, Claudio M.N.A.; Schirru, Roberto; Pinheiro, André, E-mail: jovitamarcelo@gmail.com, E-mail: cmnap@ien.gov.br, E-mail: schirru@lmp.ufrj.br, E-mail: apinheiro99@gmail.com [Instituto de Engenharia Nuclear (IEN/CNEN-RJ), Rio de Janeiro, RJ (Brazil); Coordenacao de Pos-Graduacao e Pesquisa de Engenharia (COPPE/UFRJ), Rio de Janeiro, RJ (Brazil). Programa de Engenharia Nuclear

    2017-07-01

    Atmospheric radionuclide dispersion systems (ARDS) are essential mechanisms to predict the consequences of unexpected radioactive releases from nuclear power plants. Considering, that during an eventuality of an accident with a radioactive material release, an accurate forecast is vital to guide the evacuation plan of the possible affected areas. However, in order to predict the dispersion of the radioactive material and its impact on the environment, the model must process information about source term (radioactive materials released, activities and location), weather condition (wind, humidity and precipitation) and geographical characteristics (topography). Furthermore, ARDS is basically composed of 4 main modules: Source Term, Wind Field, Plume Dispersion and Doses Calculations. The Wind Field and Plume Dispersion modules are the ones that require a high computational performance to achieve accurate results within an acceptable time. Taking this into account, this work focuses on the development of a GPU-based parallel Plume Dispersion module, focusing on the radionuclide transport and diffusion calculations, which use a given wind field and a released source term as parameters. The program is being developed using the C ++ programming language, allied with CUDA libraries. In comparative case study between a parallel and sequential version of the slower function of the Plume Dispersion module, a speedup of 11.63 times could be observed. (author)

  14. Parallel Implementation of Triangular Cellular Automata for Computing Two-Dimensional Elastodynamic Response on Arbitrary Domains

    Science.gov (United States)

    Leamy, Michael J.; Springer, Adam C.

    In this research we report parallel implementation of a Cellular Automata-based simulation tool for computing elastodynamic response on complex, two-dimensional domains. Elastodynamic simulation using Cellular Automata (CA) has recently been presented as an alternative, inherently object-oriented technique for accurately and efficiently computing linear and nonlinear wave propagation in arbitrarily-shaped geometries. The local, autonomous nature of the method should lead to straight-forward and efficient parallelization. We address this notion on symmetric multiprocessor (SMP) hardware using a Java-based object-oriented CA code implementing triangular state machines (i.e., automata) and the MPI bindings written in Java (MPJ Express). We use MPJ Express to reconfigure our existing CA code to distribute a domain's automata to cores present on a dual quad-core shared-memory system (eight total processors). We note that this message passing parallelization strategy is directly applicable to computer clustered computing, which will be the focus of follow-on research. Results on the shared memory platform indicate nearly-ideal, linear speed-up. We conclude that the CA-based elastodynamic simulator is easily configured to run in parallel, and yields excellent speed-up on SMP hardware.

  15. The boat hull model : adapting the roofline model to enable performance prediction for parallel computing

    NARCIS (Netherlands)

    Nugteren, C.; Corporaal, H.

    2012-01-01

    Multi-core and many-core were already major trends for the past six years, and are expected to continue for the next decades. With these trends of parallel computing, it becomes increasingly difficult to decide on which architecture to run a given application. In this work, we use an algorithm

  16. The boat hull model : enabling performance prediction for parallel computing prior to code development

    NARCIS (Netherlands)

    Nugteren, C.; Corporaal, H.

    2012-01-01

    Multi-core and many-core were already major trends for the past six years and are expected to continue for the next decade. With these trends of parallel computing, it becomes increasingly difficult to decide on which processor to run a given application, mainly because the programming of these

  17. Parallel Structures of Computer-Assisted Signature Pedagogy: The Case of Integrated Spreadsheets

    Science.gov (United States)

    Abramovich, Sergei; Easton, Jonathan; Hayes, Victoria O.

    2012-01-01

    This article was motivated by the authors' work on a project with a group of 2nd-grade students in a computer lab of a rural school in upstate New York. From this project, one goal of which was to provide a capstone experience for a teacher candidate in teaching application-oriented mathematics with technology, the ideas about parallel structures…

  18. High Performance Parallel Processing Project: Industrial computing initiative. Progress reports for fiscal year 1995

    Energy Technology Data Exchange (ETDEWEB)

    Koniges, A.

    1996-02-09

    This project is a package of 11 individual CRADA`s plus hardware. This innovative project established a three-year multi-party collaboration that is significantly accelerating the availability of commercial massively parallel processing computing software technology to U.S. government, academic, and industrial end-users. This report contains individual presentations from nine principal investigators along with overall program information.

  19. Alleviating Search Uncertainty through Concept Associations: Automatic Indexing, Co-Occurrence Analysis, and Parallel Computing.

    Science.gov (United States)

    Chen, Hsinchun; Martinez, Joanne; Kirchhoff, Amy; Ng, Tobun D.; Schatz, Bruce R.

    1998-01-01

    Grounded on object filtering, automatic indexing, and co-occurrence analysis, an experiment was performed using a parallel supercomputer to analyze over 400,000 abstracts in an INSPEC computer engineering collection. A user evaluation revealed that system-generated thesauri were better than the human-generated INSPEC subject thesaurus in concept…

  20. Use of massively parallel computing to improve modelling accuracy within the nuclear sector

    Directory of Open Access Journals (Sweden)

    L M Evans

    2016-06-01

    This work presents recent advancements in three techniques: Uncertainty quantification (UQ; Cellular automata finite element (CAFE; Image based finite element methods (IBFEM. Case studies are presented demonstrating their suitability for use in nuclear engineering made possible by advancements in parallel computing hardware that is projected to be available for industry within the next decade costing of the order of $100k.

  1. Fast parallel algorithm for three-dimensional distance-driven model in iterative computed tomography reconstruction

    International Nuclear Information System (INIS)

    Chen Jian-Lin; Li Lei; Wang Lin-Yuan; Cai Ai-Long; Xi Xiao-Qi; Zhang Han-Ming; Li Jian-Xin; Yan Bin

    2015-01-01

    The projection matrix model is used to describe the physical relationship between reconstructed object and projection. Such a model has a strong influence on projection and backprojection, two vital operations in iterative computed tomographic reconstruction. The distance-driven model (DDM) is a state-of-the-art technology that simulates forward and back projections. This model has a low computational complexity and a relatively high spatial resolution; however, it includes only a few methods in a parallel operation with a matched model scheme. This study introduces a fast and parallelizable algorithm to improve the traditional DDM for computing the parallel projection and backprojection operations. Our proposed model has been implemented on a GPU (graphic processing unit) platform and has achieved satisfactory computational efficiency with no approximation. The runtime for the projection and backprojection operations with our model is approximately 4.5 s and 10.5 s per loop, respectively, with an image size of 256×256×256 and 360 projections with a size of 512×512. We compare several general algorithms that have been proposed for maximizing GPU efficiency by using the unmatched projection/backprojection models in a parallel computation. The imaging resolution is not sacrificed and remains accurate during computed tomographic reconstruction. (paper)

  2. Fast Simulation of Large-Scale Floods Based on GPU Parallel Computing

    Directory of Open Access Journals (Sweden)

    Qiang Liu

    2018-05-01

    Full Text Available Computing speed is a significant issue of large-scale flood simulations for real-time response to disaster prevention and mitigation. Even today, most of the large-scale flood simulations are generally run on supercomputers due to the massive amounts of data and computations necessary. In this work, a two-dimensional shallow water model based on an unstructured Godunov-type finite volume scheme was proposed for flood simulation. To realize a fast simulation of large-scale floods on a personal computer, a Graphics Processing Unit (GPU-based, high-performance computing method using the OpenACC application was adopted to parallelize the shallow water model. An unstructured data management method was presented to control the data transportation between the GPU and CPU (Central Processing Unit with minimum overhead, and then both computation and data were offloaded from the CPU to the GPU, which exploited the computational capability of the GPU as much as possible. The parallel model was validated using various benchmarks and real-world case studies. The results demonstrate that speed-ups of up to one order of magnitude can be achieved in comparison with the serial model. The proposed parallel model provides a fast and reliable tool with which to quickly assess flood hazards in large-scale areas and, thus, has a bright application prospect for dynamic inundation risk identification and disaster assessment.

  3. In-cylinder diesel spray combustion simulations using parallel computation: A performance benchmarking study

    International Nuclear Information System (INIS)

    Pang, Kar Mun; Ng, Hoon Kiat; Gan, Suyin

    2012-01-01

    Highlights: ► A performance benchmarking exercise is conducted for diesel combustion simulations. ► The reduced chemical mechanism shows its advantages over base and skeletal models. ► High efficiency and great reduction of CPU runtime are achieved through 4-node solver. ► Increasing ISAT memory from 0.1 to 2 GB reduces the CPU runtime by almost 35%. ► Combustion and soot processes are predicted well with minimal computational cost. - Abstract: In the present study, in-cylinder diesel combustion simulation was performed with parallel processing on an Intel Xeon Quad-Core platform to allow both fluid dynamics and chemical kinetics of the surrogate diesel fuel model to be solved simultaneously on multiple processors. Here, Cartesian Z-Coordinate was selected as the most appropriate partitioning algorithm since it computationally bisects the domain such that the dynamic load associated with fuel particle tracking was evenly distributed during parallel computations. Other variables examined included number of compute nodes, chemistry sizes and in situ adaptive tabulation (ISAT) parameters. Based on the performance benchmarking test conducted, parallel configuration of 4-compute node was found to reduce the computational runtime most efficiently whereby a parallel efficiency of up to 75.4% was achieved. The simulation results also indicated that accuracy level was insensitive to the number of partitions or the partitioning algorithms. The effect of reducing the number of species on computational runtime was observed to be more significant than reducing the number of reactions. Besides, the study showed that an increase in the ISAT maximum storage of up to 2 GB reduced the computational runtime by 50%. Also, the ISAT error tolerance of 10 −3 was chosen to strike a balance between results accuracy and computational runtime. The optimised parameters in parallel processing and ISAT, as well as the use of the in-house reduced chemistry model allowed accurate

  4. Debunking the Computer Science Digital Library: Lessons Learned in Collection Development at Seneca College of Applied Arts & Technology

    Science.gov (United States)

    Buczynski, James Andrew

    2005-01-01

    Developing a library collection to support the curriculum of Canada's largest computer studies school has debunked many myths about collecting computer science and technology information resources. Computer science students are among the heaviest print book and e-book users in the library. Circulation statistics indicate that the demand for print…

  5. Some computational challenges of developing efficient parallel algorithms for data-dependent computations in thermal-hydraulics supercomputer applications

    International Nuclear Information System (INIS)

    Woodruff, S.B.

    1992-01-01

    The Transient Reactor Analysis Code (TRAC), which features a two- fluid treatment of thermal-hydraulics, is designed to model transients in water reactors and related facilities. One of the major computational costs associated with TRAC and similar codes is calculating constitutive coefficients. Although the formulations for these coefficients are local the costs are flow-regime- or data-dependent; i.e., the computations needed for a given spatial node often vary widely as a function of time. Consequently, poor load balancing will degrade efficiency on either vector or data parallel architectures when the data are organized according to spatial location. Unfortunately, a general automatic solution to the load-balancing problem associated with data-dependent computations is not yet available for massively parallel architectures. This document discusses why developers algorithms, such as a neural net representation, that do not exhibit algorithms, such as a neural net representation, that do not exhibit load-balancing problems

  6. Just-in-Time Compilation-Inspired Methodology for Parallelization of Compute Intensive Java Code

    Directory of Open Access Journals (Sweden)

    GHULAM MUSTAFA

    2017-01-01

    Full Text Available Compute intensive programs generally consume significant fraction of execution time in a small amount of repetitive code. Such repetitive code is commonly known as hotspot code. We observed that compute intensive hotspots often possess exploitable loop level parallelism. A JIT (Just-in-Time compiler profiles a running program to identify its hotspots. Hotspots are then translated into native code, for efficient execution. Using similar approach, we propose a methodology to identify hotspots and exploit their parallelization potential on multicore systems. Proposed methodology selects and parallelizes each DOALL loop that is either contained in a hotspot method or calls a hotspot method. The methodology could be integrated in front-end of a JIT compiler to parallelize sequential code, just before native translation. However, compilation to native code is out of scope of this work. As a case study, we analyze eighteen JGF (Java Grande Forum benchmarks to determine parallelization potential of hotspots. Eight benchmarks demonstrate a speedup of up to 7.6x on an 8-core system

  7. Just-in-time compilation-inspired methodology for parallelization of compute intensive java code

    International Nuclear Information System (INIS)

    Mustafa, G.; Ghani, M.U.

    2017-01-01

    Compute intensive programs generally consume significant fraction of execution time in a small amount of repetitive code. Such repetitive code is commonly known as hotspot code. We observed that compute intensive hotspots often possess exploitable loop level parallelism. A JIT (Just-in-Time) compiler profiles a running program to identify its hotspots. Hotspots are then translated into native code, for efficient execution. Using similar approach, we propose a methodology to identify hotspots and exploit their parallelization potential on multicore systems. Proposed methodology selects and parallelizes each DOALL loop that is either contained in a hotspot method or calls a hotspot method. The methodology could be integrated in front-end of a JIT compiler to parallelize sequential code, just before native translation. However, compilation to native code is out of scope of this work. As a case study, we analyze eighteen JGF (Java Grande Forum) benchmarks to determine parallelization potential of hotspots. Eight benchmarks demonstrate a speedup of up to 7.6x on an 8-core system. (author)

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

    Science.gov (United States)

    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.

  9. BEAGLE: an application programming interface and high-performance computing library for statistical phylogenetics.

    Science.gov (United States)

    Ayres, Daniel L; Darling, Aaron; Zwickl, Derrick J; Beerli, Peter; Holder, Mark T; Lewis, Paul O; Huelsenbeck, John P; Ronquist, Fredrik; Swofford, David L; Cummings, Michael P; Rambaut, Andrew; Suchard, Marc A

    2012-01-01

    Phylogenetic inference is fundamental to our understanding of most aspects of the origin and evolution of life, and in recent years, there has been a concentration of interest in statistical approaches such as Bayesian inference and maximum likelihood estimation. Yet, for large data sets and realistic or interesting models of evolution, these approaches remain computationally demanding. High-throughput sequencing can yield data for thousands of taxa, but scaling to such problems using serial computing often necessitates the use of nonstatistical or approximate approaches. The recent emergence of graphics processing units (GPUs) provides an opportunity to leverage their excellent floating-point computational performance to accelerate statistical phylogenetic inference. A specialized library for phylogenetic calculation would allow existing software packages to make more effective use of available computer hardware, including GPUs. Adoption of a common library would also make it easier for other emerging computing architectures, such as field programmable gate arrays, to be used in the future. We present BEAGLE, an application programming interface (API) and library for high-performance statistical phylogenetic inference. The API provides a uniform interface for performing phylogenetic likelihood calculations on a variety of compute hardware platforms. The library includes a set of efficient implementations and can currently exploit hardware including GPUs using NVIDIA CUDA, central processing units (CPUs) with Streaming SIMD Extensions and related processor supplementary instruction sets, and multicore CPUs via OpenMP. To demonstrate the advantages of a common API, we have incorporated the library into several popular phylogenetic software packages. The BEAGLE library is free open source software licensed under the Lesser GPL and available from http://beagle-lib.googlecode.com. An example client program is available as public domain software.

  10. Library

    OpenAIRE

    Dulaney, Ronald E. Jr.

    1997-01-01

    This study began with the desire to design a public town library of the future and became a search for an inkling of what is essential to Architecture. It is murky and full of contradictions. It asks more than it proposes, and the traces of its windings are better ordered through collage than logical synthesis. This study is neither a thesis nor a synthesis. When drawing out the measure of this study it may be beneficial to state what it attempts to place at the ...

  11. Architecture and VHDL behavioural validation of a parallel processor dedicated to computer vision

    International Nuclear Information System (INIS)

    Collette, Thierry

    1992-01-01

    Speeding up image processing is mainly obtained using parallel computers; SIMD processors (single instruction stream, multiple data stream) have been developed, and have proven highly efficient regarding low-level image processing operations. Nevertheless, their performances drop for most intermediate of high level operations, mainly when random data reorganisations in processor memories are involved. The aim of this thesis was to extend the SIMD computer capabilities to allow it to perform more efficiently at the image processing intermediate level. The study of some representative algorithms of this class, points out the limits of this computer. Nevertheless, these limits can be erased by architectural modifications. This leads us to propose SYMPATIX, a new SIMD parallel computer. To valid its new concept, a behavioural model written in VHDL - Hardware Description Language - has been elaborated. With this model, the new computer performances have been estimated running image processing algorithm simulations. VHDL modeling approach allows to perform the system top down electronic design giving an easy coupling between system architectural modifications and their electronic cost. The obtained results show SYMPATIX to be an efficient computer for low and intermediate level image processing. It can be connected to a high level computer, opening up the development of new computer vision applications. This thesis also presents, a top down design method, based on the VHDL, intended for electronic system architects. (author) [fr

  12. A learnable parallel processing architecture towards unity of memory and computing.

    Science.gov (United States)

    Li, H; Gao, B; Chen, Z; Zhao, Y; Huang, P; Ye, H; Liu, L; Liu, X; Kang, J

    2015-08-14

    Developing energy-efficient parallel information processing systems beyond von Neumann architecture is a long-standing goal of modern information technologies. The widely used von Neumann computer architecture separates memory and computing units, which leads to energy-hungry data movement when computers work. In order to meet the need of efficient information processing for the data-driven applications such as big data and Internet of Things, an energy-efficient processing architecture beyond von Neumann is critical for the information society. Here we show a non-von Neumann architecture built of resistive switching (RS) devices named "iMemComp", where memory and logic are unified with single-type devices. Leveraging nonvolatile nature and structural parallelism of crossbar RS arrays, we have equipped "iMemComp" with capabilities of computing in parallel and learning user-defined logic functions for large-scale information processing tasks. Such architecture eliminates the energy-hungry data movement in von Neumann computers. Compared with contemporary silicon technology, adder circuits based on "iMemComp" can improve the speed by 76.8% and the power dissipation by 60.3%, together with a 700 times aggressive reduction in the circuit area.

  13. A conceptual design of multidisciplinary-integrated C.F.D. simulation on parallel computers

    International Nuclear Information System (INIS)

    Onishi, Ryoichi; Ohta, Takashi; Kimura, Toshiya.

    1996-11-01

    A design of a parallel aeroelastic code for aircraft integrated simulations is conducted. The method for integrating aerodynamics and structural dynamics software on parallel computers is devised by using the Euler/Navier-Stokes equations coupled with wing-box finite element structures. A synthesis of modern aircraft requires the optimizations of aerodynamics, structures, controls, operabilities, or other design disciplines, and the R and D efforts to implement Multidisciplinary Design Optimization environments using high performance computers are made especially among the U.S. aerospace industries. This report describes a Multiple Program Multiple Data (MPMD) parallelization of aerodynamics and structural dynamics codes with a dynamic deformation grid. A three-dimensional computation of a flowfield with dynamic deformation caused by a structural deformation is performed, and a pressure data calculated is used for a computation of the structural deformation which is input again to a fluid dynamics code. This process is repeated exchanging the computed data of pressures and deformations between flowfield grids and structural elements. It enables to simulate the structure movements which take into account of the interaction of fluid and structure. The conceptual design for achieving the aforementioned various functions is reported. Also the future extensions to incorporate control systems, which enable to simulate a realistic aircraft configuration to be a major tool for Aircraft Integrated Simulation, are investigated. (author)

  14. A learnable parallel processing architecture towards unity of memory and computing

    Science.gov (United States)

    Li, H.; Gao, B.; Chen, Z.; Zhao, Y.; Huang, P.; Ye, H.; Liu, L.; Liu, X.; Kang, J.

    2015-08-01

    Developing energy-efficient parallel information processing systems beyond von Neumann architecture is a long-standing goal of modern information technologies. The widely used von Neumann computer architecture separates memory and computing units, which leads to energy-hungry data movement when computers work. In order to meet the need of efficient information processing for the data-driven applications such as big data and Internet of Things, an energy-efficient processing architecture beyond von Neumann is critical for the information society. Here we show a non-von Neumann architecture built of resistive switching (RS) devices named “iMemComp”, where memory and logic are unified with single-type devices. Leveraging nonvolatile nature and structural parallelism of crossbar RS arrays, we have equipped “iMemComp” with capabilities of computing in parallel and learning user-defined logic functions for large-scale information processing tasks. Such architecture eliminates the energy-hungry data movement in von Neumann computers. Compared with contemporary silicon technology, adder circuits based on “iMemComp” can improve the speed by 76.8% and the power dissipation by 60.3%, together with a 700 times aggressive reduction in the circuit area.

  15. Parallel computation of aerodynamic influence coefficients for aeroelastic analysis on a transputer network

    Science.gov (United States)

    Janetzke, D. C.; Murthy, D. V.

    1991-01-01

    Aeroelastic analysis is mult-disciplinary and computationally expensive. Hence, it can greatly benefit from parallel processing. As part of an effort to develop an aeroelastic analysis capability on a distributed-memory transputer network, a parallel algorithm for the computation of aerodynamic influence coefficients is implemented on a network of 32 transputers. The aerodynamic influence coefficients are calculated using a three-dimensional unsteady aerodynamic model and a panel discretization. Efficiencies up to 85 percent are demonstrated using 32 processors. The effects of subtask ordering, problem size and network topology are presented. A comparison to results on a shared-memory computer indicates that higher speedup is achieved on the distributed-memory system.

  16. Studies of electron collisions with polyatomic molecules using distributed-memory parallel computers

    International Nuclear Information System (INIS)

    Winstead, C.; Hipes, P.G.; Lima, M.A.P.; McKoy, V.

    1991-01-01

    Elastic electron scattering cross sections from 5--30 eV are reported for the molecules C 2 H 4 , C 2 H 6 , C 3 H 8 , Si 2 H 6 , and GeH 4 , obtained using an implementation of the Schwinger multichannel method for distributed-memory parallel computer architectures. These results, obtained within the static-exchange approximation, are in generally good agreement with the available experimental data. These calculations demonstrate the potential of highly parallel computation in the study of collisions between low-energy electrons and polyatomic gases. The computational methodology discussed is also directly applicable to the calculation of elastic cross sections at higher levels of approximation (target polarization) and of electronic excitation cross sections

  17. Animated computer graphics models of space and earth sciences data generated via the massively parallel processor

    Science.gov (United States)

    Treinish, Lloyd A.; Gough, Michael L.; Wildenhain, W. David

    1987-01-01

    The capability was developed of rapidly producing visual representations of large, complex, multi-dimensional space and earth sciences data sets via the implementation of computer graphics modeling techniques on the Massively Parallel Processor (MPP) by employing techniques recently developed for typically non-scientific applications. Such capabilities can provide a new and valuable tool for the understanding of complex scientific data, and a new application of parallel computing via the MPP. A prototype system with such capabilities was developed and integrated into the National Space Science Data Center's (NSSDC) Pilot Climate Data System (PCDS) data-independent environment for computer graphics data display to provide easy access to users. While developing these capabilities, several problems had to be solved independently of the actual use of the MPP, all of which are outlined.

  18. 3-D electromagnetic plasma particle simulations on the Intel Delta parallel computer

    International Nuclear Information System (INIS)

    Wang, J.; Liewer, P.C.

    1994-01-01

    A three-dimensional electromagnetic PIC code has been developed on the 512 node Intel Touchstone Delta MIMD parallel computer. This code is based on the General Concurrent PIC algorithm which uses a domain decomposition to divide the computation among the processors. The 3D simulation domain can be partitioned into 1-, 2-, or 3-dimensional sub-domains. Particles must be exchanged between processors as they move among the subdomains. The Intel Delta allows one to use this code for very-large-scale simulations (i.e. over 10 8 particles and 10 6 grid cells). The parallel efficiency of this code is measured, and the overall code performance on the Delta is compared with that on Cray supercomputers. It is shown that their code runs with a high parallel efficiency of ≥ 95% for large size problems. The particle push time achieved is 115 nsecs/particle/time step for 162 million particles on 512 nodes. Comparing with the performance on a single processor Cray C90, this represents a factor of 58 speedup. The code uses a finite-difference leap frog method for field solve which is significantly more efficient than fast fourier transforms on parallel computers. The performance of this code on the 128 node Cray T3D will also be discussed

  19. SequenceL: Automated Parallel Algorithms Derived from CSP-NT Computational Laws

    Science.gov (United States)

    Cooke, Daniel; Rushton, Nelson

    2013-01-01

    With the introduction of new parallel architectures like the cell and multicore chips from IBM, Intel, AMD, and ARM, as well as the petascale processing available for highend computing, a larger number of programmers will need to write parallel codes. Adding the parallel control structure to the sequence, selection, and iterative control constructs increases the complexity of code development, which often results in increased development costs and decreased reliability. SequenceL is a high-level programming language that is, a programming language that is closer to a human s way of thinking than to a machine s. Historically, high-level languages have resulted in decreased development costs and increased reliability, at the expense of performance. In recent applications at JSC and in industry, SequenceL has demonstrated the usual advantages of high-level programming in terms of low cost and high reliability. SequenceL programs, however, have run at speeds typically comparable with, and in many cases faster than, their counterparts written in C and C++ when run on single-core processors. Moreover, SequenceL is able to generate parallel executables automatically for multicore hardware, gaining parallel speedups without any extra effort from the programmer beyond what is required to write the sequen tial/singlecore code. A SequenceL-to-C++ translator has been developed that automatically renders readable multithreaded C++ from a combination of a SequenceL program and sample data input. The SequenceL language is based on two fundamental computational laws, Consume-Simplify- Produce (CSP) and Normalize-Trans - pose (NT), which enable it to automate the creation of parallel algorithms from high-level code that has no annotations of parallelism whatsoever. In our anecdotal experience, SequenceL development has been in every case less costly than development of the same algorithm in sequential (that is, single-core, single process) C or C++, and an order of magnitude less

  20. Parallel Monte Carlo simulations on an ARC-enabled computing grid

    International Nuclear Information System (INIS)

    Nilsen, Jon K; Samset, Bjørn H

    2011-01-01

    Grid computing opens new possibilities for running heavy Monte Carlo simulations of physical systems in parallel. The presentation gives an overview of GaMPI, a system for running an MPI-based random walker simulation on grid resources. Integrating the ARC middleware and the new storage system Chelonia with the Ganga grid job submission and control system, we show that MPI jobs can be run on a world-wide computing grid with good performance and promising scaling properties. Results for relatively communication-heavy Monte Carlo simulations run on multiple heterogeneous, ARC-enabled computing clusters in several countries are presented.