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

The language parallel Pascal and other aspects of the massively parallel processor

Science.gov (United States)

Reeves, A. P.; Bruner, J. D.

1982-01-01

A high level language for the Massively Parallel Processor (MPP) was designed. This language, called Parallel Pascal, is described in detail. A description of the language design, a description of the intermediate language, Parallel P-Code, and details for the MPP implementation are included. Formal descriptions of Parallel Pascal and Parallel P-Code are given. A compiler was developed which converts programs in Parallel Pascal into the intermediate Parallel P-Code language. The code generator to complete the compiler for the MPP is being developed independently. A Parallel Pascal to Pascal translator was also developed. The architecture design for a VLSI version of the MPP was completed with a description of fault tolerant interconnection networks. The memory arrangement aspects of the MPP are discussed and a survey of other high level languages is given.

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.

A Programming Model for Massive Data Parallelism with Data Dependencies

International Nuclear Information System (INIS)

Cui, Xiaohui; Mueller, Frank; Potok, Thomas E.; Zhang, Yongpeng

2009-01-01

Accelerating processors can often be more cost and energy effective for a wide range of data-parallel computing problems than general-purpose processors. For graphics processor units (GPUs), this is particularly the case when program development is aided by environments such as NVIDIA s Compute Unified Device Architecture (CUDA), which dramatically reduces the gap between domain-specific architectures and general purpose programming. Nonetheless, general-purpose GPU (GPGPU) programming remains subject to several restrictions. Most significantly, the separation of host (CPU) and accelerator (GPU) address spaces requires explicit management of GPU memory resources, especially for massive data parallelism that well exceeds the memory capacity of GPUs. One solution to this problem is to transfer data between the GPU and host memories frequently. In this work, we investigate another approach. We run massively data-parallel applications on GPU clusters. We further propose a programming model for massive data parallelism with data dependencies for this scenario. Experience from micro benchmarks and real-world applications shows that our model provides not only ease of programming but also significant performance gains

Massively parallel red-black algorithms for x-y-z response matrix equations

International Nuclear Information System (INIS)

Hanebutte, U.R.; Laurin-Kovitz, K.; Lewis, E.E.

1992-01-01

Recently, both discrete ordinates and spherical harmonic (S n and P n ) methods have been cast in the form of response matrices. In x-y geometry, massively parallel algorithms have been developed to solve the resulting response matrix equations on the Connection Machine family of parallel computers, the CM-2, CM-200, and CM-5. These algorithms utilize two-cycle iteration on a red-black checkerboard. In this work we examine the use of massively parallel red-black algorithms to solve response matric equations in three dimensions. This longer term objective is to utilize massively parallel algorithms to solve S n and/or P n response matrix problems. In this exploratory examination, however, we consider the simple 6 x 6 response matrices that are derivable from fine-mesh diffusion approximations in three dimensions

A massively parallel discrete ordinates response matrix method for neutron transport

International Nuclear Information System (INIS)

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

1992-01-01

In this paper a discrete ordinates response matrix method is formulated with anisotropic scattering for the solution of neutron transport problems on massively parallel computers. The response matrix formulation eliminates iteration on the scattering source. The nodal matrices that result from the diamond-differenced equations are utilized in a factored form that minimizes memory requirements and significantly reduces the number of arithmetic operations required per node. The red-black solution algorithm utilizes massive parallelism by assigning each spatial node to one or more processors. The algorithm is accelerated by a synthetic method in which the low-order diffusion equations are also solved by massively parallel red-black iterations. The method is implemented on a 16K Connection Machine-2, and S 8 and S 16 solutions are obtained for fixed-source benchmark problems in x-y geometry

Massively Parallel, Molecular Analysis Platform Developed Using a CMOS Integrated Circuit With Biological Nanopores

Science.gov (United States)

Roever, Stefan

2012-01-01

A massively parallel, low cost molecular analysis platform will dramatically change the nature of protein, molecular and genomics research, DNA sequencing, and ultimately, molecular diagnostics. An integrated circuit (IC) with 264 sensors was fabricated using standard CMOS semiconductor processing technology. Each of these sensors is individually controlled with precision analog circuitry and is capable of single molecule measurements. Under electronic and software control, the IC was used to demonstrate the feasibility of creating and detecting lipid bilayers and biological nanopores using wild type α-hemolysin. The ability to dynamically create bilayers over each of the sensors will greatly accelerate pore development and pore mutation analysis. In addition, the noise performance of the IC was measured to be 30fA(rms). With this noise performance, single base detection of DNA was demonstrated using α-hemolysin. The data shows that a single molecule, electrical detection platform using biological nanopores can be operationalized and can ultimately scale to millions of sensors. Such a massively parallel platform will revolutionize molecular analysis and will completely change the field of molecular diagnostics in the future.

Increasing the reach of forensic genetics with massively parallel sequencing.

Science.gov (United States)

Budowle, Bruce; Schmedes, Sarah E; Wendt, Frank R

2017-09-01

The field of forensic genetics has made great strides in the analysis of biological evidence related to criminal and civil matters. More so, the discipline has set a standard of performance and quality in the forensic sciences. The advent of massively parallel sequencing will allow the field to expand its capabilities substantially. This review describes the salient features of massively parallel sequencing and how it can impact forensic genetics. The features of this technology offer increased number and types of genetic markers that can be analyzed, higher throughput of samples, and the capability of targeting different organisms, all by one unifying methodology. While there are many applications, three are described where massively parallel sequencing will have immediate impact: molecular autopsy, microbial forensics and differentiation of monozygotic twins. The intent of this review is to expose the forensic science community to the potential enhancements that have or are soon to arrive and demonstrate the continued expansion the field of forensic genetics and its service in the investigation of legal matters.

Neural nets for massively parallel optimization

Science.gov (United States)

Dixon, Laurence C. W.; Mills, David

1992-07-01

To apply massively parallel processing systems to the solution of large scale optimization problems it is desirable to be able to evaluate any function f(z), z (epsilon) Rn in a parallel manner. The theorem of Cybenko, Hecht Nielsen, Hornik, Stinchcombe and White, and Funahasi shows that this can be achieved by a neural network with one hidden layer. In this paper we address the problem of the number of nodes required in the layer to achieve a given accuracy in the function and gradient values at all points within a given n dimensional interval. The type of activation function needed to obtain nonsingular Hessian matrices is described and a strategy for obtaining accurate minimal networks presented.

First massively parallel algorithm to be implemented in Apollo-II code

International Nuclear Information System (INIS)

Stankovski, Z.

1994-01-01

The collision probability (CP) method in neutron transport, as applied to arbitrary 2D XY geometries, like the TDT module in APOLLO-II, is very time consuming. Consequently RZ or 3D extensions became prohibitive. Fortunately, this method is very suitable for parallelization. Massively parallel computer architectures, especially MIMD machines, bring a new breath to this method. In this paper we present a CM5 implementation of the CP method. Parallelization is applied to the energy groups, using the CMMD message passing library. In our case we use 32 processors for the standard 99-group APOLLIB-II library. The real advantage of this algorithm will appear in the calculation of the future fine multigroup library (about 8000 groups) of the SAPHYR project with a massively parallel computer (to the order of hundreds of processors). (author). 3 tabs., 4 figs., 4 refs

First massively parallel algorithm to be implemented in APOLLO-II code

International Nuclear Information System (INIS)

Stankovski, Z.

1994-01-01

The collision probability method in neutron transport, as applied to arbitrary 2-dimensional geometries, like the two dimensional transport module in APOLLO-II is very time consuming. Consequently 3-dimensional extension became prohibitive. Fortunately, this method is very suitable for parallelization. Massively parallel computer architectures, especially MIMD machines, bring a new breath to this method. In this paper we present a CM5 implementation of the collision probability method. Parallelization is applied to the energy groups, using the CMMD massage passing library. In our case we used 32 processors for the standard 99-group APOLLIB-II library. The real advantage of this algorithm will appear in the calculation of the future multigroup library (about 8000 groups) of the SAPHYR project with a massively parallel computer (to the order of hundreds of processors). (author). 4 refs., 4 figs., 3 tabs

PARALLEL SPATIOTEMPORAL SPECTRAL CLUSTERING WITH MASSIVE TRAJECTORY DATA

Directory of Open Access Journals (Sweden)

Y. Z. Gu

2017-09-01

Full Text Available Massive trajectory data contains wealth useful information and knowledge. Spectral clustering, which has been shown to be effective in finding clusters, becomes an important clustering approaches in the trajectory data mining. However, the traditional spectral clustering lacks the temporal expansion on the algorithm and limited in its applicability to large-scale problems due to its high computational complexity. This paper presents a parallel spatiotemporal spectral clustering based on multiple acceleration solutions to make the algorithm more effective and efficient, the performance is proved due to the experiment carried out on the massive taxi trajectory dataset in Wuhan city, China.

Development of massively parallel quantum chemistry program SMASH

International Nuclear Information System (INIS)

Ishimura, Kazuya

2015-01-01

A massively parallel program for quantum chemistry calculations SMASH was released under the Apache License 2.0 in September 2014. The SMASH program is written in the Fortran90/95 language with MPI and OpenMP standards for parallelization. Frequently used routines, such as one- and two-electron integral calculations, are modularized to make program developments simple. The speed-up of the B3LYP energy calculation for (C 150 H 30 ) 2 with the cc-pVDZ basis set (4500 basis functions) was 50,499 on 98,304 cores of the K computer

Massively Parallel Sort-Merge Joins in Main Memory Multi-Core Database Systems

OpenAIRE

Albutiu, Martina-Cezara; Kemper, Alfons; Neumann, Thomas

2012-01-01

Two emerging hardware trends will dominate the database system technology in the near future: increasing main memory capacities of several TB per server and massively parallel multi-core processing. Many algorithmic and control techniques in current database technology were devised for disk-based systems where I/O dominated the performance. In this work we take a new look at the well-known sort-merge join which, so far, has not been in the focus of research in scalable massively parallel mult...

Proxy-equation paradigm: A strategy for massively parallel asynchronous computations

Science.gov (United States)

Mittal, Ankita; Girimaji, Sharath

2017-09-01

Massively parallel simulations of transport equation systems call for a paradigm change in algorithm development to achieve efficient scalability. Traditional approaches require time synchronization of processing elements (PEs), which severely restricts scalability. Relaxing synchronization requirement introduces error and slows down convergence. In this paper, we propose and develop a novel "proxy equation" concept for a general transport equation that (i) tolerates asynchrony with minimal added error, (ii) preserves convergence order and thus, (iii) expected to scale efficiently on massively parallel machines. The central idea is to modify a priori the transport equation at the PE boundaries to offset asynchrony errors. Proof-of-concept computations are performed using a one-dimensional advection (convection) diffusion equation. The results demonstrate the promise and advantages of the present strategy.

Development of massively parallel quantum chemistry program SMASH

Energy Technology Data Exchange (ETDEWEB)

Ishimura, Kazuya [Department of Theoretical and Computational Molecular Science, Institute for Molecular Science 38 Nishigo-Naka, Myodaiji, Okazaki, Aichi 444-8585 (Japan)

2015-12-31

A massively parallel program for quantum chemistry calculations SMASH was released under the Apache License 2.0 in September 2014. The SMASH program is written in the Fortran90/95 language with MPI and OpenMP standards for parallelization. Frequently used routines, such as one- and two-electron integral calculations, are modularized to make program developments simple. The speed-up of the B3LYP energy calculation for (C{sub 150}H{sub 30}){sub 2} with the cc-pVDZ basis set (4500 basis functions) was 50,499 on 98,304 cores of the K computer.

Massively parallel sparse matrix function calculations with NTPoly

Science.gov (United States)

Dawson, William; Nakajima, Takahito

2018-04-01

We present NTPoly, a massively parallel library for computing the functions of sparse, symmetric matrices. The theory of matrix functions is a well developed framework with a wide range of applications including differential equations, graph theory, and electronic structure calculations. One particularly important application area is diagonalization free methods in quantum chemistry. When the input and output of the matrix function are sparse, methods based on polynomial expansions can be used to compute matrix functions in linear time. We present a library based on these methods that can compute a variety of matrix functions. Distributed memory parallelization is based on a communication avoiding sparse matrix multiplication algorithm. OpenMP task parallellization is utilized to implement hybrid parallelization. We describe NTPoly's interface and show how it can be integrated with programs written in many different programming languages. We demonstrate the merits of NTPoly by performing large scale calculations on the K computer.

Massively parallel Fokker-Planck calculations

International Nuclear Information System (INIS)

Mirin, A.A.

1990-01-01

This paper reports that the Fokker-Planck package FPPAC, which solves the complete nonlinear multispecies Fokker-Planck collision operator for a plasma in two-dimensional velocity space, has been rewritten for the Connection Machine 2. This has involved allocation of variables either to the front end or the CM2, minimization of data flow, and replacement of Cray-optimized algorithms with ones suitable for a massively parallel architecture. Calculations have been carried out on various Connection Machines throughout the country. Results and timings on these machines have been compared to each other and to those on the static memory Cray-2. For large problem size, the Connection Machine 2 is found to be cost-efficient

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....

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...

Massive parallel 3D PIC simulation of negative ion extraction

Science.gov (United States)

Revel, Adrien; Mochalskyy, Serhiy; Montellano, Ivar Mauricio; Wünderlich, Dirk; Fantz, Ursel; Minea, Tiberiu

2017-09-01

The 3D PIC-MCC code ONIX is dedicated to modeling Negative hydrogen/deuterium Ion (NI) extraction and co-extraction of electrons from radio-frequency driven, low pressure plasma sources. It provides valuable insight on the complex phenomena involved in the extraction process. In previous calculations, a mesh size larger than the Debye length was used, implying numerical electron heating. Important steps have been achieved in terms of computation performance and parallelization efficiency allowing successful massive parallel calculations (4096 cores), imperative to resolve the Debye length. In addition, the numerical algorithms have been improved in terms of grid treatment, i.e., the electric field near the complex geometry boundaries (plasma grid) is calculated more accurately. The revised model preserves the full 3D treatment, but can take advantage of a highly refined mesh. ONIX was used to investigate the role of the mesh size, the re-injection scheme for lost particles (extracted or wall absorbed), and the electron thermalization process on the calculated extracted current and plasma characteristics. It is demonstrated that all numerical schemes give the same NI current distribution for extracted ions. Concerning the electrons, the pair-injection technique is found well-adapted to simulate the sheath in front of the plasma grid.

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.

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...

Decreasing Data Analytics Time: Hybrid Architecture MapReduce-Massive Parallel Processing for a Smart Grid

Directory of Open Access Journals (Sweden)

Abdeslam Mehenni

2017-03-01

Full Text Available As our populations grow in a world of limited resources enterprise seek ways to lighten our load on the planet. The idea of modifying consumer behavior appears as a foundation for smart grids. Enterprise demonstrates the value available from deep analysis of electricity consummation histories, consumers’ messages, and outage alerts, etc. Enterprise mines massive structured and unstructured data. In a nutshell, smart grids result in a flood of data that needs to be analyzed, for better adjust to demand and give customers more ability to delve into their power consumption. Simply put, smart grids will increasingly have a flexible data warehouse attached to them. The key driver for the adoption of data management strategies is clearly the need to handle and analyze the large amounts of information utilities are now faced with. New approaches to data integration are nauseating moment; Hadoop is in fact now being used by the utility to help manage the huge growth in data whilst maintaining coherence of the Data Warehouse. In this paper we define a new Meter Data Management System Architecture repository that differ with three leaders MDMS, where we use MapReduce programming model for ETL and Parallel DBMS in Query statements(Massive Parallel Processing MPP.

Massively-parallel best subset selection for ordinary least-squares regression

DEFF Research Database (Denmark)

Gieseke, Fabian; Polsterer, Kai Lars; Mahabal, Ashish

2017-01-01

Selecting an optimal subset of k out of d features for linear regression models given n training instances is often considered intractable for feature spaces with hundreds or thousands of dimensions. We propose an efficient massively-parallel implementation for selecting such optimal feature...

Massive Asynchronous Parallelization of Sparse Matrix Factorizations

Energy Technology Data Exchange (ETDEWEB)

Chow, Edmond [Georgia Inst. of Technology, Atlanta, GA (United States)

2018-01-08

Solving sparse problems is at the core of many DOE computational science applications. We focus on the challenge of developing sparse algorithms that can fully exploit the parallelism in extreme-scale computing systems, in particular systems with massive numbers of cores per node. Our approach is to express a sparse matrix factorization as a large number of bilinear constraint equations, and then solving these equations via an asynchronous iterative method. The unknowns in these equations are the matrix entries of the factorization that is desired.

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.

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

A Massively Parallel Code for Polarization Calculations

Science.gov (United States)

Akiyama, Shizuka; Höflich, Peter

2001-03-01

We present an implementation of our Monte-Carlo radiation transport method for rapidly expanding, NLTE atmospheres for massively parallel computers which utilizes both the distributed and shared memory models. This allows us to take full advantage of the fast communication and low latency inherent to nodes with multiple CPUs, and to stretch the limits of scalability with the number of nodes compared to a version which is based on the shared memory model. Test calculations on a local 20-node Beowulf cluster with dual CPUs showed an improved scalability by about 40%.

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.

A massively-parallel electronic-structure calculations based on real-space density functional theory

International Nuclear Information System (INIS)

Iwata, Jun-Ichi; Takahashi, Daisuke; Oshiyama, Atsushi; Boku, Taisuke; Shiraishi, Kenji; Okada, Susumu; Yabana, Kazuhiro

2010-01-01

Based on the real-space finite-difference method, we have developed a first-principles density functional program that efficiently performs large-scale calculations on massively-parallel computers. In addition to efficient parallel implementation, we also implemented several computational improvements, substantially reducing the computational costs of O(N 3 ) operations such as the Gram-Schmidt procedure and subspace diagonalization. Using the program on a massively-parallel computer cluster with a theoretical peak performance of several TFLOPS, we perform electronic-structure calculations for a system consisting of over 10,000 Si atoms, and obtain a self-consistent electronic-structure in a few hundred hours. We analyze in detail the costs of the program in terms of computation and of inter-node communications to clarify the efficiency, the applicability, and the possibility for further improvements.

Massive hybrid parallelism for fully implicit multiphysics

International Nuclear Information System (INIS)

Gaston, D. R.; Permann, C. J.; Andrs, D.; Peterson, J. W.

2013-01-01

As hardware advances continue to modify the supercomputing landscape, traditional scientific software development practices will become more outdated, ineffective, and inefficient. The process of rewriting/retooling existing software for new architectures is a Sisyphean task, and results in substantial hours of development time, effort, and money. Software libraries which provide an abstraction of the resources provided by such architectures are therefore essential if the computational engineering and science communities are to continue to flourish in this modern computing environment. The Multiphysics Object Oriented Simulation Environment (MOOSE) framework enables complex multiphysics analysis tools to be built rapidly by scientists, engineers, and domain specialists, while also allowing them to both take advantage of current HPC architectures, and efficiently prepare for future supercomputer designs. MOOSE employs a hybrid shared-memory and distributed-memory parallel model and provides a complete and consistent interface for creating multiphysics analysis tools. In this paper, a brief discussion of the mathematical algorithms underlying the framework and the internal object-oriented hybrid parallel design are given. Representative massively parallel results from several applications areas are presented, and a brief discussion of future areas of research for the framework are provided. (authors)

Massive hybrid parallelism for fully implicit multiphysics

Energy Technology Data Exchange (ETDEWEB)

Gaston, D. R.; Permann, C. J.; Andrs, D.; Peterson, J. W. [Idaho National Laboratory, 2525 N. Fremont Ave., Idaho Falls, ID 83415 (United States)

2013-07-01

As hardware advances continue to modify the supercomputing landscape, traditional scientific software development practices will become more outdated, ineffective, and inefficient. The process of rewriting/retooling existing software for new architectures is a Sisyphean task, and results in substantial hours of development time, effort, and money. Software libraries which provide an abstraction of the resources provided by such architectures are therefore essential if the computational engineering and science communities are to continue to flourish in this modern computing environment. The Multiphysics Object Oriented Simulation Environment (MOOSE) framework enables complex multiphysics analysis tools to be built rapidly by scientists, engineers, and domain specialists, while also allowing them to both take advantage of current HPC architectures, and efficiently prepare for future supercomputer designs. MOOSE employs a hybrid shared-memory and distributed-memory parallel model and provides a complete and consistent interface for creating multiphysics analysis tools. In this paper, a brief discussion of the mathematical algorithms underlying the framework and the internal object-oriented hybrid parallel design are given. Representative massively parallel results from several applications areas are presented, and a brief discussion of future areas of research for the framework are provided. (authors)

MASSIVE HYBRID PARALLELISM FOR FULLY IMPLICIT MULTIPHYSICS

Energy Technology Data Exchange (ETDEWEB)

Cody J. Permann; David Andrs; John W. Peterson; Derek R. Gaston

2013-05-01

As hardware advances continue to modify the supercomputing landscape, traditional scientific software development practices will become more outdated, ineffective, and inefficient. The process of rewriting/retooling existing software for new architectures is a Sisyphean task, and results in substantial hours of development time, effort, and money. Software libraries which provide an abstraction of the resources provided by such architectures are therefore essential if the computational engineering and science communities are to continue to flourish in this modern computing environment. The Multiphysics Object Oriented Simulation Environment (MOOSE) framework enables complex multiphysics analysis tools to be built rapidly by scientists, engineers, and domain specialists, while also allowing them to both take advantage of current HPC architectures, and efficiently prepare for future supercomputer designs. MOOSE employs a hybrid shared-memory and distributed-memory parallel model and provides a complete and consistent interface for creating multiphysics analysis tools. In this paper, a brief discussion of the mathematical algorithms underlying the framework and the internal object-oriented hybrid parallel design are given. Representative massively parallel results from several applications areas are presented, and a brief discussion of future areas of research for the framework are provided.

Massively parallel Monte Carlo for many-particle simulations on GPUs

Energy Technology Data Exchange (ETDEWEB)

Anderson, Joshua A.; Jankowski, Eric [Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109 (United States); Grubb, Thomas L. [Department of Materials Science and Engineering, University of Michigan, Ann Arbor, MI 48109 (United States); Engel, Michael [Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109 (United States); Glotzer, Sharon C., E-mail: sglotzer@umich.edu [Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109 (United States); Department of Materials Science and Engineering, University of Michigan, Ann Arbor, MI 48109 (United States)

2013-12-01

Current trends in parallel processors call for the design of efficient massively parallel algorithms for scientific computing. Parallel algorithms for Monte Carlo simulations of thermodynamic ensembles of particles have received little attention because of the inherent serial nature of the statistical sampling. In this paper, we present a massively parallel method that obeys detailed balance and implement it for a system of hard disks on the GPU. We reproduce results of serial high-precision Monte Carlo runs to verify the method. This is a good test case because the hard disk equation of state over the range where the liquid transforms into the solid is particularly sensitive to small deviations away from the balance conditions. On a Tesla K20, our GPU implementation executes over one billion trial moves per second, which is 148 times faster than on a single Intel Xeon E5540 CPU core, enables 27 times better performance per dollar, and cuts energy usage by a factor of 13. With this improved performance we are able to calculate the equation of state for systems of up to one million hard disks. These large system sizes are required in order to probe the nature of the melting transition, which has been debated for the last forty years. In this paper we present the details of our computational method, and discuss the thermodynamics of hard disks separately in a companion paper.

Parallel electric fields from ionospheric winds

International Nuclear Information System (INIS)

Nakada, M.P.

1987-01-01

The possible production of electric fields parallel to the magnetic field by dynamo winds in the E region is examined, using a jet stream wind model. Current return paths through the F region above the stream are examined as well as return paths through the conjugate ionosphere. The Wulf geometry with horizontal winds moving in opposite directions one above the other is also examined. Parallel electric fields are found to depend strongly on the width of current sheets at the edges of the jet stream. If these are narrow enough, appreciable parallel electric fields are produced. These appear to be sufficient to heat the electrons which reduces the conductivity and produces further increases in parallel electric fields and temperatures. Calculations indicate that high enough temperatures for optical emission can be produced in less than 0.3 s. Some properties of auroras that might be produced by dynamo winds are examined; one property is a time delay in brightening at higher and lower altitudes

A massively parallel corpus: the Bible in 100 languages.

Science.gov (United States)

Christodouloupoulos, Christos; Steedman, Mark

We describe the creation of a massively parallel corpus based on 100 translations of the Bible. We discuss some of the difficulties in acquiring and processing the raw material as well as the potential of the Bible as a corpus for natural language processing. Finally we present a statistical analysis of the corpora collected and a detailed comparison between the English translation and other English corpora.

Scientific programming on massively parallel processor CP-PACS

International Nuclear Information System (INIS)

Boku, Taisuke

1998-01-01

The massively parallel processor CP-PACS takes various problems of calculation physics as the object, and it has been designed so that its architecture has been devised to do various numerical processings. In this report, the outline of the CP-PACS and the example of programming in the Kernel CG benchmark in NAS Parallel Benchmarks, version 1, are shown, and the pseudo vector processing mechanism and the parallel processing tuning of scientific and technical computation utilizing the three-dimensional hyper crossbar net, which are two great features of the architecture of the CP-PACS are described. As for the CP-PACS, the PUs based on RISC processor and added with pseudo vector processor are used. Pseudo vector processing is realized as the loop processing by scalar command. The features of the connection net of PUs are explained. The algorithm of the NPB version 1 Kernel CG is shown. The part that takes the time for processing most in the main loop is the product of matrix and vector (matvec), and the parallel processing of the matvec is explained. The time for the computation by the CPU is determined. As the evaluation of the performance, the evaluation of the time for execution, the short vector processing of pseudo vector processor based on slide window, and the comparison with other parallel computers are reported. (K.I.)

Engineering-Based Thermal CFD Simulations on Massive Parallel Systems

KAUST Repository

Frisch, Jérôme

2015-05-22

The development of parallel Computational Fluid Dynamics (CFD) codes is a challenging task that entails efficient parallelization concepts and strategies in order to achieve good scalability values when running those codes on modern supercomputers with several thousands to millions of cores. In this paper, we present a hierarchical data structure for massive parallel computations that supports the coupling of a Navier–Stokes-based fluid flow code with the Boussinesq approximation in order to address complex thermal scenarios for energy-related assessments. The newly designed data structure is specifically designed with the idea of interactive data exploration and visualization during runtime of the simulation code; a major shortcoming of traditional high-performance computing (HPC) simulation codes. We further show and discuss speed-up values obtained on one of Germany’s top-ranked supercomputers with up to 140,000 processes and present simulation results for different engineering-based thermal problems.

ARTS - adaptive runtime system for massively parallel systems. Final report; ARTS - optimale Ausfuehrungsunterstuetzung fuer komplexe Anwendungen auf massiv parallelen Systemen. Teilprojekt: Parallele Stroemungsmechanik. Abschlussbericht

Energy Technology Data Exchange (ETDEWEB)

Gentzsch, W.; Ferstl, F.; Paap, H.G.; Riedel, E.

1998-03-20

In the ARTS project, system software has been developed to support smog and fluid dynamic applications on massively parallel systems. The aim is to implement and test specific software structures within an adaptive run-time system to separate the parallel core algorithms of the applications from the platform independent runtime aspects. Only slight modifications is existing Fortran and C code are necessary to integrate the application code into the new object oriented parallel integrated ARTS framework. The OO-design offers easy control, re-use and adaptation of the system services, resulting in a dramatic decrease in development time of the application and in ease of maintainability of the application software in the future. (orig.) [Deutsch] Im Projekt ARTS wird Basissoftware zur Unterstuetzung von Anwendungen aus den Bereichen Smoganalyse und Stroemungsmechanik auf massiv parallelen Systemen entwickelt und optimiert. Im Vordergrund steht die Erprobung geeigneter Strukturen, um systemnahe Funktionalitaeten in einer Laufzeitumgebung anzusiedeln und dadurch die parallelen Kernalgorithmen der Anwendungsprogramme von den plattformunabhaengigen Laufzeitaspekten zu trennen. Es handelt sich dabei um herkoemmlich strukturierten Fortran-Code, der unter minimalen Aenderungen auch weiterhin nutzbar sein muss, sowie um objektbasiert entworfenen C-Code, der die volle Funktionalitaet der ARTS-Plattform ausnutzen kann. Ein objektorientiertes Design erlaubt eine einfache Kontrolle, Wiederverwendung und Adaption der vom System vorgegebenen Basisdienste. Daraus resultiert ein deutlich reduzierter Entwicklungs- und Laufzeitaufwand fuer die Anwendung. ARTS schafft eine integrierende Plattform, die moderne Technologien aus dem Bereich objektorientierter Laufzeitsysteme mit praxisrelevanten Anforderungen aus dem Bereich des wissenschaftlichen Hoechstleistungsrechnens kombiniert. (orig.)

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

Micro-mechanical Simulations of Soils using Massively Parallel Supercomputers

Directory of Open Access Journals (Sweden)

David W. Washington

2004-06-01

Full Text Available In this research a computer program, Trubal version 1.51, based on the Discrete Element Method was converted to run on a Connection Machine (CM-5,a massively parallel supercomputer with 512 nodes, to expedite the computational times of simulating Geotechnical boundary value problems. The dynamic memory algorithm in Trubal program did not perform efficiently in CM-2 machine with the Single Instruction Multiple Data (SIMD architecture. This was due to the communication overhead involving global array reductions, global array broadcast and random data movement. Therefore, a dynamic memory algorithm in Trubal program was converted to a static memory arrangement and Trubal program was successfully converted to run on CM-5 machines. The converted program was called "TRUBAL for Parallel Machines (TPM." Simulating two physical triaxial experiments and comparing simulation results with Trubal simulations validated the TPM program. With a 512 nodes CM-5 machine TPM produced a nine-fold speedup demonstrating the inherent parallelism within algorithms based on the Discrete Element Method.

Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes

Directory of Open Access Journals (Sweden)

Cronn Richard

2009-12-01

Full Text Available Abstract Background Molecular evolutionary studies share the common goal of elucidating historical relationships, and the common challenge of adequately sampling taxa and characters. Particularly at low taxonomic levels, recent divergence, rapid radiations, and conservative genome evolution yield limited sequence variation, and dense taxon sampling is often desirable. Recent advances in massively parallel sequencing make it possible to rapidly obtain large amounts of sequence data, and multiplexing makes extensive sampling of megabase sequences feasible. Is it possible to efficiently apply massively parallel sequencing to increase phylogenetic resolution at low taxonomic levels? Results We reconstruct the infrageneric phylogeny of Pinus from 37 nearly-complete chloroplast genomes (average 109 kilobases each of an approximately 120 kilobase genome generated using multiplexed massively parallel sequencing. 30/33 ingroup nodes resolved with ≥ 95% bootstrap support; this is a substantial improvement relative to prior studies, and shows massively parallel sequencing-based strategies can produce sufficient high quality sequence to reach support levels originally proposed for the phylogenetic bootstrap. Resampling simulations show that at least the entire plastome is necessary to fully resolve Pinus, particularly in rapidly radiating clades. Meta-analysis of 99 published infrageneric phylogenies shows that whole plastome analysis should provide similar gains across a range of plant genera. A disproportionate amount of phylogenetic information resides in two loci (ycf1, ycf2, highlighting their unusual evolutionary properties. Conclusion Plastome sequencing is now an efficient option for increasing phylogenetic resolution at lower taxonomic levels in plant phylogenetic and population genetic analyses. With continuing improvements in sequencing capacity, the strategies herein should revolutionize efforts requiring dense taxon and character sampling

Visualizing Network Traffic to Understand the Performance of Massively Parallel Simulations

KAUST Repository

Landge, A. G.

2012-12-01

The performance of massively parallel applications is often heavily impacted by the cost of communication among compute nodes. However, determining how to best use the network is a formidable task, made challenging by the ever increasing size and complexity of modern supercomputers. This paper applies visualization techniques to aid parallel application developers in understanding the network activity by enabling a detailed exploration of the flow of packets through the hardware interconnect. In order to visualize this large and complex data, we employ two linked views of the hardware network. The first is a 2D view, that represents the network structure as one of several simplified planar projections. This view is designed to allow a user to easily identify trends and patterns in the network traffic. The second is a 3D view that augments the 2D view by preserving the physical network topology and providing a context that is familiar to the application developers. Using the massively parallel multi-physics code pF3D as a case study, we demonstrate that our tool provides valuable insight that we use to explain and optimize pF3D-s performance on an IBM Blue Gene/P system. © 1995-2012 IEEE.

Reduced complexity and latency for a massive MIMO system using a parallel detection algorithm

Directory of Open Access Journals (Sweden)

Shoichi Higuchi

2017-09-01

Full Text Available In recent years, massive MIMO systems have been widely researched to realize high-speed data transmission. Since massive MIMO systems use a large number of antennas, these systems require huge complexity to detect the signal. In this paper, we propose a novel detection method for massive MIMO using parallel detection with maximum likelihood detection with QR decomposition and M-algorithm (QRM-MLD to reduce the complexity and latency. The proposed scheme obtains an R matrix after permutation of an H matrix and QR decomposition. The R matrix is also eliminated using a Gauss–Jordan elimination method. By using a modified R matrix, the proposed method can detect the transmitted signal using parallel detection. From the simulation results, the proposed scheme can achieve a reduced complexity and latency with a little degradation of the bit error rate (BER performance compared with the conventional method.

Design and performance characterization of electronic structure calculations on massively parallel supercomputers

DEFF Research Database (Denmark)

Romero, N. A.; Glinsvad, Christian; Larsen, Ask Hjorth

2013-01-01

Density function theory (DFT) is the most widely employed electronic structure method because of its favorable scaling with system size and accuracy for a broad range of molecular and condensed-phase systems. The advent of massively parallel supercomputers has enhanced the scientific community...

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

Implementation of a Monte Carlo algorithm for neutron transport on a massively parallel SIMD machine

International Nuclear Information System (INIS)

Baker, R.S.

1992-01-01

We present some results from the recent adaptation of a vectorized Monte Carlo algorithm to a massively parallel architecture. The performance of the algorithm on a single processor Cray Y-MP and a Thinking Machine Corporations CM-2 and CM-200 is compared for several test problems. The results show that significant speedups are obtainable for vectorized Monte Carlo algorithms on massively parallel machines, even when the algorithms are applied to realistic problems which require extensive variance reduction. However, the architecture of the Connection Machine does place some limitations on the regime in which the Monte Carlo algorithm may be expected to perform well

Implementation of a Monte Carlo algorithm for neutron transport on a massively parallel SIMD machine

International Nuclear Information System (INIS)

Baker, R.S.

1993-01-01

We present some results from the recent adaptation of a vectorized Monte Carlo algorithm to a massively parallel architecture. The performance of the algorithm on a single processor Cray Y-MP and a Thinking Machine Corporations CM-2 and CM-200 is compared for several test problems. The results show that significant speedups are obtainable for vectorized Monte Carlo algorithms on massively parallel machines, even when the algorithms are applied to realistic problems which require extensive variance reduction. However, the architecture of the Connection Machine does place some limitations on the regime in which the Monte Carlo algorithm may be expected to perform well. (orig.)

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....

Massively Parallel Single-Molecule Manipulation Using Centrifugal Force

Science.gov (United States)

Wong, Wesley; Halvorsen, Ken

2011-03-01

Precise manipulation of single molecules has led to remarkable insights in physics, chemistry, biology, and medicine. However, two issues that have impeded the widespread adoption of these techniques are equipment cost and the laborious nature of making measurements one molecule at a time. To meet these challenges, we have developed an approach that enables massively parallel single- molecule force measurements using centrifugal force. This approach is realized in the centrifuge force microscope, an instrument in which objects in an orbiting sample are subjected to a calibration-free, macroscopically uniform force- field while their micro-to-nanoscopic motions are observed. We demonstrate high- throughput single-molecule force spectroscopy with this technique by performing thousands of rupture experiments in parallel, characterizing force-dependent unbinding kinetics of an antibody-antigen pair in minutes rather than days. Currently, we are taking steps to integrate high-resolution detection, fluorescence, temperature control and a greater dynamic range in force. With significant benefits in efficiency, cost, simplicity, and versatility, single-molecule centrifugation has the potential to expand single-molecule experimentation to a wider range of researchers and experimental systems.

MADmap: A Massively Parallel Maximum-Likelihood Cosmic Microwave Background Map-Maker

Energy Technology Data Exchange (ETDEWEB)

Cantalupo, Christopher; Borrill, Julian; Jaffe, Andrew; Kisner, Theodore; Stompor, Radoslaw

2009-06-09

MADmap is a software application used to produce maximum-likelihood images of the sky from time-ordered data which include correlated noise, such as those gathered by Cosmic Microwave Background (CMB) experiments. It works efficiently on platforms ranging from small workstations to the most massively parallel supercomputers. Map-making is a critical step in the analysis of all CMB data sets, and the maximum-likelihood approach is the most accurate and widely applicable algorithm; however, it is a computationally challenging task. This challenge will only increase with the next generation of ground-based, balloon-borne and satellite CMB polarization experiments. The faintness of the B-mode signal that these experiments seek to measure requires them to gather enormous data sets. MADmap is already being run on up to O(1011) time samples, O(108) pixels and O(104) cores, with ongoing work to scale to the next generation of data sets and supercomputers. We describe MADmap's algorithm based around a preconditioned conjugate gradient solver, fast Fourier transforms and sparse matrix operations. We highlight MADmap's ability to address problems typically encountered in the analysis of realistic CMB data sets and describe its application to simulations of the Planck and EBEX experiments. The massively parallel and distributed implementation is detailed and scaling complexities are given for the resources required. MADmap is capable of analysing the largest data sets now being collected on computing resources currently available, and we argue that, given Moore's Law, MADmap will be capable of reducing the most massive projected data sets.

Comparison of Pre-Analytical FFPE Sample Preparation Methods and Their Impact on Massively Parallel Sequencing in Routine Diagnostics

Science.gov (United States)

Heydt, Carina; Fassunke, Jana; Künstlinger, Helen; Ihle, Michaela Angelika; König, Katharina; Heukamp, Lukas Carl; Schildhaus, Hans-Ulrich; Odenthal, Margarete; Büttner, Reinhard; Merkelbach-Bruse, Sabine

2014-01-01

Over the last years, massively parallel sequencing has rapidly evolved and has now transitioned into molecular pathology routine laboratories. It is an attractive platform for analysing multiple genes at the same time with very little input material. Therefore, the need for high quality DNA obtained from automated DNA extraction systems has increased, especially to those laboratories which are dealing with formalin-fixed paraffin-embedded (FFPE) material and high sample throughput. This study evaluated five automated FFPE DNA extraction systems as well as five DNA quantification systems using the three most common techniques, UV spectrophotometry, fluorescent dye-based quantification and quantitative PCR, on 26 FFPE tissue samples. Additionally, the effects on downstream applications were analysed to find the most suitable pre-analytical methods for massively parallel sequencing in routine diagnostics. The results revealed that the Maxwell 16 from Promega (Mannheim, Germany) seems to be the superior system for DNA extraction from FFPE material. The extracts had a 1.3–24.6-fold higher DNA concentration in comparison to the other extraction systems, a higher quality and were most suitable for downstream applications. The comparison of the five quantification methods showed intermethod variations but all methods could be used to estimate the right amount for PCR amplification and for massively parallel sequencing. Interestingly, the best results in massively parallel sequencing were obtained with a DNA input of 15 ng determined by the NanoDrop 2000c spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA). No difference could be detected in mutation analysis based on the results of the quantification methods. These findings emphasise, that it is particularly important to choose the most reliable and constant DNA extraction system, especially when using small biopsies and low elution volumes, and that all common DNA quantification techniques can be used for

Comparison of pre-analytical FFPE sample preparation methods and their impact on massively parallel sequencing in routine diagnostics.

Directory of Open Access Journals (Sweden)

Carina Heydt

Full Text Available Over the last years, massively parallel sequencing has rapidly evolved and has now transitioned into molecular pathology routine laboratories. It is an attractive platform for analysing multiple genes at the same time with very little input material. Therefore, the need for high quality DNA obtained from automated DNA extraction systems has increased, especially to those laboratories which are dealing with formalin-fixed paraffin-embedded (FFPE material and high sample throughput. This study evaluated five automated FFPE DNA extraction systems as well as five DNA quantification systems using the three most common techniques, UV spectrophotometry, fluorescent dye-based quantification and quantitative PCR, on 26 FFPE tissue samples. Additionally, the effects on downstream applications were analysed to find the most suitable pre-analytical methods for massively parallel sequencing in routine diagnostics. The results revealed that the Maxwell 16 from Promega (Mannheim, Germany seems to be the superior system for DNA extraction from FFPE material. The extracts had a 1.3-24.6-fold higher DNA concentration in comparison to the other extraction systems, a higher quality and were most suitable for downstream applications. The comparison of the five quantification methods showed intermethod variations but all methods could be used to estimate the right amount for PCR amplification and for massively parallel sequencing. Interestingly, the best results in massively parallel sequencing were obtained with a DNA input of 15 ng determined by the NanoDrop 2000c spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA. No difference could be detected in mutation analysis based on the results of the quantification methods. These findings emphasise, that it is particularly important to choose the most reliable and constant DNA extraction system, especially when using small biopsies and low elution volumes, and that all common DNA quantification techniques can

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.

Massively Parallel and Scalable Implicit Time Integration Algorithms for Structural Dynamics

Science.gov (United States)

Farhat, Charbel

1997-01-01

Explicit codes are often used to simulate the nonlinear dynamics of large-scale structural systems, even for low frequency response, because the storage and CPU requirements entailed by the repeated factorizations traditionally found in implicit codes rapidly overwhelm the available computing resources. With the advent of parallel processing, this trend is accelerating because of the following additional facts: (a) explicit schemes are easier to parallelize than implicit ones, and (b) explicit schemes induce short range interprocessor communications that are relatively inexpensive, while the factorization methods used in most implicit schemes induce long range interprocessor communications that often ruin the sought-after speed-up. However, the time step restriction imposed by the Courant stability condition on all explicit schemes cannot yet be offset by the speed of the currently available parallel hardware. Therefore, it is essential to develop efficient alternatives to direct methods that are also amenable to massively parallel processing because implicit codes using unconditionally stable time-integration algorithms are computationally more efficient when simulating the low-frequency dynamics of aerospace structures.

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.

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.

Intelligent trigger by massively parallel processors for high energy physics experiments

International Nuclear Information System (INIS)

Rohrbach, F.; Vesztergombi, G.

1992-01-01

The CERN-MPPC collaboration concentrates its effort on the development of machines based on massive parallelism with thousands of integrated processing elements, arranged in a string. Seven applications are under detailed studies within the collaboration: three for LHC, one for SSC, two for fixed target high energy physics at CERN and one for HDTV. Preliminary results are presented. They show that the objectives should be reached with the use of the ASP architecture. (author)

Developing a Massively Parallel Forward Projection Radiography Model for Large-Scale Industrial Applications

Energy Technology Data Exchange (ETDEWEB)

Bauerle, Matthew [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

2014-08-01

This project utilizes Graphics Processing Units (GPUs) to compute radiograph simulations for arbitrary objects. The generation of radiographs, also known as the forward projection imaging model, is computationally intensive and not widely utilized. The goal of this research is to develop a massively parallel algorithm that can compute forward projections for objects with a trillion voxels (3D pixels). To achieve this end, the data are divided into blocks that can each t into GPU memory. The forward projected image is also divided into segments to allow for future parallelization and to avoid needless computations.

Massively parallel fabrication of repetitive nanostructures: nanolithography for nanoarrays

International Nuclear Information System (INIS)

Luttge, Regina

2009-01-01

This topical review provides an overview of nanolithographic techniques for nanoarrays. Using patterning techniques such as lithography, normally we aim for a higher order architecture similarly to functional systems in nature. Inspired by the wealth of complexity in nature, these architectures are translated into technical devices, for example, found in integrated circuitry or other systems in which structural elements work as discrete building blocks in microdevices. Ordered artificial nanostructures (arrays of pillars, holes and wires) have shown particular properties and bring about the opportunity to modify and tune the device operation. Moreover, these nanostructures deliver new applications, for example, the nanoscale control of spin direction within a nanomagnet. Subsequently, we can look for applications where this unique property of the smallest manufactured element is repetitively used such as, for example with respect to spin, in nanopatterned magnetic media for data storage. These nanostructures are generally called nanoarrays. Most of these applications require massively parallel produced nanopatterns which can be directly realized by laser interference (areas up to 4 cm 2 are easily achieved with a Lloyd's mirror set-up). In this topical review we will further highlight the application of laser interference as a tool for nanofabrication, its limitations and ultimate advantages towards a variety of devices including nanostructuring for photonic crystal devices, high resolution patterned media and surface modifications of medical implants. The unique properties of nanostructured surfaces have also found applications in biomedical nanoarrays used either for diagnostic or functional assays including catalytic reactions on chip. Bio-inspired templated nanoarrays will be presented in perspective to other massively parallel nanolithography techniques currently discussed in the scientific literature. (topical review)

Massively parallel DNA sequencing facilitates diagnosis of patients with Usher syndrome type 1.

Directory of Open Access Journals (Sweden)

Hidekane Yoshimura

Full Text Available Usher syndrome is an autosomal recessive disorder manifesting hearing loss, retinitis pigmentosa and vestibular dysfunction, and having three clinical subtypes. Usher syndrome type 1 is the most severe subtype due to its profound hearing loss, lack of vestibular responses, and retinitis pigmentosa that appears in prepuberty. Six of the corresponding genes have been identified, making early diagnosis through DNA testing possible, with many immediate and several long-term advantages for patients and their families. However, the conventional genetic techniques, such as direct sequence analysis, are both time-consuming and expensive. Targeted exon sequencing of selected genes using the massively parallel DNA sequencing technology will potentially enable us to systematically tackle previously intractable monogenic disorders and improve molecular diagnosis. Using this technique combined with direct sequence analysis, we screened 17 unrelated Usher syndrome type 1 patients and detected probable pathogenic variants in the 16 of them (94.1% who carried at least one mutation. Seven patients had the MYO7A mutation (41.2%, which is the most common type in Japanese. Most of the mutations were detected by only the massively parallel DNA sequencing. We report here four patients, who had probable pathogenic mutations in two different Usher syndrome type 1 genes, and one case of MYO7A/PCDH15 digenic inheritance. This is the first report of Usher syndrome mutation analysis using massively parallel DNA sequencing and the frequency of Usher syndrome type 1 genes in Japanese. Mutation screening using this technique has the power to quickly identify mutations of many causative genes while maintaining cost-benefit performance. In addition, the simultaneous mutation analysis of large numbers of genes is useful for detecting mutations in different genes that are possibly disease modifiers or of digenic inheritance.

Massively parallel DNA sequencing facilitates diagnosis of patients with Usher syndrome type 1.

Science.gov (United States)

Yoshimura, Hidekane; Iwasaki, Satoshi; Nishio, Shin-Ya; Kumakawa, Kozo; Tono, Tetsuya; Kobayashi, Yumiko; Sato, Hiroaki; Nagai, Kyoko; Ishikawa, Kotaro; Ikezono, Tetsuo; Naito, Yasushi; Fukushima, Kunihiro; Oshikawa, Chie; Kimitsuki, Takashi; Nakanishi, Hiroshi; Usami, Shin-Ichi

2014-01-01

Usher syndrome is an autosomal recessive disorder manifesting hearing loss, retinitis pigmentosa and vestibular dysfunction, and having three clinical subtypes. Usher syndrome type 1 is the most severe subtype due to its profound hearing loss, lack of vestibular responses, and retinitis pigmentosa that appears in prepuberty. Six of the corresponding genes have been identified, making early diagnosis through DNA testing possible, with many immediate and several long-term advantages for patients and their families. However, the conventional genetic techniques, such as direct sequence analysis, are both time-consuming and expensive. Targeted exon sequencing of selected genes using the massively parallel DNA sequencing technology will potentially enable us to systematically tackle previously intractable monogenic disorders and improve molecular diagnosis. Using this technique combined with direct sequence analysis, we screened 17 unrelated Usher syndrome type 1 patients and detected probable pathogenic variants in the 16 of them (94.1%) who carried at least one mutation. Seven patients had the MYO7A mutation (41.2%), which is the most common type in Japanese. Most of the mutations were detected by only the massively parallel DNA sequencing. We report here four patients, who had probable pathogenic mutations in two different Usher syndrome type 1 genes, and one case of MYO7A/PCDH15 digenic inheritance. This is the first report of Usher syndrome mutation analysis using massively parallel DNA sequencing and the frequency of Usher syndrome type 1 genes in Japanese. Mutation screening using this technique has the power to quickly identify mutations of many causative genes while maintaining cost-benefit performance. In addition, the simultaneous mutation analysis of large numbers of genes is useful for detecting mutations in different genes that are possibly disease modifiers or of digenic inheritance.

Optimization of multi-phase compressible lattice Boltzmann codes on massively parallel multi-core systems

NARCIS (Netherlands)

Biferale, L.; Mantovani, F.; Pivanti, M.; Pozzati, F.; Sbragaglia, M.; Schifano, S.F.; Toschi, F.; Tripiccione, R.

2011-01-01

We develop a Lattice Boltzmann code for computational fluid-dynamics and optimize it for massively parallel systems based on multi-core processors. Our code describes 2D multi-phase compressible flows. We analyze the performance bottlenecks that we find as we gradually expose a larger fraction of

Enhanced memory architecture for massively parallel vision chip

Science.gov (United States)

Chen, Zhe; Yang, Jie; Liu, Liyuan; Wu, Nanjian

2015-04-01

Local memory architecture plays an important role in high performance massively parallel vision chip. In this paper, we propose an enhanced memory architecture with compact circuit area designed in a full-custom flow. The memory consists of separate master-stage static latches and shared slave-stage dynamic latches. We use split transmission transistors on the input data path to enhance tolerance for charge sharing and to achieve random read/write capabilities. The memory is designed in a 0.18 μm CMOS process. The area overhead of the memory achieves 16.6 μm2/bit. Simulation results show that the maximum operating frequency reaches 410 MHz and the corresponding peak dynamic power consumption for a 64-bit memory unit is 190 μW under 1.8 V supply voltage.

PUMA: An Operating System for Massively Parallel Systems

Directory of Open Access Journals (Sweden)

Stephen R. Wheat

1994-01-01

Full Text Available This article presents an overview of PUMA (Performance-oriented, User-managed Messaging Architecture, a message-passing kernel for massively parallel systems. Message passing in PUMA is based on portals – an opening in the address space of an application process. Once an application process has established a portal, other processes can write values into the portal using a simple send operation. Because messages are written directly into the address space of the receiving process, there is no need to buffer messages in the PUMA kernel and later copy them into the applications address space. PUMA consists of two components: the quintessential kernel (Q-Kernel and the process control thread (PCT. Although the PCT provides management decisions, the Q-Kernel controls access and implements the policies specified by the PCT.

Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes

Science.gov (United States)

Matthew Parks; Richard Cronn; Aaron Liston

2009-01-01

We reconstruct the infrageneric phylogeny of Pinus from 37 nearly-complete chloroplast genomes (average 109 kilobases each of an approximately 120 kilobase genome) generated using multiplexed massively parallel sequencing. We found that 30/33 ingroup nodes resolved wlth > 95-percent bootstrap support; this is a substantial improvement relative...

Massively parallel data processing for quantitative total flow imaging with optical coherence microscopy and tomography

Science.gov (United States)

Sylwestrzak, Marcin; Szlag, Daniel; Marchand, Paul J.; Kumar, Ashwin S.; Lasser, Theo

2017-08-01

We present an application of massively parallel processing of quantitative flow measurements data acquired using spectral optical coherence microscopy (SOCM). The need for massive signal processing of these particular datasets has been a major hurdle for many applications based on SOCM. In view of this difficulty, we implemented and adapted quantitative total flow estimation algorithms on graphics processing units (GPU) and achieved a 150 fold reduction in processing time when compared to a former CPU implementation. As SOCM constitutes the microscopy counterpart to spectral optical coherence tomography (SOCT), the developed processing procedure can be applied to both imaging modalities. We present the developed DLL library integrated in MATLAB (with an example) and have included the source code for adaptations and future improvements. Catalogue identifier: AFBT_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AFBT_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU GPLv3 No. of lines in distributed program, including test data, etc.: 913552 No. of bytes in distributed program, including test data, etc.: 270876249 Distribution format: tar.gz Programming language: CUDA/C, MATLAB. Computer: Intel x64 CPU, GPU supporting CUDA technology. Operating system: 64-bit Windows 7 Professional. Has the code been vectorized or parallelized?: Yes, CPU code has been vectorized in MATLAB, CUDA code has been parallelized. RAM: Dependent on users parameters, typically between several gigabytes and several tens of gigabytes Classification: 6.5, 18. Nature of problem: Speed up of data processing in optical coherence microscopy Solution method: Utilization of GPU for massively parallel data processing Additional comments: Compiled DLL library with source code and documentation, example of utilization (MATLAB script with raw data) Running time: 1,8 s for one B-scan (150 × faster in comparison to the CPU

MCBooster: a tool for MC generation for massively parallel platforms

CERN Multimedia

Alves Junior, Antonio Augusto

2016-01-01

MCBooster is a header-only, C++11-compliant library for the generation of large samples of phase-space Monte Carlo events on massively parallel platforms. It was released on GitHub in the spring of 2016. The library core algorithms implement the Raubold-Lynch method; they are able to generate the full kinematics of decays with up to nine particles in the final state. The library supports the generation of sequential decays as well as the parallel evaluation of arbitrary functions over the generated events. The output of MCBooster completely accords with popular and well-tested software packages such as GENBOD (W515 from CERNLIB) and TGenPhaseSpace from the ROOT framework. MCBooster is developed on top of the Thrust library and runs on Linux systems. It deploys transparently on NVidia CUDA-enabled GPUs as well as multicore CPUs. 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 perfor...

A highly scalable massively parallel fast marching method for the Eikonal equation

Science.gov (United States)

Yang, Jianming; Stern, Frederick

2017-03-01

The fast marching method is a widely used numerical method for solving the Eikonal equation arising from a variety of scientific and engineering fields. It is long deemed inherently sequential and an efficient parallel algorithm applicable to large-scale practical applications is not available in the literature. In this study, we present a highly scalable massively parallel implementation of the fast marching method using a domain decomposition approach. Central to this algorithm is a novel restarted narrow band approach that coordinates the frequency of communications and the amount of computations extra to a sequential run for achieving an unprecedented parallel performance. Within each restart, the narrow band fast marching method is executed; simple synchronous local exchanges and global reductions are adopted for communicating updated data in the overlapping regions between neighboring subdomains and getting the latest front status, respectively. The independence of front characteristics is exploited through special data structures and augmented status tags to extract the masked parallelism within the fast marching method. The efficiency, flexibility, and applicability of the parallel algorithm are demonstrated through several examples. These problems are extensively tested on six grids with up to 1 billion points using different numbers of processes ranging from 1 to 65536. Remarkable parallel speedups are achieved using tens of thousands of processes. Detailed pseudo-codes for both the sequential and parallel algorithms are provided to illustrate the simplicity of the parallel implementation and its similarity to the sequential narrow band fast marching algorithm.

Massively parallel whole genome amplification for single-cell sequencing using droplet microfluidics.

Science.gov (United States)

Hosokawa, Masahito; Nishikawa, Yohei; Kogawa, Masato; Takeyama, Haruko

2017-07-12

Massively parallel single-cell genome sequencing is required to further understand genetic diversities in complex biological systems. Whole genome amplification (WGA) is the first step for single-cell sequencing, but its throughput and accuracy are insufficient in conventional reaction platforms. Here, we introduce single droplet multiple displacement amplification (sd-MDA), a method that enables massively parallel amplification of single cell genomes while maintaining sequence accuracy and specificity. Tens of thousands of single cells are compartmentalized in millions of picoliter droplets and then subjected to lysis and WGA by passive droplet fusion in microfluidic channels. Because single cells are isolated in compartments, their genomes are amplified to saturation without contamination. This enables the high-throughput acquisition of contamination-free and cell specific sequence reads from single cells (21,000 single-cells/h), resulting in enhancement of the sequence data quality compared to conventional methods. This method allowed WGA of both single bacterial cells and human cancer cells. The obtained sequencing coverage rivals those of conventional techniques with superior sequence quality. In addition, we also demonstrate de novo assembly of uncultured soil bacteria and obtain draft genomes from single cell sequencing. This sd-MDA is promising for flexible and scalable use in single-cell sequencing.

Block iterative restoration of astronomical images with the massively parallel processor

International Nuclear Information System (INIS)

Heap, S.R.; Lindler, D.J.

1987-01-01

A method is described for algebraic image restoration capable of treating astronomical images. For a typical 500 x 500 image, direct algebraic restoration would require the solution of a 250,000 x 250,000 linear system. The block iterative approach is used to reduce the problem to solving 4900 121 x 121 linear systems. The algorithm was implemented on the Goddard Massively Parallel Processor, which can solve a 121 x 121 system in approximately 0.06 seconds. Examples are shown of the results for various astronomical images

Scalable Parallel Distributed Coprocessor System for Graph Searching Problems with Massive Data

Directory of Open Access Journals (Sweden)

Wanrong Huang

2017-01-01

Full Text Available The Internet applications, such as network searching, electronic commerce, and modern medical applications, produce and process massive data. Considerable data parallelism exists in computation processes of data-intensive applications. A traversal algorithm, breadth-first search (BFS, is fundamental in many graph processing applications and metrics when a graph grows in scale. A variety of scientific programming methods have been proposed for accelerating and parallelizing BFS because of the poor temporal and spatial locality caused by inherent irregular memory access patterns. However, new parallel hardware could provide better improvement for scientific methods. To address small-world graph problems, we propose a scalable and novel field-programmable gate array-based heterogeneous multicore system for scientific programming. The core is multithread for streaming processing. And the communication network InfiniBand is adopted for scalability. We design a binary search algorithm to address mapping to unify all processor addresses. Within the limits permitted by the Graph500 test bench after 1D parallel hybrid BFS algorithm testing, our 8-core and 8-thread-per-core system achieved superior performance and efficiency compared with the prior work under the same degree of parallelism. Our system is efficient not as a special acceleration unit but as a processor platform that deals with graph searching applications.

Massively Parallel Sort-Merge Joins in Main Memory Multi-Core Database Systems

OpenAIRE

Martina-Cezara Albutiu, Alfons Kemper, Thomas Neumann

2012-01-01

Two emerging hardware trends will dominate the database system technology in the near future: increasing main memory capacities of several TB per server and massively parallel multi-core processing. Many algorithmic and control techniques in current database technology were devised for disk-based systems where I/O dominated the performance. In this work we take a new look at the well-known sort-merge join which, so far, has not been in the focus of research ...

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.

The Fortran-P Translator: Towards Automatic Translation of Fortran 77 Programs for Massively Parallel Processors

Directory of Open Access Journals (Sweden)

Matthew O'keefe

1995-01-01

Full Text Available Massively parallel processors (MPPs hold the promise of extremely high performance that, if realized, could be used to study problems of unprecedented size and complexity. One of the primary stumbling blocks to this promise has been the lack of tools to translate application codes to MPP form. In this article we show how applications codes written in a subset of Fortran 77, called Fortran-P, can be translated to achieve good performance on several massively parallel machines. This subset can express codes that are self-similar, where the algorithm applied to the global data domain is also applied to each subdomain. We have found many codes that match the Fortran-P programming style and have converted them using our tools. We believe a self-similar coding style will accomplish what a vectorizable style has accomplished for vector machines by allowing the construction of robust, user-friendly, automatic translation systems that increase programmer productivity and generate fast, efficient code for MPPs.

Massive Parallelism of Monte-Carlo Simulation on Low-End Hardware using Graphic Processing Units

International Nuclear Information System (INIS)

Mburu, Joe Mwangi; Hah, Chang Joo Hah

2014-01-01

Within the past decade, research has been done on utilizing GPU massive parallelization in core simulation with impressive results but unfortunately, not much commercial application has been done in the nuclear field especially in reactor core simulation. The purpose of this paper is to give an introductory concept on the topic and illustrate the potential of exploiting the massive parallel nature of GPU computing on a simple monte-carlo simulation with very minimal hardware specifications. To do a comparative analysis, a simple two dimension monte-carlo simulation is implemented for both the CPU and GPU in order to evaluate performance gain based on the computing devices. The heterogeneous platform utilized in this analysis is done on a slow notebook with only 1GHz processor. The end results are quite surprising whereby high speedups obtained are almost a factor of 10. In this work, we have utilized heterogeneous computing in a GPU-based approach in applying potential high arithmetic intensive calculation. By applying a complex monte-carlo simulation on GPU platform, we have speed up the computational process by almost a factor of 10 based on one million neutrons. This shows how easy, cheap and efficient it is in using GPU in accelerating scientific computing and the results should encourage in exploring further this avenue especially in nuclear reactor physics simulation where deterministic and stochastic calculations are quite favourable in parallelization

Massive Parallelism of Monte-Carlo Simulation on Low-End Hardware using Graphic Processing Units

Energy Technology Data Exchange (ETDEWEB)

Mburu, Joe Mwangi; Hah, Chang Joo Hah [KEPCO International Nuclear Graduate School, Ulsan (Korea, Republic of)

2014-05-15

Within the past decade, research has been done on utilizing GPU massive parallelization in core simulation with impressive results but unfortunately, not much commercial application has been done in the nuclear field especially in reactor core simulation. The purpose of this paper is to give an introductory concept on the topic and illustrate the potential of exploiting the massive parallel nature of GPU computing on a simple monte-carlo simulation with very minimal hardware specifications. To do a comparative analysis, a simple two dimension monte-carlo simulation is implemented for both the CPU and GPU in order to evaluate performance gain based on the computing devices. The heterogeneous platform utilized in this analysis is done on a slow notebook with only 1GHz processor. The end results are quite surprising whereby high speedups obtained are almost a factor of 10. In this work, we have utilized heterogeneous computing in a GPU-based approach in applying potential high arithmetic intensive calculation. By applying a complex monte-carlo simulation on GPU platform, we have speed up the computational process by almost a factor of 10 based on one million neutrons. This shows how easy, cheap and efficient it is in using GPU in accelerating scientific computing and the results should encourage in exploring further this avenue especially in nuclear reactor physics simulation where deterministic and stochastic calculations are quite favourable in parallelization.

Massively Parallel Dimension Independent Adaptive Metropolis

KAUST Repository

Chen, Yuxin

2015-05-14

This work considers black-box Bayesian inference over high-dimensional parameter spaces. The well-known and widely respected adaptive Metropolis (AM) algorithm is extended herein to asymptotically scale uniformly with respect to the underlying parameter dimension, by respecting the variance, for Gaussian targets. The result- ing algorithm, referred to as the dimension-independent adaptive Metropolis (DIAM) algorithm, also shows improved performance with respect to adaptive Metropolis on non-Gaussian targets. This algorithm is further improved, and the possibility of probing high-dimensional targets is enabled, via GPU-accelerated numerical libraries and periodically synchronized concurrent chains (justified a posteriori). Asymptoti- cally in dimension, this massively parallel dimension-independent adaptive Metropolis (MPDIAM) GPU implementation exhibits a factor of four improvement versus the CPU-based Intel MKL version alone, which is itself already a factor of three improve- ment versus the serial version. The scaling to multiple CPUs and GPUs exhibits a form of strong scaling in terms of the time necessary to reach a certain convergence criterion, through a combination of longer time per sample batch (weak scaling) and yet fewer necessary samples to convergence. This is illustrated by e ciently sampling from several Gaussian and non-Gaussian targets for dimension d 1000.

Effect of parallel electric fields on the whistler mode wave propagation in the magnetosphere

International Nuclear Information System (INIS)

Gupta, G.P.; Singh, R.N.

1975-01-01

The effect of parallel electric fields on whistler mode wave propagation has been studied. To account for the parallel electric fields, the dispersion equation has been analyzed, and refractive index surfaces for magnetospheric plasma have been constructed. The presence of parallel electric fields deforms the refractive index surfaces which diffuse the energy flow and produce defocusing of the whistler mode waves. The parallel electric field induces an instability in the whistler mode waves propagating through the magnetosphere. The growth or decay of whistler mode instability depends on the direction of parallel electric fields. It is concluded that the analyses of whistler wave records received on the ground should account for the role of parallel electric fields

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).

Time-dependent density-functional theory in massively parallel computer architectures: the OCTOPUS project.

Science.gov (United States)

Andrade, Xavier; Alberdi-Rodriguez, Joseba; Strubbe, David A; Oliveira, Micael J T; Nogueira, Fernando; Castro, Alberto; Muguerza, Javier; Arruabarrena, Agustin; Louie, Steven G; Aspuru-Guzik, Alán; Rubio, Angel; Marques, Miguel A L

2012-06-13

Octopus is a general-purpose density-functional theory (DFT) code, with a particular emphasis on the time-dependent version of DFT (TDDFT). In this paper we present the ongoing efforts to achieve the parallelization of octopus. We focus on the real-time variant of TDDFT, where the time-dependent Kohn-Sham equations are directly propagated in time. This approach has great potential for execution in massively parallel systems such as modern supercomputers with thousands of processors and graphics processing units (GPUs). For harvesting the potential of conventional supercomputers, the main strategy is a multi-level parallelization scheme that combines the inherent scalability of real-time TDDFT with a real-space grid domain-partitioning approach. A scalable Poisson solver is critical for the efficiency of this scheme. For GPUs, we show how using blocks of Kohn-Sham states provides the required level of data parallelism and that this strategy is also applicable for code optimization on standard processors. Our results show that real-time TDDFT, as implemented in octopus, can be the method of choice for studying the excited states of large molecular systems in modern parallel architectures.

Time-dependent density-functional theory in massively parallel computer architectures: the octopus project

Science.gov (United States)

Andrade, Xavier; Alberdi-Rodriguez, Joseba; Strubbe, David A.; Oliveira, Micael J. T.; Nogueira, Fernando; Castro, Alberto; Muguerza, Javier; Arruabarrena, Agustin; Louie, Steven G.; Aspuru-Guzik, Alán; Rubio, Angel; Marques, Miguel A. L.

2012-06-01

Octopus is a general-purpose density-functional theory (DFT) code, with a particular emphasis on the time-dependent version of DFT (TDDFT). In this paper we present the ongoing efforts to achieve the parallelization of octopus. We focus on the real-time variant of TDDFT, where the time-dependent Kohn-Sham equations are directly propagated in time. This approach has great potential for execution in massively parallel systems such as modern supercomputers with thousands of processors and graphics processing units (GPUs). For harvesting the potential of conventional supercomputers, the main strategy is a multi-level parallelization scheme that combines the inherent scalability of real-time TDDFT with a real-space grid domain-partitioning approach. A scalable Poisson solver is critical for the efficiency of this scheme. For GPUs, we show how using blocks of Kohn-Sham states provides the required level of data parallelism and that this strategy is also applicable for code optimization on standard processors. Our results show that real-time TDDFT, as implemented in octopus, can be the method of choice for studying the excited states of large molecular systems in modern parallel architectures.

Time-dependent density-functional theory in massively parallel computer architectures: the octopus project

International Nuclear Information System (INIS)

Andrade, Xavier; Aspuru-Guzik, Alán; Alberdi-Rodriguez, Joseba; Rubio, Angel; Strubbe, David A; Louie, Steven G; Oliveira, Micael J T; Nogueira, Fernando; Castro, Alberto; Muguerza, Javier; Arruabarrena, Agustin; Marques, Miguel A L

2012-01-01

Octopus is a general-purpose density-functional theory (DFT) code, with a particular emphasis on the time-dependent version of DFT (TDDFT). In this paper we present the ongoing efforts to achieve the parallelization of octopus. We focus on the real-time variant of TDDFT, where the time-dependent Kohn-Sham equations are directly propagated in time. This approach has great potential for execution in massively parallel systems such as modern supercomputers with thousands of processors and graphics processing units (GPUs). For harvesting the potential of conventional supercomputers, the main strategy is a multi-level parallelization scheme that combines the inherent scalability of real-time TDDFT with a real-space grid domain-partitioning approach. A scalable Poisson solver is critical for the efficiency of this scheme. For GPUs, we show how using blocks of Kohn-Sham states provides the required level of data parallelism and that this strategy is also applicable for code optimization on standard processors. Our results show that real-time TDDFT, as implemented in octopus, can be the method of choice for studying the excited states of large molecular systems in modern parallel architectures. (topical review)

Tolerating correlated failures in Massively Parallel Stream Processing Engines

DEFF Research Database (Denmark)

Su, L.; Zhou, Y.

2016-01-01

Fault-tolerance techniques for stream processing engines can be categorized into passive and active approaches. A typical passive approach periodically checkpoints a processing task's runtime states and can recover a failed task by restoring its runtime state using its latest checkpoint. On the o......Fault-tolerance techniques for stream processing engines can be categorized into passive and active approaches. A typical passive approach periodically checkpoints a processing task's runtime states and can recover a failed task by restoring its runtime state using its latest checkpoint....... On the other hand, an active approach usually employs backup nodes to run replicated tasks. Upon failure, the active replica can take over the processing of the failed task with minimal latency. However, both approaches have their own inadequacies in Massively Parallel Stream Processing Engines (MPSPE...

cellGPU: Massively parallel simulations of dynamic vertex models

Science.gov (United States)

Sussman, Daniel M.

2017-10-01

Vertex models represent confluent tissue by polygonal or polyhedral tilings of space, with the individual cells interacting via force laws that depend on both the geometry of the cells and the topology of the tessellation. This dependence on the connectivity of the cellular network introduces several complications to performing molecular-dynamics-like simulations of vertex models, and in particular makes parallelizing the simulations difficult. cellGPU addresses this difficulty and lays the foundation for massively parallelized, GPU-based simulations of these models. This article discusses its implementation for a pair of two-dimensional models, and compares the typical performance that can be expected between running cellGPU entirely on the CPU versus its performance when running on a range of commercial and server-grade graphics cards. By implementing the calculation of topological changes and forces on cells in a highly parallelizable fashion, cellGPU enables researchers to simulate time- and length-scales previously inaccessible via existing single-threaded CPU implementations. Program Files doi:http://dx.doi.org/10.17632/6j2cj29t3r.1 Licensing provisions: MIT Programming language: CUDA/C++ Nature of problem: Simulations of off-lattice "vertex models" of cells, in which the interaction forces depend on both the geometry and the topology of the cellular aggregate. Solution method: Highly parallelized GPU-accelerated dynamical simulations in which the force calculations and the topological features can be handled on either the CPU or GPU. Additional comments: The code is hosted at https://gitlab.com/dmsussman/cellGPU, with documentation additionally maintained at http://dmsussman.gitlab.io/cellGPUdocumentation

ASSET: Analysis of Sequences of Synchronous Events in Massively Parallel Spike Trains

Science.gov (United States)

Canova, Carlos; Denker, Michael; Gerstein, George; Helias, Moritz

2016-01-01

With the ability to observe the activity from large numbers of neurons simultaneously using modern recording technologies, the chance to identify sub-networks involved in coordinated processing increases. Sequences of synchronous spike events (SSEs) constitute one type of such coordinated spiking that propagates activity in a temporally precise manner. The synfire chain was proposed as one potential model for such network processing. Previous work introduced a method for visualization of SSEs in massively parallel spike trains, based on an intersection matrix that contains in each entry the degree of overlap of active neurons in two corresponding time bins. Repeated SSEs are reflected in the matrix as diagonal structures of high overlap values. The method as such, however, leaves the task of identifying these diagonal structures to visual inspection rather than to a quantitative analysis. Here we present ASSET (Analysis of Sequences of Synchronous EvenTs), an improved, fully automated method which determines diagonal structures in the intersection matrix by a robust mathematical procedure. The method consists of a sequence of steps that i) assess which entries in the matrix potentially belong to a diagonal structure, ii) cluster these entries into individual diagonal structures and iii) determine the neurons composing the associated SSEs. We employ parallel point processes generated by stochastic simulations as test data to demonstrate the performance of the method under a wide range of realistic scenarios, including different types of non-stationarity of the spiking activity and different correlation structures. Finally, the ability of the method to discover SSEs is demonstrated on complex data from large network simulations with embedded synfire chains. Thus, ASSET represents an effective and efficient tool to analyze massively parallel spike data for temporal sequences of synchronous activity. PMID:27420734

A Massively Parallel Solver for the Mechanical Harmonic Analysis of Accelerator Cavities

International Nuclear Information System (INIS)

2015-01-01

ACE3P is a 3D massively parallel simulation suite that developed at SLAC National Accelerator Laboratory that can perform coupled electromagnetic, thermal and mechanical study. Effectively utilizing supercomputer resources, ACE3P has become a key simulation tool for particle accelerator R and D. A new frequency domain solver to perform mechanical harmonic response analysis of accelerator components is developed within the existing parallel framework. This solver is designed to determine the frequency response of the mechanical system to external harmonic excitations for time-efficient accurate analysis of the large-scale problems. Coupled with the ACE3P electromagnetic modules, this capability complements a set of multi-physics tools for a comprehensive study of microphonics in superconducting accelerating cavities in order to understand the RF response and feedback requirements for the operational reliability of a particle accelerator. (auth)

Application of Massively Parallel Sequencing in the Clinical Diagnostic Testing of Inherited Cardiac Conditions

Directory of Open Access Journals (Sweden)

Ivone U. S. Leong

2014-06-01

Full Text Available Sudden cardiac death in people between the ages of 1–40 years is a devastating event and is frequently caused by several heritable cardiac disorders. These disorders include cardiac ion channelopathies, such as long QT syndrome, catecholaminergic polymorphic ventricular tachycardia and Brugada syndrome and cardiomyopathies, such as hypertrophic cardiomyopathy and arrhythmogenic right ventricular cardiomyopathy. Through careful molecular genetic evaluation of DNA from sudden death victims, the causative gene mutation can be uncovered, and the rest of the family can be screened and preventative measures implemented in at-risk individuals. The current screening approach in most diagnostic laboratories uses Sanger-based sequencing; however, this method is time consuming and labour intensive. The development of massively parallel sequencing has made it possible to produce millions of sequence reads simultaneously and is potentially an ideal approach to screen for mutations in genes that are associated with sudden cardiac death. This approach offers mutation screening at reduced cost and turnaround time. Here, we will review the current commercially available enrichment kits, massively parallel sequencing (MPS platforms, downstream data analysis and its application to sudden cardiac death in a diagnostic environment.

Massive parallel electromagnetic field simulation program JEMS-FDTD design and implementation on jasmin

International Nuclear Information System (INIS)

Li Hanyu; Zhou Haijing; Dong Zhiwei; Liao Cheng; Chang Lei; Cao Xiaolin; Xiao Li

2010-01-01

A large-scale parallel electromagnetic field simulation program JEMS-FDTD(J Electromagnetic Solver-Finite Difference Time Domain) is designed and implemented on JASMIN (J parallel Adaptive Structured Mesh applications INfrastructure). This program can simulate propagation, radiation, couple of electromagnetic field by solving Maxwell equations on structured mesh explicitly with FDTD method. JEMS-FDTD is able to simulate billion-mesh-scale problems on thousands of processors. In this article, the program is verified by simulating the radiation of an electric dipole. A beam waveguide is simulated to demonstrate the capability of large scale parallel computation. A parallel performance test indicates that a high parallel efficiency is obtained. (authors)

From Massively Parallel Algorithms and Fluctuating Time Horizons to Nonequilibrium Surface Growth

International Nuclear Information System (INIS)

Korniss, G.; Toroczkai, Z.; Novotny, M. A.; Rikvold, P. A.

2000-01-01

We study the asymptotic scaling properties of a massively parallel algorithm for discrete-event simulations where the discrete events are Poisson arrivals. The evolution of the simulated time horizon is analogous to a nonequilibrium surface. Monte Carlo simulations and a coarse-grained approximation indicate that the macroscopic landscape in the steady state is governed by the Edwards-Wilkinson Hamiltonian. Since the efficiency of the algorithm corresponds to the density of local minima in the associated surface, our results imply that the algorithm is asymptotically scalable. (c) 2000 The American Physical Society

Passive and partially active fault tolerance for massively parallel stream processing engines

DEFF Research Database (Denmark)

Su, Li; Zhou, Yongluan

2018-01-01

. On the other hand, an active approach usually employs backup nodes to run replicated tasks. Upon failure, the active replica can take over the processing of the failed task with minimal latency. However, both approaches have their own inadequacies in Massively Parallel Stream Processing Engines (MPSPE...... also propose effective and efficient algorithms to optimize a partially active replication plan to maximize the quality of tentative outputs. We implemented PPA on top of Storm, an open-source MPSPE and conducted extensive experiments using both real and synthetic datasets to verify the effectiveness...

Massively Parallel Interrogation of Aptamer Sequence, Structure and Function

Energy Technology Data Exchange (ETDEWEB)

Fischer, N O; Tok, J B; Tarasow, T M

2008-02-08

Optimization of high affinity reagents is a significant bottleneck in medicine and the life sciences. The ability to synthetically create thousands of permutations of a lead high-affinity reagent and survey the properties of individual permutations in parallel could potentially relieve this bottleneck. Aptamers are single stranded oligonucleotides affinity reagents isolated by in vitro selection processes and as a class have been shown to bind a wide variety of target molecules. Methodology/Principal Findings. High density DNA microarray technology was used to synthesize, in situ, arrays of approximately 3,900 aptamer sequence permutations in triplicate. These sequences were interrogated on-chip for their ability to bind the fluorescently-labeled cognate target, immunoglobulin E, resulting in the parallel execution of thousands of experiments. Fluorescence intensity at each array feature was well resolved and shown to be a function of the sequence present. The data demonstrated high intra- and interchip correlation between the same features as well as among the sequence triplicates within a single array. Consistent with aptamer mediated IgE binding, fluorescence intensity correlated strongly with specific aptamer sequences and the concentration of IgE applied to the array. The massively parallel sequence-function analyses provided by this approach confirmed the importance of a consensus sequence found in all 21 of the original IgE aptamer sequences and support a common stem:loop structure as being the secondary structure underlying IgE binding. The microarray application, data and results presented illustrate an efficient, high information content approach to optimizing aptamer function. It also provides a foundation from which to better understand and manipulate this important class of high affinity biomolecules.

Massively parallel interrogation of aptamer sequence, structure and function.

Directory of Open Access Journals (Sweden)

Nicholas O Fischer

Full Text Available BACKGROUND: Optimization of high affinity reagents is a significant bottleneck in medicine and the life sciences. The ability to synthetically create thousands of permutations of a lead high-affinity reagent and survey the properties of individual permutations in parallel could potentially relieve this bottleneck. Aptamers are single stranded oligonucleotides affinity reagents isolated by in vitro selection processes and as a class have been shown to bind a wide variety of target molecules. METHODOLOGY/PRINCIPAL FINDINGS: High density DNA microarray technology was used to synthesize, in situ, arrays of approximately 3,900 aptamer sequence permutations in triplicate. These sequences were interrogated on-chip for their ability to bind the fluorescently-labeled cognate target, immunoglobulin E, resulting in the parallel execution of thousands of experiments. Fluorescence intensity at each array feature was well resolved and shown to be a function of the sequence present. The data demonstrated high intra- and inter-chip correlation between the same features as well as among the sequence triplicates within a single array. Consistent with aptamer mediated IgE binding, fluorescence intensity correlated strongly with specific aptamer sequences and the concentration of IgE applied to the array. CONCLUSION AND SIGNIFICANCE: The massively parallel sequence-function analyses provided by this approach confirmed the importance of a consensus sequence found in all 21 of the original IgE aptamer sequences and support a common stem:loop structure as being the secondary structure underlying IgE binding. The microarray application, data and results presented illustrate an efficient, high information content approach to optimizing aptamer function. It also provides a foundation from which to better understand and manipulate this important class of high affinity biomolecules.

Parallel dispatch: a new paradigm of electrical power system dispatch

Energy Technology Data Exchange (ETDEWEB)

Zhang, Jun Jason; Wang, Fei-Yue; Wang, Qiang; Hao, Dazhi; Yang, Xiaojing; Gao, David Wenzhong; Zhao, Xiangyang; Zhang, Yingchen

2018-01-01

Modern power systems are evolving into sociotechnical systems with massive complexity, whose real-time operation and dispatch go beyond human capability. Thus, the need for developing and applying new intelligent power system dispatch tools are of great practical significance. In this paper, we introduce the overall business model of power system dispatch, the top level design approach of an intelligent dispatch system, and the parallel intelligent technology with its dispatch applications. We expect that a new dispatch paradigm, namely the parallel dispatch, can be established by incorporating various intelligent technologies, especially the parallel intelligent technology, to enable secure operation of complex power grids, extend system operators U+02BC capabilities, suggest optimal dispatch strategies, and to provide decision-making recommendations according to power system operational goals.

DGDFT: A massively parallel method for large scale density functional theory calculations.

Science.gov (United States)

Hu, Wei; Lin, Lin; Yang, Chao

2015-09-28

We describe a massively parallel implementation of the recently developed discontinuous Galerkin density functional theory (DGDFT) method, for efficient large-scale Kohn-Sham DFT based electronic structure calculations. The DGDFT method uses adaptive local basis (ALB) functions generated on-the-fly during the self-consistent field iteration to represent the solution to the Kohn-Sham equations. The use of the ALB set provides a systematic way to improve the accuracy of the approximation. By using the pole expansion and selected inversion technique to compute electron density, energy, and atomic forces, we can make the computational complexity of DGDFT scale at most quadratically with respect to the number of electrons for both insulating and metallic systems. We show that for the two-dimensional (2D) phosphorene systems studied here, using 37 basis functions per atom allows us to reach an accuracy level of 1.3 × 10(-4) Hartree/atom in terms of the error of energy and 6.2 × 10(-4) Hartree/bohr in terms of the error of atomic force, respectively. DGDFT can achieve 80% parallel efficiency on 128,000 high performance computing cores when it is used to study the electronic structure of 2D phosphorene systems with 3500-14 000 atoms. This high parallel efficiency results from a two-level parallelization scheme that we will describe in detail.

DGDFT: A massively parallel method for large scale density functional theory calculations

International Nuclear Information System (INIS)

Hu, Wei; Yang, Chao; Lin, Lin

2015-01-01

We describe a massively parallel implementation of the recently developed discontinuous Galerkin density functional theory (DGDFT) method, for efficient large-scale Kohn-Sham DFT based electronic structure calculations. The DGDFT method uses adaptive local basis (ALB) functions generated on-the-fly during the self-consistent field iteration to represent the solution to the Kohn-Sham equations. The use of the ALB set provides a systematic way to improve the accuracy of the approximation. By using the pole expansion and selected inversion technique to compute electron density, energy, and atomic forces, we can make the computational complexity of DGDFT scale at most quadratically with respect to the number of electrons for both insulating and metallic systems. We show that for the two-dimensional (2D) phosphorene systems studied here, using 37 basis functions per atom allows us to reach an accuracy level of 1.3 × 10 −4 Hartree/atom in terms of the error of energy and 6.2 × 10 −4 Hartree/bohr in terms of the error of atomic force, respectively. DGDFT can achieve 80% parallel efficiency on 128,000 high performance computing cores when it is used to study the electronic structure of 2D phosphorene systems with 3500-14 000 atoms. This high parallel efficiency results from a two-level parallelization scheme that we will describe in detail

DGDFT: A massively parallel method for large scale density functional theory calculations

Energy Technology Data Exchange (ETDEWEB)

Hu, Wei, E-mail: whu@lbl.gov; Yang, Chao, E-mail: cyang@lbl.gov [Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (United States); Lin, Lin, E-mail: linlin@math.berkeley.edu [Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (United States); Department of Mathematics, University of California, Berkeley, California 94720 (United States)

2015-09-28

We describe a massively parallel implementation of the recently developed discontinuous Galerkin density functional theory (DGDFT) method, for efficient large-scale Kohn-Sham DFT based electronic structure calculations. The DGDFT method uses adaptive local basis (ALB) functions generated on-the-fly during the self-consistent field iteration to represent the solution to the Kohn-Sham equations. The use of the ALB set provides a systematic way to improve the accuracy of the approximation. By using the pole expansion and selected inversion technique to compute electron density, energy, and atomic forces, we can make the computational complexity of DGDFT scale at most quadratically with respect to the number of electrons for both insulating and metallic systems. We show that for the two-dimensional (2D) phosphorene systems studied here, using 37 basis functions per atom allows us to reach an accuracy level of 1.3 × 10{sup −4} Hartree/atom in terms of the error of energy and 6.2 × 10{sup −4} Hartree/bohr in terms of the error of atomic force, respectively. DGDFT can achieve 80% parallel efficiency on 128,000 high performance computing cores when it is used to study the electronic structure of 2D phosphorene systems with 3500-14 000 atoms. This high parallel efficiency results from a two-level parallelization scheme that we will describe in detail.

Multiplexed microsatellite recovery using massively parallel sequencing

Science.gov (United States)

Jennings, T.N.; Knaus, B.J.; Mullins, T.D.; Haig, S.M.; Cronn, R.C.

2011-01-01

Conservation and management of natural populations requires accurate and inexpensive genotyping methods. Traditional microsatellite, or simple sequence repeat (SSR), marker analysis remains a popular genotyping method because of the comparatively low cost of marker development, ease of analysis and high power of genotype discrimination. With the availability of massively parallel sequencing (MPS), it is now possible to sequence microsatellite-enriched genomic libraries in multiplex pools. To test this approach, we prepared seven microsatellite-enriched, barcoded genomic libraries from diverse taxa (two conifer trees, five birds) and sequenced these on one lane of the Illumina Genome Analyzer using paired-end 80-bp reads. In this experiment, we screened 6.1 million sequences and identified 356958 unique microreads that contained di- or trinucleotide microsatellites. Examination of four species shows that our conversion rate from raw sequences to polymorphic markers compares favourably to Sanger- and 454-based methods. The advantage of multiplexed MPS is that the staggering capacity of modern microread sequencing is spread across many libraries; this reduces sample preparation and sequencing costs to less than $400 (USD) per species. This price is sufficiently low that microsatellite libraries could be prepared and sequenced for all 1373 organisms listed as 'threatened' and 'endangered' in the United States for under $0.5M (USD).

GPAW - massively parallel electronic structure calculations with Python-based software

DEFF Research Database (Denmark)

Enkovaara, Jussi; Romero, Nichols A.; Shende, Sameer

2011-01-01

of the productivity enhancing features together with a good numerical performance. We have used this approach in implementing an electronic structure simulation software GPAW using the combination of Python and C programming languages. While the chosen approach works well in standard workstations and Unix...... popular choice. While dynamic, interpreted languages, such as Python, can increase the effciency of programmer, they cannot compete directly with the raw performance of compiled languages. However, by using an interpreted language together with a compiled language, it is possible to have most...... environments, massively parallel supercomputing systems can present some challenges in porting, debugging and profiling the software. In this paper we describe some details of the implementation and discuss the advantages and challenges of the combined Python/C approach. We show that despite the challenges...

Massively Parallel Finite Element Programming

KAUST Repository

Heister, Timo; Kronbichler, Martin; Bangerth, Wolfgang

2010-01-01

Today's large finite element simulations require parallel algorithms to scale on clusters with thousands or tens of thousands of processor cores. We present data structures and algorithms to take advantage of the power of high performance computers in generic finite element codes. Existing generic finite element libraries often restrict the parallelization to parallel linear algebra routines. This is a limiting factor when solving on more than a few hundreds of cores. We describe routines for distributed storage of all major components coupled with efficient, scalable algorithms. We give an overview of our effort to enable the modern and generic finite element library deal.II to take advantage of the power of large clusters. In particular, we describe the construction of a distributed mesh and develop algorithms to fully parallelize the finite element calculation. Numerical results demonstrate good scalability. © 2010 Springer-Verlag.

Massively Parallel Finite Element Programming

KAUST Repository

Heister, Timo

2010-01-01

Today\\'s large finite element simulations require parallel algorithms to scale on clusters with thousands or tens of thousands of processor cores. We present data structures and algorithms to take advantage of the power of high performance computers in generic finite element codes. Existing generic finite element libraries often restrict the parallelization to parallel linear algebra routines. This is a limiting factor when solving on more than a few hundreds of cores. We describe routines for distributed storage of all major components coupled with efficient, scalable algorithms. We give an overview of our effort to enable the modern and generic finite element library deal.II to take advantage of the power of large clusters. In particular, we describe the construction of a distributed mesh and develop algorithms to fully parallelize the finite element calculation. Numerical results demonstrate good scalability. © 2010 Springer-Verlag.

Massively parallel de novo protein design for targeted therapeutics

KAUST Repository

Chevalier, Aaron

2017-09-26

De novo protein design holds promise for creating small stable proteins with shapes customized to bind therapeutic targets. We describe a massively parallel approach for designing, manufacturing and screening mini-protein binders, integrating large-scale computational design, oligonucleotide synthesis, yeast display screening and next-generation sequencing. We designed and tested 22,660 mini-proteins of 37-43 residues that target influenza haemagglutinin and botulinum neurotoxin B, along with 6,286 control sequences to probe contributions to folding and binding, and identified 2,618 high-affinity binders. Comparison of the binding and non-binding design sets, which are two orders of magnitude larger than any previously investigated, enabled the evaluation and improvement of the computational model. Biophysical characterization of a subset of the binder designs showed that they are extremely stable and, unlike antibodies, do not lose activity after exposure to high temperatures. The designs elicit little or no immune response and provide potent prophylactic and therapeutic protection against influenza, even after extensive repeated dosing.

Massively parallel de novo protein design for targeted therapeutics

KAUST Repository

Chevalier, Aaron; Silva, Daniel-Adriano; Rocklin, Gabriel J.; Hicks, Derrick R.; Vergara, Renan; Murapa, Patience; Bernard, Steffen M.; Zhang, Lu; Lam, Kwok-Ho; Yao, Guorui; Bahl, Christopher D.; Miyashita, Shin-Ichiro; Goreshnik, Inna; Fuller, James T.; Koday, Merika T.; Jenkins, Cody M.; Colvin, Tom; Carter, Lauren; Bohn, Alan; Bryan, Cassie M.; Ferná ndez-Velasco, D. Alejandro; Stewart, Lance; Dong, Min; Huang, Xuhui; Jin, Rongsheng; Wilson, Ian A.; Fuller, Deborah H.; Baker, David

2017-01-01

De novo protein design holds promise for creating small stable proteins with shapes customized to bind therapeutic targets. We describe a massively parallel approach for designing, manufacturing and screening mini-protein binders, integrating large-scale computational design, oligonucleotide synthesis, yeast display screening and next-generation sequencing. We designed and tested 22,660 mini-proteins of 37-43 residues that target influenza haemagglutinin and botulinum neurotoxin B, along with 6,286 control sequences to probe contributions to folding and binding, and identified 2,618 high-affinity binders. Comparison of the binding and non-binding design sets, which are two orders of magnitude larger than any previously investigated, enabled the evaluation and improvement of the computational model. Biophysical characterization of a subset of the binder designs showed that they are extremely stable and, unlike antibodies, do not lose activity after exposure to high temperatures. The designs elicit little or no immune response and provide potent prophylactic and therapeutic protection against influenza, even after extensive repeated dosing.

Massively parallel performance of neutron transport response matrix algorithms

International Nuclear Information System (INIS)

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

1993-01-01

Massively parallel red/black response matrix algorithms for the solution of within-group neutron transport problems are implemented on the Connection Machines-2, 200 and 5. The response matrices are dericed from the diamond-differences and linear-linear nodal discrete ordinate and variational nodal P 3 approximations. The unaccelerated performance of the iterative procedure is examined relative to the maximum rated performances of the machines. The effects of processor partitions size, of virtual processor ratio and of problems size are examined in detail. For the red/black algorithm, the ratio of inter-node communication to computing times is found to be quite small, normally of the order of ten percent or less. Performance increases with problems size and with virtual processor ratio, within the memeory per physical processor limitation. Algorithm adaptation to courser grain machines is straight-forward, with total computing time being virtually inversely proportional to the number of physical processors. (orig.)

Massively parallel de novo protein design for targeted therapeutics

Science.gov (United States)

Chevalier, Aaron; Silva, Daniel-Adriano; Rocklin, Gabriel J.; Hicks, Derrick R.; Vergara, Renan; Murapa, Patience; Bernard, Steffen M.; Zhang, Lu; Lam, Kwok-Ho; Yao, Guorui; Bahl, Christopher D.; Miyashita, Shin-Ichiro; Goreshnik, Inna; Fuller, James T.; Koday, Merika T.; Jenkins, Cody M.; Colvin, Tom; Carter, Lauren; Bohn, Alan; Bryan, Cassie M.; Fernández-Velasco, D. Alejandro; Stewart, Lance; Dong, Min; Huang, Xuhui; Jin, Rongsheng; Wilson, Ian A.; Fuller, Deborah H.; Baker, David

2018-01-01

De novo protein design holds promise for creating small stable proteins with shapes customized to bind therapeutic targets. We describe a massively parallel approach for designing, manufacturing and screening mini-protein binders, integrating large-scale computational design, oligonucleotide synthesis, yeast display screening and next-generation sequencing. We designed and tested 22,660 mini-proteins of 37–43 residues that target influenza haemagglutinin and botulinum neurotoxin B, along with 6,286 control sequences to probe contributions to folding and binding, and identified 2,618 high-affinity binders. Comparison of the binding and non-binding design sets, which are two orders of magnitude larger than any previously investigated, enabled the evaluation and improvement of the computational model. Biophysical characterization of a subset of the binder designs showed that they are extremely stable and, unlike antibodies, do not lose activity after exposure to high temperatures. The designs elicit little or no immune response and provide potent prophylactic and therapeutic protection against influenza, even after extensive repeated dosing. PMID:28953867

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....

Massive parallel sequencing in sarcoma pathobiology: state of the art and perspectives.

Science.gov (United States)

Brenca, Monica; Maestro, Roberta

2015-01-01

Sarcomas are an aggressive and highly heterogeneous group of mesenchymal malignancies with different morphologies and clinical behavior. Current therapeutic strategies remain unsatisfactory. Cytogenetic and molecular characterization of these tumors is resulting in the breakdown of the classical histopathological categories into molecular subgroups that better define sarcoma pathobiology and pave the way to more precise diagnostic criteria and novel therapeutic opportunities. The purpose of this short review is to summarize the state-of-the-art on the exploitation of massive parallel sequencing technologies, also known as next generation sequencing, in the elucidation of sarcoma pathobiology and to discuss how these applications may impact on diagnosis, prognosis and therapy of these tumors.

Parallel time domain solvers for electrically large transient scattering problems

KAUST Repository

Liu, Yang

2014-09-26

Marching on in time (MOT)-based integral equation solvers represent an increasingly appealing avenue for analyzing transient electromagnetic interactions with large and complex structures. MOT integral equation solvers for analyzing electromagnetic scattering from perfect electrically conducting objects are obtained by enforcing electric field boundary conditions and implicitly time advance electric surface current densities by iteratively solving sparse systems of equations at all time steps. Contrary to finite difference and element competitors, these solvers apply to nonlinear and multi-scale structures comprising geometrically intricate and deep sub-wavelength features residing atop electrically large platforms. Moreover, they are high-order accurate, stable in the low- and high-frequency limits, and applicable to conducting and penetrable structures represented by highly irregular meshes. This presentation reviews some recent advances in the parallel implementations of time domain integral equation solvers, specifically those that leverage multilevel plane-wave time-domain algorithm (PWTD) on modern manycore computer architectures including graphics processing units (GPUs) and distributed memory supercomputers. The GPU-based implementation achieves at least one order of magnitude speedups compared to serial implementations while the distributed parallel implementation are highly scalable to thousands of compute-nodes. A distributed parallel PWTD kernel has been adopted to solve time domain surface/volume integral equations (TDSIE/TDVIE) for analyzing transient scattering from large and complex-shaped perfectly electrically conducting (PEC)/dielectric objects involving ten million/tens of millions of spatial unknowns.

Massively parallel simulator of optical coherence tomography of inhomogeneous turbid media.

Science.gov (United States)

Malektaji, Siavash; Lima, Ivan T; Escobar I, Mauricio R; Sherif, Sherif S

2017-10-01

An accurate and practical simulator for Optical Coherence Tomography (OCT) could be an important tool to study the underlying physical phenomena in OCT such as multiple light scattering. Recently, many researchers have investigated simulation of OCT of turbid media, e.g., tissue, using Monte Carlo methods. The main drawback of these earlier simulators is the long computational time required to produce accurate results. We developed a massively parallel simulator of OCT of inhomogeneous turbid media that obtains both Class I diffusive reflectivity, due to ballistic and quasi-ballistic scattered photons, and Class II diffusive reflectivity due to multiply scattered photons. This Monte Carlo-based simulator is implemented on graphic processing units (GPUs), using the Compute Unified Device Architecture (CUDA) platform and programming model, to exploit the parallel nature of propagation of photons in tissue. It models an arbitrary shaped sample medium as a tetrahedron-based mesh and uses an advanced importance sampling scheme. This new simulator speeds up simulations of OCT of inhomogeneous turbid media by about two orders of magnitude. To demonstrate this result, we have compared the computation times of our new parallel simulator and its serial counterpart using two samples of inhomogeneous turbid media. We have shown that our parallel implementation reduced simulation time of OCT of the first sample medium from 407 min to 92 min by using a single GPU card, to 12 min by using 8 GPU cards and to 7 min by using 16 GPU cards. For the second sample medium, the OCT simulation time was reduced from 209 h to 35.6 h by using a single GPU card, and to 4.65 h by using 8 GPU cards, and to only 2 h by using 16 GPU cards. Therefore our new parallel simulator is considerably more practical to use than its central processing unit (CPU)-based counterpart. Our new parallel OCT simulator could be a practical tool to study the different physical phenomena underlying OCT

Massive Exploration of Perturbed Conditions of the Blood Coagulation Cascade through GPU Parallelization

Directory of Open Access Journals (Sweden)

Paolo Cazzaniga

2014-01-01

high-performance computing solutions is motivated by the need of performing large numbers of in silico analysis to study the behavior of biological systems in different conditions, which necessitate a computing power that usually overtakes the capability of standard desktop computers. In this work we present coagSODA, a CUDA-powered computational tool that was purposely developed for the analysis of a large mechanistic model of the blood coagulation cascade (BCC, defined according to both mass-action kinetics and Hill functions. coagSODA allows the execution of parallel simulations of the dynamics of the BCC by automatically deriving the system of ordinary differential equations and then exploiting the numerical integration algorithm LSODA. We present the biological results achieved with a massive exploration of perturbed conditions of the BCC, carried out with one-dimensional and bi-dimensional parameter sweep analysis, and show that GPU-accelerated parallel simulations of this model can increase the computational performances up to a 181× speedup compared to the corresponding sequential simulations.

Beam dynamics calculations and particle tracking using massively parallel processors

International Nuclear Information System (INIS)

Ryne, R.D.; Habib, S.

1995-01-01

During the past decade massively parallel processors (MPPs) have slowly gained acceptance within the scientific community. At present these machines typically contain a few hundred to one thousand off-the-shelf microprocessors and a total memory of up to 32 GBytes. The potential performance of these machines is illustrated by the fact that a month long job on a high end workstation might require only a few hours on an MPP. The acceptance of MPPs has been slow for a variety of reasons. For example, some algorithms are not easily parallelizable. Also, in the past these machines were difficult to program. But in recent years the development of Fortran-like languages such as CM Fortran and High Performance Fortran have made MPPs much easier to use. In the following we will describe how MPPs can be used for beam dynamics calculations and long term particle tracking

Implementation, capabilities, and benchmarking of Shift, a massively parallel Monte Carlo radiation transport code

International Nuclear Information System (INIS)

Pandya, Tara M.; Johnson, Seth R.; Evans, Thomas M.; Davidson, Gregory G.; Hamilton, Steven P.; Godfrey, Andrew T.

2015-01-01

This paper discusses the implementation, capabilities, and validation of Shift, a massively parallel Monte Carlo radiation transport package developed and maintained at Oak Ridge National Laboratory. It has been developed to scale well from laptop to small computing clusters to advanced supercomputers. Special features of Shift include hybrid capabilities for variance reduction such as CADIS and FW-CADIS, and advanced parallel decomposition and tally methods optimized for scalability on supercomputing architectures. Shift has been validated and verified against various reactor physics benchmarks and compares well to other state-of-the-art Monte Carlo radiation transport codes such as MCNP5, CE KENO-VI, and OpenMC. Some specific benchmarks used for verification and validation include the CASL VERA criticality test suite and several Westinghouse AP1000 ® problems. These benchmark and scaling studies show promising results

Convergence analysis of a class of massively parallel direction splitting algorithms for the Navier-Stokes equations in simple domains

KAUST Repository

Guermond, Jean-Luc; Minev, Peter D.; Salgado, Abner J.

2012-01-01

We provide a convergence analysis for a new fractional timestepping technique for the incompressible Navier-Stokes equations based on direction splitting. This new technique is of linear complexity, unconditionally stable and convergent, and suitable for massive parallelization. © 2012 American Mathematical Society.

A scalable approach to modeling groundwater flow on massively parallel computers

International Nuclear Information System (INIS)

Ashby, S.F.; Falgout, R.D.; Tompson, A.F.B.

1995-12-01

We describe a fully scalable approach to the simulation of groundwater flow on a hierarchy of computing platforms, ranging from workstations to massively parallel computers. Specifically, we advocate the use of scalable conceptual models in which the subsurface model is defined independently of the computational grid on which the simulation takes place. We also describe a scalable multigrid algorithm for computing the groundwater flow velocities. We axe thus able to leverage both the engineer's time spent developing the conceptual model and the computing resources used in the numerical simulation. We have successfully employed this approach at the LLNL site, where we have run simulations ranging in size from just a few thousand spatial zones (on workstations) to more than eight million spatial zones (on the CRAY T3D)-all using the same conceptual model

Inter-laboratory evaluation of the EUROFORGEN Global ancestry-informative SNP panel by massively parallel sequencing using the Ion PGM™

DEFF Research Database (Denmark)

Eduardoff, M; Gross, T E; Santos, C

2016-01-01

Seq™ PCR primers was designed for the Global AIM-SNPs to perform massively parallel sequencing using the Ion PGM™ system. This study assessed individual SNP genotyping precision using the Ion PGM™, the forensic sensitivity of the multiplex using dilution series, degraded DNA plus simple mixtures...

Detection of reverse transcriptase termination sites using cDNA ligation and massive parallel sequencing

DEFF Research Database (Denmark)

Kielpinski, Lukasz J; Boyd, Mette; Sandelin, Albin

2013-01-01

Detection of reverse transcriptase termination sites is important in many different applications, such as structural probing of RNAs, rapid amplification of cDNA 5' ends (5' RACE), cap analysis of gene expression, and detection of RNA modifications and protein-RNA cross-links. The throughput...... of these methods can be increased by applying massive parallel sequencing technologies.Here, we describe a versatile method for detection of reverse transcriptase termination sites based on ligation of an adapter to the 3' end of cDNA with bacteriophage TS2126 RNA ligase (CircLigase™). In the following PCR...

A Faster Parallel Algorithm and Efficient Multithreaded Implementations for Evaluating Betweenness Centrality on Massive Datasets

Energy Technology Data Exchange (ETDEWEB)

Madduri, Kamesh; Ediger, David; Jiang, Karl; Bader, David A.; Chavarria-Miranda, Daniel

2009-02-15

We present a new lock-free parallel algorithm for computing betweenness centralityof massive small-world networks. With minor changes to the data structures, ouralgorithm also achieves better spatial cache locality compared to previous approaches. Betweenness centrality is a key algorithm kernel in HPCS SSCA#2, a benchmark extensively used to evaluate the performance of emerging high-performance computing architectures for graph-theoretic computations. We design optimized implementations of betweenness centrality and the SSCA#2 benchmark for two hardware multithreaded systems: a Cray XMT system with the Threadstorm processor, and a single-socket Sun multicore server with the UltraSPARC T2 processor. For a small-world network of 134 million vertices and 1.073 billion edges, the 16-processor XMT system and the 8-core Sun Fire T5120 server achieve TEPS scores (an algorithmic performance count for the SSCA#2 benchmark) of 160 million and 90 million respectively, which corresponds to more than a 2X performance improvement over the previous parallel implementations. To better characterize the performance of these multithreaded systems, we correlate the SSCA#2 performance results with data from the memory-intensive STREAM and RandomAccess benchmarks. Finally, we demonstrate the applicability of our implementation to analyze massive real-world datasets by computing approximate betweenness centrality for a large-scale IMDb movie-actor network.

Massively parallel simulations of strong electronic correlations: Realistic Coulomb vertex and multiplet effects

Science.gov (United States)

Baumgärtel, M.; Ghanem, K.; Kiani, A.; Koch, E.; Pavarini, E.; Sims, H.; Zhang, G.

2017-07-01

We discuss the efficient implementation of general impurity solvers for dynamical mean-field theory. We show that both Lanczos and quantum Monte Carlo in different flavors (Hirsch-Fye, continuous-time hybridization- and interaction-expansion) exhibit excellent scaling on massively parallel supercomputers. We apply these algorithms to simulate realistic model Hamiltonians including the full Coulomb vertex, crystal-field splitting, and spin-orbit interaction. We discuss how to remove the sign problem in the presence of non-diagonal crystal-field and hybridization matrices. We show how to extract the physically observable quantities from imaginary time data, in particular correlation functions and susceptibilities. Finally, we present benchmarks and applications for representative correlated systems.

Multi-mode sensor processing on a dynamically reconfigurable massively parallel processor array

Science.gov (United States)

Chen, Paul; Butts, Mike; Budlong, Brad; Wasson, Paul

2008-04-01

This paper introduces a novel computing architecture that can be reconfigured in real time to adapt on demand to multi-mode sensor platforms' dynamic computational and functional requirements. This 1 teraOPS reconfigurable Massively Parallel Processor Array (MPPA) has 336 32-bit processors. The programmable 32-bit communication fabric provides streamlined inter-processor connections with deterministically high performance. Software programmability, scalability, ease of use, and fast reconfiguration time (ranging from microseconds to milliseconds) are the most significant advantages over FPGAs and DSPs. This paper introduces the MPPA architecture, its programming model, and methods of reconfigurability. An MPPA platform for reconfigurable computing is based on a structural object programming model. Objects are software programs running concurrently on hundreds of 32-bit RISC processors and memories. They exchange data and control through a network of self-synchronizing channels. A common application design pattern on this platform, called a work farm, is a parallel set of worker objects, with one input and one output stream. Statically configured work farms with homogeneous and heterogeneous sets of workers have been used in video compression and decompression, network processing, and graphics applications.

Performance evaluations of advanced massively parallel platforms based on gyrokinetic toroidal five-dimensional Eulerian code GT5D

International Nuclear Information System (INIS)

Idomura, Yasuhiro; Jolliet, Sebastien

2010-01-01

A gyrokinetic toroidal five dimensional Eulerian code GT5D is ported on six advanced massively parallel platforms and comprehensive benchmark tests are performed. A parallelisation technique based on physical properties of the gyrokinetic equation is presented. By extending the parallelisation technique with a hybrid parallel model, the scalability of the code is improved on platforms with multi-core processors. In the benchmark tests, a good salability is confirmed up to several thousands cores on every platforms, and the maximum sustained performance of ∼18.6 Tflops is achieved using 16384 cores of BX900. (author)

A massively parallel strategy for STR marker development, capture, and genotyping.

Science.gov (United States)

Kistler, Logan; Johnson, Stephen M; Irwin, Mitchell T; Louis, Edward E; Ratan, Aakrosh; Perry, George H

2017-09-06

Short tandem repeat (STR) variants are highly polymorphic markers that facilitate powerful population genetic analyses. STRs are especially valuable in conservation and ecological genetic research, yielding detailed information on population structure and short-term demographic fluctuations. Massively parallel sequencing has not previously been leveraged for scalable, efficient STR recovery. Here, we present a pipeline for developing STR markers directly from high-throughput shotgun sequencing data without a reference genome, and an approach for highly parallel target STR recovery. We employed our approach to capture a panel of 5000 STRs from a test group of diademed sifakas (Propithecus diadema, n = 3), endangered Malagasy rainforest lemurs, and we report extremely efficient recovery of targeted loci-97.3-99.6% of STRs characterized with ≥10x non-redundant sequence coverage. We then tested our STR capture strategy on P. diadema fecal DNA, and report robust initial results and suggestions for future implementations. In addition to STR targets, this approach also generates large, genome-wide single nucleotide polymorphism (SNP) panels from flanking regions. Our method provides a cost-effective and scalable solution for rapid recovery of large STR and SNP datasets in any species without needing a reference genome, and can be used even with suboptimal DNA more easily acquired in conservation and ecological studies. Published by Oxford University Press on behalf of Nucleic Acids Research 2017.

Differences Between Distributed and Parallel Systems

Energy Technology Data Exchange (ETDEWEB)

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

1998-10-01

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

CHOLLA: A NEW MASSIVELY PARALLEL HYDRODYNAMICS CODE FOR ASTROPHYSICAL SIMULATION

International Nuclear Information System (INIS)

Schneider, Evan E.; Robertson, Brant E.

2015-01-01

We present Computational Hydrodynamics On ParaLLel Architectures (Cholla ), a new three-dimensional hydrodynamics code that harnesses the power of graphics processing units (GPUs) to accelerate astrophysical simulations. Cholla models the Euler equations on a static mesh using state-of-the-art techniques, including the unsplit Corner Transport Upwind algorithm, a variety of exact and approximate Riemann solvers, and multiple spatial reconstruction techniques including the piecewise parabolic method (PPM). Using GPUs, Cholla evolves the fluid properties of thousands of cells simultaneously and can update over 10 million cells per GPU-second while using an exact Riemann solver and PPM reconstruction. Owing to the massively parallel architecture of GPUs and the design of the Cholla code, astrophysical simulations with physically interesting grid resolutions (≳256 3 ) can easily be computed on a single device. We use the Message Passing Interface library to extend calculations onto multiple devices and demonstrate nearly ideal scaling beyond 64 GPUs. A suite of test problems highlights the physical accuracy of our modeling and provides a useful comparison to other codes. We then use Cholla to simulate the interaction of a shock wave with a gas cloud in the interstellar medium, showing that the evolution of the cloud is highly dependent on its density structure. We reconcile the computed mixing time of a turbulent cloud with a realistic density distribution destroyed by a strong shock with the existing analytic theory for spherical cloud destruction by describing the system in terms of its median gas density

CHOLLA: A NEW MASSIVELY PARALLEL HYDRODYNAMICS CODE FOR ASTROPHYSICAL SIMULATION

Energy Technology Data Exchange (ETDEWEB)

Schneider, Evan E.; Robertson, Brant E. [Steward Observatory, University of Arizona, 933 North Cherry Avenue, Tucson, AZ 85721 (United States)

2015-04-15

We present Computational Hydrodynamics On ParaLLel Architectures (Cholla ), a new three-dimensional hydrodynamics code that harnesses the power of graphics processing units (GPUs) to accelerate astrophysical simulations. Cholla models the Euler equations on a static mesh using state-of-the-art techniques, including the unsplit Corner Transport Upwind algorithm, a variety of exact and approximate Riemann solvers, and multiple spatial reconstruction techniques including the piecewise parabolic method (PPM). Using GPUs, Cholla evolves the fluid properties of thousands of cells simultaneously and can update over 10 million cells per GPU-second while using an exact Riemann solver and PPM reconstruction. Owing to the massively parallel architecture of GPUs and the design of the Cholla code, astrophysical simulations with physically interesting grid resolutions (≳256{sup 3}) can easily be computed on a single device. We use the Message Passing Interface library to extend calculations onto multiple devices and demonstrate nearly ideal scaling beyond 64 GPUs. A suite of test problems highlights the physical accuracy of our modeling and provides a useful comparison to other codes. We then use Cholla to simulate the interaction of a shock wave with a gas cloud in the interstellar medium, showing that the evolution of the cloud is highly dependent on its density structure. We reconcile the computed mixing time of a turbulent cloud with a realistic density distribution destroyed by a strong shock with the existing analytic theory for spherical cloud destruction by describing the system in terms of its median gas density.

Electron Cooling and Isotropization during Magnetotail Current Sheet Thinning: Implications for Parallel Electric Fields

Science.gov (United States)

Lu, San; Artemyev, A. V.; Angelopoulos, V.

2017-11-01

Magnetotail current sheet thinning is a distinctive feature of substorm growth phase, during which magnetic energy is stored in the magnetospheric lobes. Investigation of charged particle dynamics in such thinning current sheets is believed to be important for understanding the substorm energy storage and the current sheet destabilization responsible for substorm expansion phase onset. We use Time History of Events and Macroscale Interactions during Substorms (THEMIS) B and C observations in 2008 and 2009 at 18 - 25 RE to show that during magnetotail current sheet thinning, the electron temperature decreases (cooling), and the parallel temperature decreases faster than the perpendicular temperature, leading to a decrease of the initially strong electron temperature anisotropy (isotropization). This isotropization cannot be explained by pure adiabatic cooling or by pitch angle scattering. We use test particle simulations to explore the mechanism responsible for the cooling and isotropization. We find that during the thinning, a fast decrease of a parallel electric field (directed toward the Earth) can speed up the electron parallel cooling, causing it to exceed the rate of perpendicular cooling, and thus lead to isotropization, consistent with observation. If the parallel electric field is too small or does not change fast enough, the electron parallel cooling is slower than the perpendicular cooling, so the parallel electron anisotropy grows, contrary to observation. The same isotropization can also be accomplished by an increasing parallel electric field directed toward the equatorial plane. Our study reveals the existence of a large-scale parallel electric field, which plays an important role in magnetotail particle dynamics during the current sheet thinning process.

Phase space simulation of collisionless stellar systems on the massively parallel processor

International Nuclear Information System (INIS)

White, R.L.

1987-01-01

A numerical technique for solving the collisionless Boltzmann equation describing the time evolution of a self gravitating fluid in phase space was implemented on the Massively Parallel Processor (MPP). The code performs calculations for a two dimensional phase space grid (with one space and one velocity dimension). Some results from calculations are presented. The execution speed of the code is comparable to the speed of a single processor of a Cray-XMP. Advantages and disadvantages of the MPP architecture for this type of problem are discussed. The nearest neighbor connectivity of the MPP array does not pose a significant obstacle. Future MPP-like machines should have much more local memory and easier access to staging memory and disks in order to be effective for this type of problem

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.

Massively Parallel Assimilation of TOGA/TAO and Topex/Poseidon Measurements into a Quasi Isopycnal Ocean General Circulation Model Using an Ensemble Kalman Filter

Science.gov (United States)

Keppenne, Christian L.; Rienecker, Michele; Borovikov, Anna Y.; Suarez, Max

1999-01-01

A massively parallel ensemble Kalman filter (EnKF)is used to assimilate temperature data from the TOGA/TAO array and altimetry from TOPEX/POSEIDON into a Pacific basin version of the NASA Seasonal to Interannual Prediction Project (NSIPP)ls quasi-isopycnal ocean general circulation model. The EnKF is an approximate Kalman filter in which the error-covariance propagation step is modeled by the integration of multiple instances of a numerical model. An estimate of the true error covariances is then inferred from the distribution of the ensemble of model state vectors. This inplementation of the filter takes advantage of the inherent parallelism in the EnKF algorithm by running all the model instances concurrently. The Kalman filter update step also occurs in parallel by having each processor process the observations that occur in the region of physical space for which it is responsible. The massively parallel data assimilation system is validated by withholding some of the data and then quantifying the extent to which the withheld information can be inferred from the assimilation of the remaining data. The distributions of the forecast and analysis error covariances predicted by the ENKF are also examined.

Massive parallelization of a 3D finite difference electromagnetic forward solution using domain decomposition methods on multiple CUDA enabled GPUs

Science.gov (United States)

Schultz, A.

2010-12-01

3D forward solvers lie at the core of inverse formulations used to image the variation of electrical conductivity within the Earth's interior. This property is associated with variations in temperature, composition, phase, presence of volatiles, and in specific settings, the presence of groundwater, geothermal resources, oil/gas or minerals. The high cost of 3D solutions has been a stumbling block to wider adoption of 3D methods. Parallel algorithms for modeling frequency domain 3D EM problems have not achieved wide scale adoption, with emphasis on fairly coarse grained parallelism using MPI and similar approaches. The communications bandwidth as well as the latency required to send and receive network communication packets is a limiting factor in implementing fine grained parallel strategies, inhibiting wide adoption of these algorithms. Leading Graphics Processor Unit (GPU) companies now produce GPUs with hundreds of GPU processor cores per die. The footprint, in silicon, of the GPU's restricted instruction set is much smaller than the general purpose instruction set required of a CPU. Consequently, the density of processor cores on a GPU can be much greater than on a CPU. GPUs also have local memory, registers and high speed communication with host CPUs, usually through PCIe type interconnects. The extremely low cost and high computational power of GPUs provides the EM geophysics community with an opportunity to achieve fine grained (i.e. massive) parallelization of codes on low cost hardware. The current generation of GPUs (e.g. NVidia Fermi) provides 3 billion transistors per chip die, with nearly 500 processor cores and up to 6 GB of fast (DDR5) GPU memory. This latest generation of GPU supports fast hardware double precision (64 bit) floating point operations of the type required for frequency domain EM forward solutions. Each Fermi GPU board can sustain nearly 1 TFLOP in double precision, and multiple boards can be installed in the host computer system. We

Stochastic Optimal Control of Parallel Hybrid Electric Vehicles

Directory of Open Access Journals (Sweden)

Feiyan Qin

2017-02-01

Full Text Available Energy management strategies (EMSs in hybrid electric vehicles (HEVs are highly related to the fuel economy and emission performances. However, EMS constitutes a challenging problem due to the complex structure of a HEV and the unknown or partially known driving cycles. To meet this problem, this paper adopts a stochastic dynamic programming (SDP method for the EMS of a specially designed vehicle, a pre-transmission single-shaft torque-coupling parallel HEV. In this parallel HEV, the auto clutch output is connected to the transmission input through an electric motor, which benefits an efficient motor assist operation. In this EMS, demanded torque of driver is modeled as a one-state Markov process to represent the uncertainty of future driving situations. The obtained EMS has been evaluated with ADVISOR2002 over two standard government drive cycles and a self-defined one, and compared with a dynamic programming (DP one and a rule-based one. Simulation results have shown the real-time performance of the proposed approach, and potential vehicle performance improvement relative to the rule-based one.

Reduction of momentum transfer rates by parallel electric fields: A two-fluid demonstration

International Nuclear Information System (INIS)

Delamere, P.A.; Stenbaek-Nielsen, H.C.; Otto, A.

2002-01-01

Momentum transfer between an ionized gas cloud moving relative to an ambient magnetized plasma is a general problem in space plasma physics. Obvious examples include the Io-Jupiter interaction, comets, and coronal mass ejections. Active plasma experiments have demonstrated that momentum transfer rates associated with Alfven wave propagation are poorly understood. Barium injection experiments from the Combined Release and Radiation Effects Satellite (CRRES) have shown that dense ionized clouds are capable of ExB drifting over large distances perpendicular to the magnetic field. The CRRES 'skidding' distances were much larger than predicted by magnetohydrodynamic theory and it has been proposed that parallel electric fields were a key component in the skidding phenomenon. A two-fluid code was used to demonstrate the role of parallel electric fields in reducing momentum transfer between two distinct plasma populations. In this study, a dense plasma was initialized moving relative to an ambient plasma and perpendicular to B. Parallel electric fields were introduced via a friction term in the electron momentum equation and the collision frequency was scaled in proportion to the field-aligned current density. The simulation results showed that parallel electric fields decreased the decelerating magnetic tension force on the plasma cloud through a magnetic diffusion/reconnection process

Massive Electrical Storm at Disease Onset in a Patient with Brugada Syndrome

DEFF Research Database (Denmark)

Pallisgaard, Jannik L; Gang, Uffe; Kanters, Jørgen K.

2014-01-01

Background Brugada syndrome (BrS) is a genetic arrhythmogenic disease characterized by ST-segment elevations in the right precordial leads of the electrocardiogram (ECG). These ECG changes may be concealed and BrS may present with electrical storm characterized by recurrent ventricular tachycardia...... and fibrillation. Case Report A 49-year-old previously healthy man was admitted with electrical storm. The patient received direct current (DC) cardioversion shocks and only after intravenous lidocaine did the electrical storm slowly subside with a total of 255 DC shocks administered during the first 24 h after...... admission. He fully recovered and received an implantable cardioverter-defibrillator. Subsequent drug challenge with flecainide revealed type 1 BrS. Conclusions Massive electrical storm can be the first symptom of BrS and the diagnostic ECG changes may be concealed at presentation. Although hundreds of DC...

Detection of arboviruses and other micro-organisms in experimentally infected mosquitoes using massively parallel sequencing.

Directory of Open Access Journals (Sweden)

Sonja Hall-Mendelin

Full Text Available Human disease incidence attributed to arbovirus infection is increasing throughout the world, with effective control interventions limited by issues of sustainability, insecticide resistance and the lack of effective vaccines. Several promising control strategies are currently under development, such as the release of mosquitoes trans-infected with virus-blocking Wolbachia bacteria. Implementation of any control program is dependent on effective virus surveillance and a thorough understanding of virus-vector interactions. Massively parallel sequencing has enormous potential for providing comprehensive genomic information that can be used to assess many aspects of arbovirus ecology, as well as to evaluate novel control strategies. To demonstrate proof-of-principle, we analyzed Aedes aegypti or Aedes albopictus experimentally infected with dengue, yellow fever or chikungunya viruses. Random amplification was used to prepare sufficient template for sequencing on the Personal Genome Machine. Viral sequences were present in all infected mosquitoes. In addition, in most cases, we were also able to identify the mosquito species and mosquito micro-organisms, including the bacterial endosymbiont Wolbachia. Importantly, naturally occurring Wolbachia strains could be differentiated from strains that had been trans-infected into the mosquito. The method allowed us to assemble near full-length viral genomes and detect other micro-organisms without prior sequence knowledge, in a single reaction. This is a step toward the application of massively parallel sequencing as an arbovirus surveillance tool. It has the potential to provide insight into virus transmission dynamics, and has applicability to the post-release monitoring of Wolbachia in mosquito populations.

Computations on the massively parallel processor at the Goddard Space Flight Center

Science.gov (United States)

Strong, James P.

1991-01-01

Described are four significant algorithms implemented on the massively parallel processor (MPP) at the Goddard Space Flight Center. Two are in the area of image analysis. Of the other two, one is a mathematical simulation experiment and the other deals with the efficient transfer of data between distantly separated processors in the MPP array. The first algorithm presented is the automatic determination of elevations from stereo pairs. The second algorithm solves mathematical logistic equations capable of producing both ordered and chaotic (or random) solutions. This work can potentially lead to the simulation of artificial life processes. The third algorithm is the automatic segmentation of images into reasonable regions based on some similarity criterion, while the fourth is an implementation of a bitonic sort of data which significantly overcomes the nearest neighbor interconnection constraints on the MPP for transferring data between distant processors.

An FPGA-Based Massively Parallel Neuromorphic Cortex Simulator.

Science.gov (United States)

Wang, Runchun M; Thakur, Chetan S; van Schaik, André

2018-01-01

This paper presents a massively parallel and scalable neuromorphic cortex simulator designed for simulating large and structurally connected spiking neural networks, such as complex models of various areas of the cortex. The main novelty of this work is the abstraction of a neuromorphic architecture into clusters represented by minicolumns and hypercolumns, analogously to the fundamental structural units observed in neurobiology. Without this approach, simulating large-scale fully connected networks needs prohibitively large memory to store look-up tables for point-to-point connections. Instead, we use a novel architecture, based on the structural connectivity in the neocortex, such that all the required parameters and connections can be stored in on-chip memory. The cortex simulator can be easily reconfigured for simulating different neural networks without any change in hardware structure by programming the memory. A hierarchical communication scheme allows one neuron to have a fan-out of up to 200 k neurons. As a proof-of-concept, an implementation on one Altera Stratix V FPGA was able to simulate 20 million to 2.6 billion leaky-integrate-and-fire (LIF) neurons in real time. We verified the system by emulating a simplified auditory cortex (with 100 million neurons). This cortex simulator achieved a low power dissipation of 1.62 μW per neuron. With the advent of commercially available FPGA boards, our system offers an accessible and scalable tool for the design, real-time simulation, and analysis of large-scale spiking neural networks.

An FPGA-Based Massively Parallel Neuromorphic Cortex Simulator

Directory of Open Access Journals (Sweden)

Runchun M. Wang

2018-04-01

Full Text Available This paper presents a massively parallel and scalable neuromorphic cortex simulator designed for simulating large and structurally connected spiking neural networks, such as complex models of various areas of the cortex. The main novelty of this work is the abstraction of a neuromorphic architecture into clusters represented by minicolumns and hypercolumns, analogously to the fundamental structural units observed in neurobiology. Without this approach, simulating large-scale fully connected networks needs prohibitively large memory to store look-up tables for point-to-point connections. Instead, we use a novel architecture, based on the structural connectivity in the neocortex, such that all the required parameters and connections can be stored in on-chip memory. The cortex simulator can be easily reconfigured for simulating different neural networks without any change in hardware structure by programming the memory. A hierarchical communication scheme allows one neuron to have a fan-out of up to 200 k neurons. As a proof-of-concept, an implementation on one Altera Stratix V FPGA was able to simulate 20 million to 2.6 billion leaky-integrate-and-fire (LIF neurons in real time. We verified the system by emulating a simplified auditory cortex (with 100 million neurons. This cortex simulator achieved a low power dissipation of 1.62 μW per neuron. With the advent of commercially available FPGA boards, our system offers an accessible and scalable tool for the design, real-time simulation, and analysis of large-scale spiking neural networks.

Application of Raptor-M3G to reactor dosimetry problems on massively parallel architectures - 026

International Nuclear Information System (INIS)

Longoni, G.

2010-01-01

The solution of complex 3-D radiation transport problems requires significant resources both in terms of computation time and memory availability. Therefore, parallel algorithms and multi-processor architectures are required to solve efficiently large 3-D radiation transport problems. This paper presents the application of RAPTOR-M3G (Rapid Parallel Transport Of Radiation - Multiple 3D Geometries) to reactor dosimetry problems. RAPTOR-M3G is a newly developed parallel computer code designed to solve the discrete ordinates (SN) equations on multi-processor computer architectures. This paper presents the results for a reactor dosimetry problem using a 3-D model of a commercial 2-loop pressurized water reactor (PWR). The accuracy and performance of RAPTOR-M3G will be analyzed and the numerical results obtained from the calculation will be compared directly to measurements of the neutron field in the reactor cavity air gap. The parallel performance of RAPTOR-M3G on massively parallel architectures, where the number of computing nodes is in the order of hundreds, will be analyzed up to four hundred processors. The performance results will be presented based on two supercomputing architectures: the POPLE supercomputer operated by the Pittsburgh Supercomputing Center and the Westinghouse computer cluster. The Westinghouse computer cluster is equipped with a standard Ethernet network connection and an InfiniBand R interconnects capable of a bandwidth in excess of 20 GBit/sec. Therefore, the impact of the network architecture on RAPTOR-M3G performance will be analyzed as well. (authors)

Running ATLAS workloads within massively parallel distributed applications using Athena Multi-Process framework (AthenaMP)

CERN Document Server

Calafiura, Paolo; The ATLAS collaboration; Seuster, Rolf; Tsulaia, Vakhtang; van Gemmeren, Peter

2015-01-01

AthenaMP is a multi-process version of the ATLAS reconstruction and data analysis framework Athena. By leveraging Linux fork and copy-on-write, it allows the sharing of memory pages between event processors running on the same compute node with little to no change in the application code. Originally targeted to optimize the memory footprint of reconstruction jobs, AthenaMP has demonstrated that it can reduce the memory usage of certain confugurations of ATLAS production jobs by a factor of 2. AthenaMP has also evolved to become the parallel event-processing core of the recently developed ATLAS infrastructure for fine-grained event processing (Event Service) which allows to run AthenaMP inside massively parallel distributed applications on hundreds of compute nodes simultaneously. We present the architecture of AthenaMP, various strategies implemented by AthenaMP for scheduling workload to worker processes (for example: Shared Event Queue and Shared Distributor of Event Tokens) and the usage of AthenaMP in the...

Running ATLAS workloads within massively parallel distributed applications using Athena Multi-Process framework (AthenaMP)

CERN Document Server

Calafiura, Paolo; Seuster, Rolf; Tsulaia, Vakhtang; van Gemmeren, Peter

2015-01-01

AthenaMP is a multi-process version of the ATLAS reconstruction, simulation and data analysis framework Athena. By leveraging Linux fork and copy-on-write, it allows for sharing of memory pages between event processors running on the same compute node with little to no change in the application code. Originally targeted to optimize the memory footprint of reconstruction jobs, AthenaMP has demonstrated that it can reduce the memory usage of certain configurations of ATLAS production jobs by a factor of 2. AthenaMP has also evolved to become the parallel event-processing core of the recently developed ATLAS infrastructure for fine-grained event processing (Event Service) which allows to run AthenaMP inside massively parallel distributed applications on hundreds of compute nodes simultaneously. We present the architecture of AthenaMP, various strategies implemented by AthenaMP for scheduling workload to worker processes (for example: Shared Event Queue and Shared Distributor of Event Tokens) and the usage of Ath...

LiNbO3: A photovoltaic substrate for massive parallel manipulation and patterning of nano-objects

International Nuclear Information System (INIS)

Carrascosa, M.; García-Cabañes, A.; Jubera, M.; Ramiro, J. B.; Agulló-López, F.

2015-01-01

The application of evanescent photovoltaic (PV) fields, generated by visible illumination of Fe:LiNbO 3 substrates, for parallel massive trapping and manipulation of micro- and nano-objects is critically reviewed. The technique has been often referred to as photovoltaic or photorefractive tweezers. The main advantage of the new method is that the involved electrophoretic and/or dielectrophoretic forces do not require any electrodes and large scale manipulation of nano-objects can be easily achieved using the patterning capabilities of light. The paper describes the experimental techniques for particle trapping and the main reported experimental results obtained with a variety of micro- and nano-particles (dielectric and conductive) and different illumination configurations (single beam, holographic geometry, and spatial light modulator projection). The report also pays attention to the physical basis of the method, namely, the coupling of the evanescent photorefractive fields to the dielectric response of the nano-particles. The role of a number of physical parameters such as the contrast and spatial periodicities of the illumination pattern or the particle deposition method is discussed. Moreover, the main properties of the obtained particle patterns in relation to potential applications are summarized, and first demonstrations reviewed. Finally, the PV method is discussed in comparison to other patterning strategies, such as those based on the pyroelectric response and the electric fields associated to domain poling of ferroelectric materials

User's Guide for TOUGH2-MP - A Massively Parallel Version of the TOUGH2 Code

International Nuclear Information System (INIS)

Earth Sciences Division; Zhang, Keni; Zhang, Keni; Wu, Yu-Shu; Pruess, Karsten

2008-01-01

TOUGH2-MP is a massively parallel (MP) version of the TOUGH2 code, designed for computationally efficient parallel simulation of isothermal and nonisothermal flows of multicomponent, multiphase fluids in one, two, and three-dimensional porous and fractured media. In recent years, computational requirements have become increasingly intensive in large or highly nonlinear problems for applications in areas such as radioactive waste disposal, CO2 geological sequestration, environmental assessment and remediation, reservoir engineering, and groundwater hydrology. The primary objective of developing the parallel-simulation capability is to significantly improve the computational performance of the TOUGH2 family of codes. The particular goal for the parallel simulator is to achieve orders-of-magnitude improvement in computational time for models with ever-increasing complexity. TOUGH2-MP is designed to perform parallel simulation on multi-CPU computational platforms. An earlier version of TOUGH2-MP (V1.0) was based on the TOUGH2 Version 1.4 with EOS3, EOS9, and T2R3D modules, a software previously qualified for applications in the Yucca Mountain project, and was designed for execution on CRAY T3E and IBM SP supercomputers. The current version of TOUGH2-MP (V2.0) includes all fluid property modules of the standard version TOUGH2 V2.0. It provides computationally efficient capabilities using supercomputers, Linux clusters, or multi-core PCs, and also offers many user-friendly features. The parallel simulator inherits all process capabilities from V2.0 together with additional capabilities for handling fractured media from V1.4. This report provides a quick starting guide on how to set up and run the TOUGH2-MP program for users with a basic knowledge of running the (standard) version TOUGH2 code. The report also gives a brief technical description of the code, including a discussion of parallel methodology, code structure, as well as mathematical and numerical methods used

Massive electrical storm at disease onset in a patient with Brugada syndrome.

Science.gov (United States)

Pallisgaard, Jannik L; Gang, Uffe; Kanters, Jørgen K; Hansen, Peter R

2014-12-16

Brugada syndrome (BrS) is a genetic arrhythmogenic disease characterized by ST-segment elevations in the right precordial leads of the electrocardiogram (ECG). These ECG changes may be concealed and BrS may present with electrical storm characterized by recurrent ventricular tachycardia and fibrillation. A 49-year-old previously healthy man was admitted with electrical storm. The patient received direct current (DC) cardioversion shocks and only after intravenous lidocaine did the electrical storm slowly subside with a total of 255 DC shocks administered during the first 24 h after admission. He fully recovered and received an implantable cardioverter-defibrillator. Subsequent drug challenge with flecainide revealed type 1 BrS. Massive electrical storm can be the first symptom of BrS and the diagnostic ECG changes may be concealed at presentation. Although hundreds of DC shocks may be required during initial treatment, full recovery can be achieved.

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

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.

Electron cyclotron waves in the presence of parallel electric fields in the Earth's auroral plasma

Directory of Open Access Journals (Sweden)

S. Kumar

1997-01-01

Full Text Available The electron cyclotron waves that originate at low altitudes (<0.5 RE and observed by ground facilities have been studied in the presence of a weak parallel electric field in auroral magnetoplasma consisting of trapped energetic auroral electrons and cold background electrons of ionospheric origin. The model distribution for auroral trapped electrons is taken as Maxwellian ring distribution. An expression for the growth rate has been obtained in the presence of parallel electric field assuming that the real frequency in the whistler mode is not affected by the presence of the electric field. The results show that waves grow (or damp in amplitude for a parallel (or antiparallel electric field. The influence of the electric field is more pronounced at a shorter wavelength spectrum. An increase in population of energetic electrons increases the growth rate and thus, plays a significant role in the wave excitation process in the auroral regions.

Modular and efficient ozone systems based on massively parallel chemical processing in microchannel plasma arrays: performance and commercialization

Science.gov (United States)

Kim, M.-H.; Cho, J. H.; Park, S.-J.; Eden, J. G.

2017-08-01

Plasmachemical systems based on the production of a specific molecule (O3) in literally thousands of microchannel plasmas simultaneously have been demonstrated, developed and engineered over the past seven years, and commercialized. At the heart of this new plasma technology is the plasma chip, a flat aluminum strip fabricated by photolithographic and wet chemical processes and comprising 24-48 channels, micromachined into nanoporous aluminum oxide, with embedded electrodes. By integrating 4-6 chips into a module, the mass output of an ozone microplasma system is scaled linearly with the number of modules operating in parallel. A 115 g/hr (2.7 kg/day) ozone system, for example, is realized by the combined output of 18 modules comprising 72 chips and 1,800 microchannels. The implications of this plasma processing architecture for scaling ozone production capability, and reducing capital and service costs when introducing redundancy into the system, are profound. In contrast to conventional ozone generator technology, microplasma systems operate reliably (albeit with reduced output) in ambient air and humidity levels up to 90%, a characteristic attributable to the water adsorption/desorption properties and electrical breakdown strength of nanoporous alumina. Extensive testing has documented chip and system lifetimes (MTBF) beyond 5,000 hours, and efficiencies >130 g/kWh when oxygen is the feedstock gas. Furthermore, the weight and volume of microplasma systems are a factor of 3-10 lower than those for conventional ozone systems of comparable output. Massively-parallel plasmachemical processing offers functionality, performance, and commercial value beyond that afforded by conventional technology, and is currently in operation in more than 30 countries worldwide.

Space-charge-dominated beam dynamics simulations using the massively parallel processors (MPPs) of the Cray T3D

International Nuclear Information System (INIS)

Liu, H.

1996-01-01

Computer simulations using the multi-particle code PARMELA with a three-dimensional point-by-point space charge algorithm have turned out to be very helpful in supporting injector commissioning and operations at Thomas Jefferson National Accelerator Facility (Jefferson Lab, formerly called CEBAF). However, this algorithm, which defines a typical N 2 problem in CPU time scaling, is very time-consuming when N, the number of macro-particles, is large. Therefore, it is attractive to use massively parallel processors (MPPs) to speed up the simulations. Motivated by this, the authors modified the space charge subroutine for using the MPPs of the Cray T3D. The techniques used to parallelize and optimize the code on the T3D are discussed in this paper. The performance of the code on the T3D is examined in comparison with a Parallel Vector Processing supercomputer of the Cray C90 and an HP 735/15 high-end workstation

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

OpenCL Implementation of a Parallel Universal Kriging Algorithm for Massive Spatial Data Interpolation on Heterogeneous Systems

Directory of Open Access Journals (Sweden)

Fang Huang

2016-06-01

Full Text Available In some digital Earth engineering applications, spatial interpolation algorithms are required to process and analyze large amounts of data. Due to its powerful computing capacity, heterogeneous computing has been used in many applications for data processing in various fields. In this study, we explore the design and implementation of a parallel universal kriging spatial interpolation algorithm using the OpenCL programming model on heterogeneous computing platforms for massive Geo-spatial data processing. This study focuses primarily on transforming the hotspots in serial algorithms, i.e., the universal kriging interpolation function, into the corresponding kernel function in OpenCL. We also employ parallelization and optimization techniques in our implementation to improve the code performance. Finally, based on the results of experiments performed on two different high performance heterogeneous platforms, i.e., an NVIDIA graphics processing unit system and an Intel Xeon Phi system (MIC, we show that the parallel universal kriging algorithm can achieve the highest speedup of up to 40× with a single computing device and the highest speedup of up to 80× with multiple devices.

Revealing the Physics of Galactic Winds Through Massively-Parallel Hydrodynamics Simulations

Science.gov (United States)

Schneider, Evan Elizabeth

This thesis documents the hydrodynamics code Cholla and a numerical study of multiphase galactic winds. Cholla is a massively-parallel, GPU-based code designed for astrophysical simulations that is freely available to the astrophysics community. A static-mesh Eulerian code, Cholla is ideally suited to carrying out massive simulations (> 20483 cells) that require very high resolution. The code incorporates state-of-the-art hydrodynamics algorithms including third-order spatial reconstruction, exact and linearized Riemann solvers, and unsplit integration algorithms that account for transverse fluxes on multidimensional grids. Operator-split radiative cooling and a dual-energy formalism for high mach number flows are also included. An extensive test suite demonstrates Cholla's superior ability to model shocks and discontinuities, while the GPU-native design makes the code extremely computationally efficient - speeds of 5-10 million cell updates per GPU-second are typical on current hardware for 3D simulations with all of the aforementioned physics. The latter half of this work comprises a comprehensive study of the mixing between a hot, supernova-driven wind and cooler clouds representative of those observed in multiphase galactic winds. Both adiabatic and radiatively-cooling clouds are investigated. The analytic theory of cloud-crushing is applied to the problem, and adiabatic turbulent clouds are found to be mixed with the hot wind on similar timescales as the classic spherical case (4-5 t cc) with an appropriate rescaling of the cloud-crushing time. Radiatively cooling clouds survive considerably longer, and the differences in evolution between turbulent and spherical clouds cannot be reconciled with a simple rescaling. The rapid incorporation of low-density material into the hot wind implies efficient mass-loading of hot phases of galactic winds. At the same time, the extreme compression of high-density cloud material leads to long-lived but slow-moving clumps

SWAMP+: multiple subsequence alignment using associative massive parallelism

Energy Technology Data Exchange (ETDEWEB)

Steinfadt, Shannon Irene [Los Alamos National Laboratory; Baker, Johnnie W [KENT STATE UNIV.

2010-10-18

A new parallel algorithm SWAMP+ incorporates the Smith-Waterman sequence alignment on an associative parallel model known as ASC. It is a highly sensitive parallel approach that expands traditional pairwise sequence alignment. This is the first parallel algorithm to provide multiple non-overlapping, non-intersecting subsequence alignments with the accuracy of Smith-Waterman. The efficient algorithm provides multiple alignments similar to BLAST while creating a better workflow for the end users. The parallel portions of the code run in O(m+n) time using m processors. When m = n, the algorithmic analysis becomes O(n) with a coefficient of two, yielding a linear speedup. Implementation of the algorithm on the SIMD ClearSpeed CSX620 confirms this theoretical linear speedup with real timings.

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.

Bentonite electrical conductivity: a model based on series–parallel transport

KAUST Repository

Lima, Ana T.

2010-01-30

Bentonite has significant applications nowadays, among them as landfill liners, in concrete industry as a repairing material, and as drilling mud in oil well construction. The application of an electric field to such perimeters is under wide discussion, and subject of many studies. However, to understand the behaviour of such an expansive and plastic material under the influence of an electric field, the perception of its electrical properties is essential. This work serves to compare existing data of such electrical behaviour with new laboratorial results. Electrical conductivity is a pertinent parameter since it indicates how much a material is prone to conduct electricity. In the current study, total conductivity of a compacted porous medium was established to be dependent upon density of the bentonite plug. Therefore, surface conductivity was addressed and a series-parallel transport model used to quantify/predict the total conductivity of the system. © The Author(s) 2010.

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

An explanation for parallel electric field pulses observed over thunderstorms

Science.gov (United States)

Kelley, M. C.; Barnum, B. H.

2009-10-01

Every electric field instrument flown on sounding rockets over a thunderstorm has detected pulses of electric fields parallel to the Earth's magnetic field associated with every strike. This paper describes the ionospheric signatures found during a flight from Wallops Island, Virginia, on 2 September 1995. The electric field results in a drifting Maxwellian corresponding to energies up to 1 eV. The distribution function relaxes because of elastic and inelastic collisions, resulting in electron heating up to 4000-5000 K and potentially observable red line emissions and enhanced ISR electron temperatures. The field strength scales with the current in cloud-to-ground strikes and falls off as r -1 with distance. Pulses of both polarities are found, although most electric fields are downward, parallel to the magnetic field. The pulse may be the reaction of ambient plasma to a current pulse carried at the whistler packet's highest group velocity. The charge source required to produce the electric field is very likely electrons of a few keV traveling at the packet velocity. We conjecture that the current source is the divergence of the current flowing at mesospheric heights, the phenomenon called an elve. The whistler packet's effective radiated power is as high as 25 mW at ionospheric heights, comparable to some ionospheric heater transmissions. Comparing the Poynting flux at the base of the ionosphere with flux an equal distance away along the ground, some 30 db are lost in the mesosphere. Another 10 db are lost in the transition from free space to the whistler mode.

PFLOTRAN User Manual: A Massively Parallel Reactive Flow and Transport Model for Describing Surface and Subsurface Processes

Energy Technology Data Exchange (ETDEWEB)

Lichtner, Peter C. [OFM Research, Redmond, WA (United States); Hammond, Glenn E. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Lu, Chuan [Idaho National Lab. (INL), Idaho Falls, ID (United States); Karra, Satish [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Bisht, Gautam [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Andre, Benjamin [National Center for Atmospheric Research, Boulder, CO (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Mills, Richard [Intel Corporation, Portland, OR (United States); Univ. of Tennessee, Knoxville, TN (United States); Kumar, Jitendra [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

2015-01-20

PFLOTRAN solves a system of generally nonlinear partial differential equations describing multi-phase, multicomponent and multiscale reactive flow and transport in porous materials. The code is designed to run on massively parallel computing architectures as well as workstations and laptops (e.g. Hammond et al., 2011). Parallelization is achieved through domain decomposition using the PETSc (Portable Extensible Toolkit for Scientific Computation) libraries for the parallelization framework (Balay et al., 1997). PFLOTRAN has been developed from the ground up for parallel scalability and has been run on up to 218 processor cores with problem sizes up to 2 billion degrees of freedom. Written in object oriented Fortran 90, the code requires the latest compilers compatible with Fortran 2003. At the time of this writing this requires gcc 4.7.x, Intel 12.1.x and PGC compilers. As a requirement of running problems with a large number of degrees of freedom, PFLOTRAN allows reading input data that is too large to fit into memory allotted to a single processor core. The current limitation to the problem size PFLOTRAN can handle is the limitation of the HDF5 file format used for parallel IO to 32 bit integers. Noting that 2³² = 4; 294; 967; 296, this gives an estimate of the maximum problem size that can be currently run with PFLOTRAN. Hopefully this limitation will be remedied in the near future.

Statistical method to compare massive parallel sequencing pipelines.

Science.gov (United States)

Elsensohn, M H; Leblay, N; Dimassi, S; Campan-Fournier, A; Labalme, A; Roucher-Boulez, F; Sanlaville, D; Lesca, G; Bardel, C; Roy, P

2017-03-01

Today, sequencing is frequently carried out by Massive Parallel Sequencing (MPS) that cuts drastically sequencing time and expenses. Nevertheless, Sanger sequencing remains the main validation method to confirm the presence of variants. The analysis of MPS data involves the development of several bioinformatic tools, academic or commercial. We present here a statistical method to compare MPS pipelines and test it in a comparison between an academic (BWA-GATK) and a commercial pipeline (TMAP-NextGENe®), with and without reference to a gold standard (here, Sanger sequencing), on a panel of 41 genes in 43 epileptic patients. This method used the number of variants to fit log-linear models for pairwise agreements between pipelines. To assess the heterogeneity of the margins and the odds ratios of agreement, four log-linear models were used: a full model, a homogeneous-margin model, a model with single odds ratio for all patients, and a model with single intercept. Then a log-linear mixed model was fitted considering the biological variability as a random effect. Among the 390,339 base-pairs sequenced, TMAP-NextGENe® and BWA-GATK found, on average, 2253.49 and 1857.14 variants (single nucleotide variants and indels), respectively. Against the gold standard, the pipelines had similar sensitivities (63.47% vs. 63.42%) and close but significantly different specificities (99.57% vs. 99.65%; p < 0.001). Same-trend results were obtained when only single nucleotide variants were considered (99.98% specificity and 76.81% sensitivity for both pipelines). The method allows thus pipeline comparison and selection. It is generalizable to all types of MPS data and all pipelines.

Wideband aperture array using RF channelizers and massively parallel digital 2D IIR filterbank

Science.gov (United States)

Sengupta, Arindam; Madanayake, Arjuna; Gómez-García, Roberto; Engeberg, Erik D.

2014-05-01

Wideband receive-mode beamforming applications in wireless location, electronically-scanned antennas for radar, RF sensing, microwave imaging and wireless communications require digital aperture arrays that offer a relatively constant far-field beam over several octaves of bandwidth. Several beamforming schemes including the well-known true time-delay and the phased array beamformers have been realized using either finite impulse response (FIR) or fast Fourier transform (FFT) digital filter-sum based techniques. These beamforming algorithms offer the desired selectivity at the cost of a high computational complexity and frequency-dependant far-field array patterns. A novel approach to receiver beamforming is the use of massively parallel 2-D infinite impulse response (IIR) fan filterbanks for the synthesis of relatively frequency independent RF beams at an order of magnitude lower multiplier complexity compared to FFT or FIR filter based conventional algorithms. The 2-D IIR filterbanks demand fast digital processing that can support several octaves of RF bandwidth, fast analog-to-digital converters (ADCs) for RF-to-bits type direct conversion of wideband antenna element signals. Fast digital implementation platforms that can realize high-precision recursive filter structures necessary for real-time beamforming, at RF radio bandwidths, are also desired. We propose a novel technique that combines a passive RF channelizer, multichannel ADC technology, and single-phase massively parallel 2-D IIR digital fan filterbanks, realized at low complexity using FPGA and/or ASIC technology. There exists native support for a larger bandwidth than the maximum clock frequency of the digital implementation technology. We also strive to achieve More-than-Moore throughput by processing a wideband RF signal having content with N-fold (B = N Fclk/2) bandwidth compared to the maximum clock frequency Fclk Hz of the digital VLSI platform under consideration. Such increase in bandwidth is

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

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

Parallel electric fields in a simulation of magnetotail reconnection and plasmoid evolution

International Nuclear Information System (INIS)

Hesse, M.; Birn, J.

1990-01-01

Properties of the electric field component parallel to the magnetic field are investigate in a 3D MHD simulation of plasmoid formation and evolution in the magnetotail, in the presence of a net dawn-dusk magnetic field component. The spatial localization of E-parallel, and the concept of a diffusion zone and the role of E-parallel in accelerating electrons are discussed. A localization of the region of enhanced E-parallel in all space directions is found, with a strong concentration in the z direction. This region is identified as the diffusion zone, which plays a crucial role in reconnection theory through the local break-down of magnetic flux conservation. 12 refs

Characterization of the Zoarces viviparus liver transcriptome using massively parallel pyrosequencing

Directory of Open Access Journals (Sweden)

Asker Noomi

2009-07-01

Full Text Available Abstract Background The teleost Zoarces viviparus (eelpout lives along the coasts of Northern Europe and has long been an established model organism for marine ecology and environmental monitoring. The scarce information about this species genome has however restrained the use of efficient molecular-level assays, such as gene expression microarrays. Results In the present study we present the first comprehensive characterization of the Zoarces viviparus liver transcriptome. From 400,000 reads generated by massively parallel pyrosequencing, more than 50,000 pieces of putative transcripts were assembled, annotated and functionally classified. The data was estimated to cover roughly 40% of the total transcriptome and homologues for about half of the genes of Gasterosteus aculeatus (stickleback were identified. The sequence data was consequently used to design an oligonucleotide microarray for large-scale gene expression analysis. Conclusion Our results show that one run using a Genome Sequencer FLX from 454 Life Science/Roche generates enough genomic information for adequate de novo assembly of a large number of genes in a higher vertebrate. The generated sequence data, including the validated microarray probes, are publicly available to promote genome-wide research in Zoarces viviparus.

Light scattering of rectangular slot antennas: parallel magnetic vector vs perpendicular electric vector

Science.gov (United States)

Lee, Dukhyung; Kim, Dai-Sik

2016-01-01

We study light scattering off rectangular slot nano antennas on a metal film varying incident polarization and incident angle, to examine which field vector of light is more important: electric vector perpendicular to, versus magnetic vector parallel to the long axis of the rectangle. While vector Babinet’s principle would prefer magnetic field along the long axis for optimizing slot antenna function, convention and intuition most often refer to the electric field perpendicular to it. Here, we demonstrate experimentally that in accordance with vector Babinet’s principle, the incident magnetic vector parallel to the long axis is the dominant component, with the perpendicular incident electric field making a small contribution of the factor of 1/|ε|, the reciprocal of the absolute value of the dielectric constant of the metal, owing to the non-perfectness of metals at optical frequencies.

Inter-laboratory evaluation of the EUROFORGEN Global ancestry-informative SNP panel by massively parallel sequencing using the Ion PGM™.

Science.gov (United States)

Eduardoff, M; Gross, T E; Santos, C; de la Puente, M; Ballard, D; Strobl, C; Børsting, C; Morling, N; Fusco, L; Hussing, C; Egyed, B; Souto, L; Uacyisrael, J; Syndercombe Court, D; Carracedo, Á; Lareu, M V; Schneider, P M; Parson, W; Phillips, C; Parson, W; Phillips, C

2016-07-01

The EUROFORGEN Global ancestry-informative SNP (AIM-SNPs) panel is a forensic multiplex of 128 markers designed to differentiate an individual's ancestry from amongst the five continental population groups of Africa, Europe, East Asia, Native America, and Oceania. A custom multiplex of AmpliSeq™ PCR primers was designed for the Global AIM-SNPs to perform massively parallel sequencing using the Ion PGM™ system. This study assessed individual SNP genotyping precision using the Ion PGM™, the forensic sensitivity of the multiplex using dilution series, degraded DNA plus simple mixtures, and the ancestry differentiation power of the final panel design, which required substitution of three original ancestry-informative SNPs with alternatives. Fourteen populations that had not been previously analyzed were genotyped using the custom multiplex and these studies allowed assessment of genotyping performance by comparison of data across five laboratories. Results indicate a low level of genotyping error can still occur from sequence misalignment caused by homopolymeric tracts close to the target SNP, despite careful scrutiny of candidate SNPs at the design stage. Such sequence misalignment required the exclusion of component SNP rs2080161 from the Global AIM-SNPs panel. However, the overall genotyping precision and sensitivity of this custom multiplex indicates the Ion PGM™ assay for the Global AIM-SNPs is highly suitable for forensic ancestry analysis with massively parallel sequencing. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Hydrogenic donor impurity in parallel-triangular quantum wires: Hydrostatic pressure and applied electric field effects

International Nuclear Information System (INIS)

Restrepo, R.L.; Giraldo, E.; Miranda, G.L.; Ospina, W.; Duque, C.A.

2009-01-01

The combined effects of the hydrostatic pressure and in-growth direction applied electric field on the binding energy of hydrogenic shallow-donor impurity states in parallel-coupled-GaAs-Ga 1-x Al x As-quantum-well wires are calculated using a variational procedure within the effective-mass and parabolic-band approximations. Results are obtained for several dimensions of the structure, shallow-donor impurity positions, hydrostatic pressure, and applied electric field. Our results suggest that external inputs such us hydrostatic pressure and in-growth direction electric field are two useful tools in order to modify the binding energy of a donor impurity in parallel-coupled-quantum-well wires.

Parallel PWTD-Accelerated Explicit Solution of the Time Domain Electric Field Volume Integral Equation

KAUST Repository

Liu, Yang

2016-03-25

A parallel plane-wave time-domain (PWTD)-accelerated explicit marching-on-in-time (MOT) scheme for solving the time domain electric field volume integral equation (TD-EFVIE) is presented. The proposed scheme leverages pulse functions and Lagrange polynomials to spatially and temporally discretize the electric flux density induced throughout the scatterers, and a finite difference scheme to compute the electric fields from the Hertz electric vector potentials radiated by the flux density. The flux density is explicitly updated during time marching by a predictor-corrector (PC) scheme and the vector potentials are efficiently computed by a scalar PWTD scheme. The memory requirement and computational complexity of the resulting explicit PWTD-PC-EFVIE solver scale as ( log ) s s O N N and ( ) s t O N N , respectively. Here, s N is the number of spatial basis functions and t N is the number of time steps. A scalable parallelization of the proposed MOT scheme on distributed- memory CPU clusters is described. The efficiency, accuracy, and applicability of the resulting (parallelized) PWTD-PC-EFVIE solver are demonstrated via its application to the analysis of transient electromagnetic wave interactions on canonical and real-life scatterers represented with up to 25 million spatial discretization elements.

Parallel PWTD-Accelerated Explicit Solution of the Time Domain Electric Field Volume Integral Equation

KAUST Repository

Liu, Yang; Al-Jarro, Ahmed; Bagci, Hakan; Michielssen, Eric

2016-01-01

A parallel plane-wave time-domain (PWTD)-accelerated explicit marching-on-in-time (MOT) scheme for solving the time domain electric field volume integral equation (TD-EFVIE) is presented. The proposed scheme leverages pulse functions and Lagrange polynomials to spatially and temporally discretize the electric flux density induced throughout the scatterers, and a finite difference scheme to compute the electric fields from the Hertz electric vector potentials radiated by the flux density. The flux density is explicitly updated during time marching by a predictor-corrector (PC) scheme and the vector potentials are efficiently computed by a scalar PWTD scheme. The memory requirement and computational complexity of the resulting explicit PWTD-PC-EFVIE solver scale as ( log ) s s O N N and ( ) s t O N N , respectively. Here, s N is the number of spatial basis functions and t N is the number of time steps. A scalable parallelization of the proposed MOT scheme on distributed- memory CPU clusters is described. The efficiency, accuracy, and applicability of the resulting (parallelized) PWTD-PC-EFVIE solver are demonstrated via its application to the analysis of transient electromagnetic wave interactions on canonical and real-life scatterers represented with up to 25 million spatial discretization elements.

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...

Parallel Hybrid Gas-Electric Geared Turbofan Engine Conceptual Design and Benefits Analysis

Science.gov (United States)

Lents, Charles; Hardin, Larry; Rheaume, Jonathan; Kohlman, Lee

2016-01-01

The conceptual design of a parallel gas-electric hybrid propulsion system for a conventional single aisle twin engine tube and wing vehicle has been developed. The study baseline vehicle and engine technology are discussed, followed by results of the hybrid propulsion system sizing and performance analysis. The weights analysis for the electric energy storage & conversion system and thermal management system is described. Finally, the potential system benefits are assessed.

A quantitative assessment of the Hadoop framework for analyzing massively parallel DNA sequencing data.

Science.gov (United States)

Siretskiy, Alexey; Sundqvist, Tore; Voznesenskiy, Mikhail; Spjuth, Ola

2015-01-01

New high-throughput technologies, such as massively parallel sequencing, have transformed the life sciences into a data-intensive field. The most common e-infrastructure for analyzing this data consists of batch systems that are based on high-performance computing resources; however, the bioinformatics software that is built on this platform does not scale well in the general case. Recently, the Hadoop platform has emerged as an interesting option to address the challenges of increasingly large datasets with distributed storage, distributed processing, built-in data locality, fault tolerance, and an appealing programming methodology. In this work we introduce metrics and report on a quantitative comparison between Hadoop and a single node of conventional high-performance computing resources for the tasks of short read mapping and variant calling. We calculate efficiency as a function of data size and observe that the Hadoop platform is more efficient for biologically relevant data sizes in terms of computing hours for both split and un-split data files. We also quantify the advantages of the data locality provided by Hadoop for NGS problems, and show that a classical architecture with network-attached storage will not scale when computing resources increase in numbers. Measurements were performed using ten datasets of different sizes, up to 100 gigabases, using the pipeline implemented in Crossbow. To make a fair comparison, we implemented an improved preprocessor for Hadoop with better performance for splittable data files. For improved usability, we implemented a graphical user interface for Crossbow in a private cloud environment using the CloudGene platform. All of the code and data in this study are freely available as open source in public repositories. From our experiments we can conclude that the improved Hadoop pipeline scales better than the same pipeline on high-performance computing resources, we also conclude that Hadoop is an economically viable

Development of parallel algorithms for electrical power management in space applications

Science.gov (United States)

Berry, Frederick C.

1989-01-01

The application of parallel techniques for electrical power system analysis is discussed. The Newton-Raphson method of load flow analysis was used along with the decomposition-coordination technique to perform load flow analysis. The decomposition-coordination technique enables tasks to be performed in parallel by partitioning the electrical power system into independent local problems. Each independent local problem represents a portion of the total electrical power system on which a loan flow analysis can be performed. The load flow analysis is performed on these partitioned elements by using the Newton-Raphson load flow method. These independent local problems will produce results for voltage and power which can then be passed to the coordinator portion of the solution procedure. The coordinator problem uses the results of the local problems to determine if any correction is needed on the local problems. The coordinator problem is also solved by an iterative method much like the local problem. The iterative method for the coordination problem will also be the Newton-Raphson method. Therefore, each iteration at the coordination level will result in new values for the local problems. The local problems will have to be solved again along with the coordinator problem until some convergence conditions are met.

Optimal energy management for a series-parallel hybrid electric bus

International Nuclear Information System (INIS)

Xiong Weiwei; Zhang Yong; Yin Chengliang

2009-01-01

This paper aims to present a new type of series-parallel hybrid electric bus and its energy management strategy. This hybrid bus is a post-transmission coupled system employing a novel transmission as the series-parallel configuration switcher. In this paper, the vehicle architecture, transmission scheme and numerical models are presented. The energy management system governs the mode switching between the series mode and the parallel mode as well as the instantaneous power distribution. In this work, two separated controllers using fuzzy logic called Mode Decision and Parallel-driving Energy Management are employed to fulfill these two tasks. The energy management strategy and the applications of fuzzy logic are described. The strategy is validated by a forward-facing simulation program based on the software Matlab/Simulink. The results show that the energy management strategy is effective to control the engine operating in a high-efficiency region as well as to sustain the battery charge state while satisfy the drive ability. The energy consumption is theoretically reduced by 30.3% to that of the conventional bus under transit bus driving cycle. In addition, works need future study are also presented.

Performance evaluation of parallel electric field tunnel field-effect transistor by a distributed-element circuit model

Science.gov (United States)

Morita, Yukinori; Mori, Takahiro; Migita, Shinji; Mizubayashi, Wataru; Tanabe, Akihito; Fukuda, Koichi; Matsukawa, Takashi; Endo, Kazuhiko; O'uchi, Shin-ichi; Liu, Yongxun; Masahara, Meishoku; Ota, Hiroyuki

2014-12-01

The performance of parallel electric field tunnel field-effect transistors (TFETs), in which band-to-band tunneling (BTBT) was initiated in-line to the gate electric field was evaluated. The TFET was fabricated by inserting an epitaxially-grown parallel-plate tunnel capacitor between heavily doped source wells and gate insulators. Analysis using a distributed-element circuit model indicated there should be a limit of the drain current caused by the self-voltage-drop effect in the ultrathin channel layer.

High fidelity thermal-hydraulic analysis using CFD and massively parallel computers

International Nuclear Information System (INIS)

Weber, D.P.; Wei, T.Y.C.; Brewster, R.A.; Rock, Daniel T.; Rizwan-uddin

2000-01-01

Thermal-hydraulic analyses play an important role in design and reload analysis of nuclear power plants. These analyses have historically relied on early generation computational fluid dynamics capabilities, originally developed in the 1960s and 1970s. Over the last twenty years, however, dramatic improvements in both computational fluid dynamics codes in the commercial sector and in computing power have taken place. These developments offer the possibility of performing large scale, high fidelity, core thermal hydraulics analysis. Such analyses will allow a determination of the conservatism employed in traditional design approaches and possibly justify the operation of nuclear power systems at higher powers without compromising safety margins. The objective of this work is to demonstrate such a large scale analysis approach using a state of the art CFD code, STAR-CD, and the computing power of massively parallel computers, provided by IBM. A high fidelity representation of a current generation PWR was analyzed with the STAR-CD CFD code and the results were compared to traditional analyses based on the VIPRE code. Current design methodology typically involves a simplified representation of the assemblies, where a single average pin is used in each assembly to determine the hot assembly from a whole core analysis. After determining this assembly, increased refinement is used in the hot assembly, and possibly some of its neighbors, to refine the analysis for purposes of calculating DNBR. This latter calculation is performed with sub-channel codes such as VIPRE. The modeling simplifications that are used involve the approximate treatment of surrounding assemblies and coarse representation of the hot assembly, where the subchannel is the lowest level of discretization. In the high fidelity analysis performed in this study, both restrictions have been removed. Within the hot assembly, several hundred thousand to several million computational zones have been used, to

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

International Nuclear Information System (INIS)

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

2012-01-01

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

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)

Massively parallel computing and the search for jets and black holes at the LHC

Energy Technology Data Exchange (ETDEWEB)

Halyo, V., E-mail: vhalyo@gmail.com; LeGresley, P.; Lujan, P.

2014-04-21

Massively parallel computing at the LHC could be the next leap necessary to reach an era of new discoveries at the LHC after the Higgs discovery. Scientific computing is a critical component of the LHC experiment, including operation, trigger, LHC computing GRID, simulation, and analysis. One way to improve the physics reach of the LHC is to take advantage of the flexibility of the trigger system by integrating coprocessors based on Graphics Processing Units (GPUs) or the Many Integrated Core (MIC) architecture into its server farm. This cutting edge technology provides not only the means to accelerate existing algorithms, but also the opportunity to develop new algorithms that select events in the trigger that previously would have evaded detection. In this paper we describe new algorithms that would allow us to select in the trigger new topological signatures that include non-prompt jet and black hole-like objects in the silicon tracker.

Excitation of electromagnetic proton cyclotron instability by parallel electric field in the equatorial magnetosphere

International Nuclear Information System (INIS)

Dixit, S.K.; Azif, Z.A.; Gwal, A.K.

1994-01-01

The characteristics of the growth rate of electromagnetic ion cyclotron (EMIC) instability is investigated in a mixture of cold species of ions and warm proton in the presence of weak parallel static electric field. An attempt has been made to explain the excitation of EMIC waves through linear wave-particle (W-P) interaction in the equatorial magnetospheric region. The proton cyclotron instability is modified in presence of weak parallel electric field and the growth rate is computed for equatorial magnetospheric plasma parameters. The results of theoretical investigations of the growth rate are used to explain the excitation mechanism of extremely low frequency/very low frequency (ELF/VLF) waves as observed by satellites. (author). 29 refs., 4 figs

A task parallel implementation of fast multipole methods

KAUST Repository

Taura, Kenjiro; Nakashima, Jun; Yokota, Rio; Maruyama, Naoya

2012-01-01

This paper describes a task parallel implementation of ExaFMM, an open source implementation of fast multipole methods (FMM), using a lightweight task parallel library MassiveThreads. Although there have been many attempts on parallelizing FMM

Engineering-Based Thermal CFD Simulations on Massive Parallel Systems

KAUST Repository

Frisch, Jé rô me; Mundani, Ralf-Peter; Rank, Ernst; van Treeck, Christoph

2015-01-01

The development of parallel Computational Fluid Dynamics (CFD) codes is a challenging task that entails efficient parallelization concepts and strategies in order to achieve good scalability values when running those codes on modern supercomputers

The relation between reconnected flux, the parallel electric field, and the reconnection rate in a three-dimensional kinetic simulation of magnetic reconnection

International Nuclear Information System (INIS)

Wendel, D. E.; Olson, D. K.; Hesse, M.; Kuznetsova, M.; Adrian, M. L.; Aunai, N.; Karimabadi, H.; Daughton, W.

2013-01-01

We investigate the distribution of parallel electric fields and their relationship to the location and rate of magnetic reconnection in a large particle-in-cell simulation of 3D turbulent magnetic reconnection with open boundary conditions. The simulation's guide field geometry inhibits the formation of simple topological features such as null points. Therefore, we derive the location of potential changes in magnetic connectivity by finding the field lines that experience a large relative change between their endpoints, i.e., the quasi-separatrix layer. We find a good correspondence between the locus of changes in magnetic connectivity or the quasi-separatrix layer and the map of large gradients in the integrated parallel electric field (or quasi-potential). Furthermore, we investigate the distribution of the parallel electric field along the reconnecting field lines. We find the reconnection rate is controlled by only the low-amplitude, zeroth and first–order trends in the parallel electric field while the contribution from fluctuations of the parallel electric field, such as electron holes, is negligible. The results impact the determination of reconnection sites and reconnection rates in models and in situ spacecraft observations of 3D turbulent reconnection. It is difficult through direct observation to isolate the loci of the reconnection parallel electric field amidst the large amplitude fluctuations. However, we demonstrate that a positive slope of the running sum of the parallel electric field along the field line as a function of field line length indicates where reconnection is occurring along the field line

Genetic algorithm with small population size for search feasible control parameters for parallel hybrid electric vehicles

Directory of Open Access Journals (Sweden)

Yu-Huei Cheng

2017-11-01

Full Text Available The control strategy is a major unit in hybrid electric vehicles (HEVs. In order to provide suitable control parameters for reducing fuel consumptions and engine emissions while maintaining vehicle performance requirements, the genetic algorithm (GA with small population size is applied to search for feasible control parameters in parallel HEVs. The electric assist control strategy (EACS is used as the fundamental control strategy of parallel HEVs. The dynamic performance requirements stipulated in the Partnership for a New Generation of Vehicles (PNGV is considered to maintain the vehicle performance. The known ADvanced VehIcle SimulatOR (ADVISOR is used to simulate a specific parallel HEV with urban dynamometer driving schedule (UDDS. Five population sets with size 5, 10, 15, 20, and 25 are used in the GA. The experimental results show that the GA with population size of 25 is the best for selecting feasible control parameters in parallel HEVs.

Significant Association between Sulfate-Reducing Bacteria and Uranium-Reducing Microbial Communities as Revealed by a Combined Massively Parallel Sequencing-Indicator Species Approach▿ †

OpenAIRE

Cardenas, Erick; Wu, Wei-Min; Leigh, Mary Beth; Carley, Jack; Carroll, Sue; Gentry, Terry; Luo, Jian; Watson, David; Gu, Baohua; Ginder-Vogel, Matthew; Kitanidis, Peter K.; Jardine, Philip M.; Zhou, Jizhong; Criddle, Craig S.; Marsh, Terence L.

2010-01-01

Massively parallel sequencing has provided a more affordable and high-throughput method to study microbial communities, although it has mostly been used in an exploratory fashion. We combined pyrosequencing with a strict indicator species statistical analysis to test if bacteria specifically responded to ethanol injection that successfully promoted dissimilatory uranium(VI) reduction in the subsurface of a uranium contamination plume at the Oak Ridge Field Research Center in Tennessee. Remedi...

Neural network control of a parallel hybrid-electric propulsion system for a small unmanned aerial vehicle

Science.gov (United States)

Harmon, Frederick G.

2005-11-01

Parallel hybrid-electric propulsion systems would be beneficial for small unmanned aerial vehicles (UAVs) used for military, homeland security, and disaster-monitoring missions. The benefits, due to the hybrid and electric-only modes, include increased time-on-station and greater range as compared to electric-powered UAVs and stealth modes not available with gasoline-powered UAVs. This dissertation contributes to the research fields of small unmanned aerial vehicles, hybrid-electric propulsion system control, and intelligent control. A conceptual design of a small UAV with a parallel hybrid-electric propulsion system is provided. The UAV is intended for intelligence, surveillance, and reconnaissance (ISR) missions. A conceptual design reveals the trade-offs that must be considered to take advantage of the hybrid-electric propulsion system. The resulting hybrid-electric propulsion system is a two-point design that includes an engine primarily sized for cruise speed and an electric motor and battery pack that are primarily sized for a slower endurance speed. The electric motor provides additional power for take-off, climbing, and acceleration and also serves as a generator during charge-sustaining operation or regeneration. The intelligent control of the hybrid-electric propulsion system is based on an instantaneous optimization algorithm that generates a hyper-plane from the nonlinear efficiency maps for the internal combustion engine, electric motor, and lithium-ion battery pack. The hyper-plane incorporates charge-depletion and charge-sustaining strategies. The optimization algorithm is flexible and allows the operator/user to assign relative importance between the use of gasoline, electricity, and recharging depending on the intended mission. A MATLAB/Simulink model was developed to test the control algorithms. The Cerebellar Model Arithmetic Computer (CMAC) associative memory neural network is applied to the control of the UAVs parallel hybrid-electric

Massively parallel diffuse optical tomography

Energy Technology Data Exchange (ETDEWEB)

Sandusky, John V.; Pitts, Todd A.

2017-09-05

Diffuse optical tomography systems and methods are described herein. In a general embodiment, the diffuse optical tomography system comprises a plurality of sensor heads, the plurality of sensor heads comprising respective optical emitter systems and respective sensor systems. A sensor head in the plurality of sensors heads is caused to act as an illuminator, such that its optical emitter system transmits a transillumination beam towards a portion of a sample. Other sensor heads in the plurality of sensor heads act as observers, detecting portions of the transillumination beam that radiate from the sample in the fields of view of the respective sensory systems of the other sensor heads. Thus, sensor heads in the plurality of sensors heads generate sensor data in parallel.

Mechanism of parallel electric fields inferred from observations

International Nuclear Information System (INIS)

Yeh, H.; Hill, T.W.

1981-01-01

An analysis of satellite data from regions of upward Birkeland (magnetic-field-aligned) current shows that the typical magnetic-field-aligned potential drop in the auroral zone is larger than required to provide direct acceleration of magnetospheric electrons by the field-aligned electric field against the upward magnetic force to produce the observed upward Birkeland current. A model of simple electrostatic acceleration without anomalous resistivity predicts observable relations between parallel current and parallel potential drop and between energy deposition and parallel potential drop. The temperature, density, and species of the unaccelerated charge carriers are the relevant parameters of the model. Simultaneously measurements of electron precipitation and ion drift velocities on the satellites Atmosphere Explorere C and D were used to test these relations. In a steady state the divergence of ionospheric currents must be compensated by Birkeland currents. The model current-voltage relation was applied to predict the densities of the primary charge carriers (i.e., plasma sheet electrons above the acceleration region for upward currents). In cases involving thin arc structures, where the reliable estimation of the divergence of ionospheric current is difficult and the steady-state assumption may not apply, the precipitating energy flux versus voltage relation was used to predict the densities of the unaccelerated plasma sheet electrons. Within the experimental uncertainties, reasonable agreement is found between these predicted densities and those inferred directly from the simultaneous data of the Low-Energy Electron Experiment. These results are interpreted as indicating that anomalous resistivity is not important in determining the magnitude of the field-aligned potential drop in the auroral zone

Effects of a parallel resistor on electrical characteristics of a piezoelectric transformer in open-circuit transient state.

Science.gov (United States)

Chang, Kuo-Tsai

2007-01-01

This paper investigates electrical transient characteristics of a Rosen-type piezoelectric transformer (PT), including maximum voltages, time constants, energy losses and average powers, and their improvements immediately after turning OFF. A parallel resistor connected to both input terminals of the PT is needed to improve the transient characteristics. An equivalent circuit for the PT is first given. Then, an open-circuit voltage, involving a direct current (DC) component and an alternating current (AC) component, and its related energy losses are derived from the equivalent circuit with initial conditions. Moreover, an AC power control system, including a DC-to-AC resonant inverter, a control switch and electronic instruments, is constructed to determine the electrical characteristics of the OFF transient state. Furthermore, the effects of the parallel resistor on the transient characteristics at different parallel resistances are measured. The advantages of adding the parallel resistor also are discussed. From the measured results, the DC time constant is greatly decreased from 9 to 0.04 ms by a 10 k(omega) parallel resistance under open output.

Hierarchical Image Segmentation of Remotely Sensed Data using Massively Parallel GNU-LINUX Software

Science.gov (United States)

Tilton, James C.

2003-01-01

A hierarchical set of image segmentations is a set of several image segmentations of the same image at different levels of detail in which the segmentations at coarser levels of detail can be produced from simple merges of regions at finer levels of detail. In [1], Tilton, et a1 describes an approach for producing hierarchical segmentations (called HSEG) and gave a progress report on exploiting these hierarchical segmentations for image information mining. The HSEG algorithm is a hybrid of region growing and constrained spectral clustering that produces a hierarchical set of image segmentations based on detected convergence points. In the main, HSEG employs the hierarchical stepwise optimization (HSWO) approach to region growing, which was described as early as 1989 by Beaulieu and Goldberg. The HSWO approach seeks to produce segmentations that are more optimized than those produced by more classic approaches to region growing (e.g. Horowitz and T. Pavlidis, [3]). In addition, HSEG optionally interjects between HSWO region growing iterations, merges between spatially non-adjacent regions (i.e., spectrally based merging or clustering) constrained by a threshold derived from the previous HSWO region growing iteration. While the addition of constrained spectral clustering improves the utility of the segmentation results, especially for larger images, it also significantly increases HSEG s computational requirements. To counteract this, a computationally efficient recursive, divide-and-conquer, implementation of HSEG (RHSEG) was devised, which includes special code to avoid processing artifacts caused by RHSEG s recursive subdivision of the image data. The recursive nature of RHSEG makes for a straightforward parallel implementation. This paper describes the HSEG algorithm, its recursive formulation (referred to as RHSEG), and the implementation of RHSEG using massively parallel GNU-LINUX software. Results with Landsat TM data are included comparing RHSEG with classic

Benefits of a parallel hybrid electric architecture on medium commercial vehicles

Energy Technology Data Exchange (ETDEWEB)

Boot, Marco Aimo; Consano, Ludovico [Iveco S.p.A, Turin (Italy)

2009-07-01

Hybrid electric technology is becoming an increasingly interesting solution for medium and heavy trucks involved in urban and suburban missions. The increasing demand for gas and oil, consequent price rises and environmental concerns are driving a market that is in need of alternative solutions. For these reasons, the growth in the global hybrid market significantly exceeded all the hybrid sales forecasts. The parallel hybrid electric vehicle (PHEV) employs an additional power source (electric motogenerator) in combination with the conventional diesel engine. This architecture exploits the benefits of both power sources in order to reduce the fuel consumption, increase the overall power, and above all, decrease CO2 emissions. Moreover, the emissions reduction target is lead by EU Regulations and local initiatives for traffic limitations, but the real drivers for the growth in the market are demonstrable fuel economy improvements and productivity costs optimization (global efficiency). This paper presents the results achieved by Iveco in the development and testing of parallel hybrid systems applied to medium range commercial vehicles, with the intent to evaluate the functionality, driveability performance and leading the best reduction in terms of fuel consumption and emissions in different real-world missions. The system architecture foresees one electric motor/generator and a single clutch unit. An external electrical power source for the battery recharging it is not necessary. The chosen configuration allows to implement the following functional modes: Stop and Start with Electric Launch, Hybrid Mode, Regenerative Braking Mode, Inertial Start and Creeping Mode. The software contained in the supervisor control unit has been tuned to the customer specific missions, taking in account on road data acquisition in order to demonstrate the reliability, driveability and the overall efficiency of the hybrid system. The field tests carried out in collaboration with

Three-dimensional gyrokinetic particle-in-cell simulation of plasmas on a massively parallel computer: Final report on LDRD Core Competency Project, FY 1991--FY 1993

International Nuclear Information System (INIS)

Byers, J.A.; Williams, T.J.; Cohen, B.I.; Dimits, A.M.

1994-01-01

One of the programs of the Magnetic fusion Energy (MFE) Theory and computations Program is studying the anomalous transport of thermal energy across the field lines in the core of a tokamak. We use the method of gyrokinetic particle-in-cell simulation in this study. For this LDRD project we employed massively parallel processing, new algorithms, and new algorithms, and new formal techniques to improve this research. Specifically, we sought to take steps toward: researching experimentally-relevant parameters in our simulations, learning parallel computing to have as a resource for our group, and achieving a 100 x speedup over our starting-point Cray2 simulation code's performance

Energy flow of electric dipole radiation in between parallel mirrors

Science.gov (United States)

Xu, Zhangjin; Arnoldus, Henk F.

2017-11-01

We have studied the energy flow patterns of the radiation emitted by an electric dipole located in between parallel mirrors. It appears that the field lines of the Poynting vector (the flow lines of energy) can have very intricate structures, including many singularities and vortices. The flow line patterns depend on the distance between the mirrors, the distance of the dipole to one of the mirrors and the angle of oscillation of the dipole moment with respect to the normal of the mirror surfaces. Already for the simplest case of a dipole moment oscillating perpendicular to the mirrors, singularities appear at regular intervals along the direction of propagation (parallel to the mirrors). For a parallel dipole, vortices appear in the neighbourhood of the dipole. For a dipole oscillating under a finite angle with the surface normal, the radiating tends to swirl around the dipole before travelling off parallel to the mirrors. For relatively large mirror separations, vortices appear in the pattern. When the dipole is off-centred with respect to the midway point between the mirrors, the flow line structure becomes even more complicated, with numerous vortices in the pattern, and tiny loops near the dipole. We have also investigated the locations of the vortices and singularities, and these can be found without any specific knowledge about the flow lines. This provides an independent means of studying the propagation of dipole radiation between mirrors.

Power-balancing instantaneous optimization energy management for a novel series-parallel hybrid electric bus

Science.gov (United States)

Sun, Dongye; Lin, Xinyou; Qin, Datong; Deng, Tao

2012-11-01

Energy management(EM) is a core technique of hybrid electric bus(HEB) in order to advance fuel economy performance optimization and is unique for the corresponding configuration. There are existing algorithms of control strategy seldom take battery power management into account with international combustion engine power management. In this paper, a type of power-balancing instantaneous optimization(PBIO) energy management control strategy is proposed for a novel series-parallel hybrid electric bus. According to the characteristic of the novel series-parallel architecture, the switching boundary condition between series and parallel mode as well as the control rules of the power-balancing strategy are developed. The equivalent fuel model of battery is implemented and combined with the fuel of engine to constitute the objective function which is to minimize the fuel consumption at each sampled time and to coordinate the power distribution in real-time between the engine and battery. To validate the proposed strategy effective and reasonable, a forward model is built based on Matlab/Simulink for the simulation and the dSPACE autobox is applied to act as a controller for hardware in-the-loop integrated with bench test. Both the results of simulation and hardware-in-the-loop demonstrate that the proposed strategy not only enable to sustain the battery SOC within its operational range and keep the engine operation point locating the peak efficiency region, but also the fuel economy of series-parallel hybrid electric bus(SPHEB) dramatically advanced up to 30.73% via comparing with the prototype bus and a similar improvement for PBIO strategy relative to rule-based strategy, the reduction of fuel consumption is up to 12.38%. The proposed research ensures the algorithm of PBIO is real-time applicability, improves the efficiency of SPHEB system, as well as suite to complicated configuration perfectly.

TIA: algorithms for development of identity-linked SNP islands for analysis by massively parallel DNA sequencing.

Science.gov (United States)

Farris, M Heath; Scott, Andrew R; Texter, Pamela A; Bartlett, Marta; Coleman, Patricia; Masters, David

2018-04-11

Single nucleotide polymorphisms (SNPs) located within the human genome have been shown to have utility as markers of identity in the differentiation of DNA from individual contributors. Massively parallel DNA sequencing (MPS) technologies and human genome SNP databases allow for the design of suites of identity-linked target regions, amenable to sequencing in a multiplexed and massively parallel manner. Therefore, tools are needed for leveraging the genotypic information found within SNP databases for the discovery of genomic targets that can be evaluated on MPS platforms. The SNP island target identification algorithm (TIA) was developed as a user-tunable system to leverage SNP information within databases. Using data within the 1000 Genomes Project SNP database, human genome regions were identified that contain globally ubiquitous identity-linked SNPs and that were responsive to targeted resequencing on MPS platforms. Algorithmic filters were used to exclude target regions that did not conform to user-tunable SNP island target characteristics. To validate the accuracy of TIA for discovering these identity-linked SNP islands within the human genome, SNP island target regions were amplified from 70 contributor genomic DNA samples using the polymerase chain reaction. Multiplexed amplicons were sequenced using the Illumina MiSeq platform, and the resulting sequences were analyzed for SNP variations. 166 putative identity-linked SNPs were targeted in the identified genomic regions. Of the 309 SNPs that provided discerning power across individual SNP profiles, 74 previously undefined SNPs were identified during evaluation of targets from individual genomes. Overall, DNA samples of 70 individuals were uniquely identified using a subset of the suite of identity-linked SNP islands. TIA offers a tunable genome search tool for the discovery of targeted genomic regions that are scalable in the population frequency and numbers of SNPs contained within the SNP island regions

Parallel plasma fluid turbulence calculations

International Nuclear Information System (INIS)

Leboeuf, J.N.; Carreras, B.A.; Charlton, L.A.; Drake, J.B.; Lynch, V.E.; Newman, D.E.; Sidikman, K.L.; Spong, D.A.

1994-01-01

The study of plasma turbulence and transport is a complex problem of critical importance for fusion-relevant plasmas. To this day, the fluid treatment of plasma dynamics is the best approach to realistic physics at the high resolution required for certain experimentally relevant calculations. Core and edge turbulence in a magnetic fusion device have been modeled using state-of-the-art, nonlinear, three-dimensional, initial-value fluid and gyrofluid codes. Parallel implementation of these models on diverse platforms--vector parallel (National Energy Research Supercomputer Center's CRAY Y-MP C90), massively parallel (Intel Paragon XP/S 35), and serial parallel (clusters of high-performance workstations using the Parallel Virtual Machine protocol)--offers a variety of paths to high resolution and significant improvements in real-time efficiency, each with its own advantages. The largest and most efficient calculations have been performed at the 200 Mword memory limit on the C90 in dedicated mode, where an overlap of 12 to 13 out of a maximum of 16 processors has been achieved with a gyrofluid model of core fluctuations. The richness of the physics captured by these calculations is commensurate with the increased resolution and efficiency and is limited only by the ingenuity brought to the analysis of the massive amounts of data generated

Engine-start Control Strategy of P2 Parallel Hybrid Electric Vehicle

Science.gov (United States)

Xiangyang, Xu; Siqi, Zhao; Peng, Dong

2017-12-01

A smooth and fast engine-start process is important to parallel hybrid electric vehicles with an electric motor mounted in front of the transmission. However, there are some challenges during the engine-start control. Firstly, the electric motor must simultaneously provide a stable driving torque to ensure the drivability and a compensative torque to drag the engine before ignition. Secondly, engine-start time is a trade-off control objective because both fast start and smooth start have to be considered. To solve these problems, this paper first analyzed the resistance of the engine start process, and established a physic model in MATLAB/Simulink. Then a model-based coordinated control strategy among engine, motor and clutch was developed. Two basic control strategy during fast start and smooth start process were studied. Simulation results showed that the control objectives were realized by applying given control strategies, which can meet different requirement from the driver.

Targeted capture massively parallel sequencing analysis of LCIS and invasive lobular cancer: Repertoire of somatic genetic alterations and clonal relationships.

Science.gov (United States)

Sakr, Rita A; Schizas, Michail; Carniello, Jose V Scarpa; Ng, Charlotte K Y; Piscuoglio, Salvatore; Giri, Dilip; Andrade, Victor P; De Brot, Marina; Lim, Raymond S; Towers, Russell; Weigelt, Britta; Reis-Filho, Jorge S; King, Tari A

2016-02-01

Lobular carcinoma in situ (LCIS) has been proposed as a non-obligate precursor of invasive lobular carcinoma (ILC). Here we sought to define the repertoire of somatic genetic alterations in pure LCIS and in synchronous LCIS and ILC using targeted massively parallel sequencing. DNA samples extracted from microdissected LCIS, ILC and matched normal breast tissue or peripheral blood from 30 patients were subjected to massively parallel sequencing targeting all exons of 273 genes, including the genes most frequently mutated in breast cancer and DNA repair-related genes. Single nucleotide variants and insertions and deletions were identified using state-of-the-art bioinformatics approaches. The constellation of somatic mutations found in LCIS (n = 34) and ILC (n = 21) were similar, with the most frequently mutated genes being CDH1 (56% and 66%, respectively), PIK3CA (41% and 52%, respectively) and CBFB (12% and 19%, respectively). Among 19 LCIS and ILC synchronous pairs, 14 (74%) had at least one identical mutation in common, including identical PIK3CA and CDH1 mutations. Paired analysis of independent foci of LCIS from 3 breasts revealed at least one common mutation in each of the 3 pairs (CDH1, PIK3CA, CBFB and PKHD1L1). LCIS and ILC have a similar repertoire of somatic mutations, with PIK3CA and CDH1 being the most frequently mutated genes. The presence of identical mutations between LCIS-LCIS and LCIS-ILC pairs demonstrates that LCIS is a clonal neoplastic lesion, and provides additional evidence that at least some LCIS are non-obligate precursors of ILC. Copyright © 2015 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Massively parallel unsupervised single-particle cryo-EM data clustering via statistical manifold learning.

Directory of Open Access Journals (Sweden)

Jiayi Wu

Full Text Available Structural heterogeneity in single-particle cryo-electron microscopy (cryo-EM data represents a major challenge for high-resolution structure determination. Unsupervised classification may serve as the first step in the assessment of structural heterogeneity. However, traditional algorithms for unsupervised classification, such as K-means clustering and maximum likelihood optimization, may classify images into wrong classes with decreasing signal-to-noise-ratio (SNR in the image data, yet demand increased computational costs. Overcoming these limitations requires further development of clustering algorithms for high-performance cryo-EM data processing. Here we introduce an unsupervised single-particle clustering algorithm derived from a statistical manifold learning framework called generative topographic mapping (GTM. We show that unsupervised GTM clustering improves classification accuracy by about 40% in the absence of input references for data with lower SNRs. Applications to several experimental datasets suggest that our algorithm can detect subtle structural differences among classes via a hierarchical clustering strategy. After code optimization over a high-performance computing (HPC environment, our software implementation was able to generate thousands of reference-free class averages within hours in a massively parallel fashion, which allows a significant improvement on ab initio 3D reconstruction and assists in the computational purification of homogeneous datasets for high-resolution visualization.

A massive parallel sequencing workflow for diagnostic genetic testing of mismatch repair genes

Science.gov (United States)

Hansen, Maren F; Neckmann, Ulrike; Lavik, Liss A S; Vold, Trine; Gilde, Bodil; Toft, Ragnhild K; Sjursen, Wenche

2014-01-01

The purpose of this study was to develop a massive parallel sequencing (MPS) workflow for diagnostic analysis of mismatch repair (MMR) genes using the GS Junior system (Roche). A pathogenic variant in one of four MMR genes, (MLH1, PMS2, MSH6, and MSH2), is the cause of Lynch Syndrome (LS), which mainly predispose to colorectal cancer. We used an amplicon-based sequencing method allowing specific and preferential amplification of the MMR genes including PMS2, of which several pseudogenes exist. The amplicons were pooled at different ratios to obtain coverage uniformity and maximize the throughput of a single-GS Junior run. In total, 60 previously identified and distinct variants (substitutions and indels), were sequenced by MPS and successfully detected. The heterozygote detection range was from 19% to 63% and dependent on sequence context and coverage. We were able to distinguish between false-positive and true-positive calls in homopolymeric regions by cross-sample comparison and evaluation of flow signal distributions. In addition, we filtered variants according to a predefined status, which facilitated variant annotation. Our study shows that implementation of MPS in routine diagnostics of LS can accelerate sample throughput and reduce costs without compromising sensitivity, compared to Sanger sequencing. PMID:24689082

Massively parallel unsupervised single-particle cryo-EM data clustering via statistical manifold learning.

Science.gov (United States)

Wu, Jiayi; Ma, Yong-Bei; Congdon, Charles; Brett, Bevin; Chen, Shuobing; Xu, Yaofang; Ouyang, Qi; Mao, Youdong

2017-01-01

Structural heterogeneity in single-particle cryo-electron microscopy (cryo-EM) data represents a major challenge for high-resolution structure determination. Unsupervised classification may serve as the first step in the assessment of structural heterogeneity. However, traditional algorithms for unsupervised classification, such as K-means clustering and maximum likelihood optimization, may classify images into wrong classes with decreasing signal-to-noise-ratio (SNR) in the image data, yet demand increased computational costs. Overcoming these limitations requires further development of clustering algorithms for high-performance cryo-EM data processing. Here we introduce an unsupervised single-particle clustering algorithm derived from a statistical manifold learning framework called generative topographic mapping (GTM). We show that unsupervised GTM clustering improves classification accuracy by about 40% in the absence of input references for data with lower SNRs. Applications to several experimental datasets suggest that our algorithm can detect subtle structural differences among classes via a hierarchical clustering strategy. After code optimization over a high-performance computing (HPC) environment, our software implementation was able to generate thousands of reference-free class averages within hours in a massively parallel fashion, which allows a significant improvement on ab initio 3D reconstruction and assists in the computational purification of homogeneous datasets for high-resolution visualization.

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.

Electric vehicles in France: A fifteen-year financing plan for massive roll-out

International Nuclear Information System (INIS)

Sartor, Oliver; Spencer, Thomas; Fryatt, Oliver

2017-03-01

Numerous studies have acknowledged the importance of massive deployment of full battery electric vehicles (BEVs) and plug-in hybrid vehicles (PHEVs), in order to reduce environmental externalities from personal road transport, in particular CO_2 emissions. Good news about declining battery costs and ambitious output pronouncements by major car manufacturers may give the misleading impression that mass-penetration of EVs is just around the corner. But current deployment rates of EVs are significantly off track for deep decarbonization of the French transport system by 2050. In the short to medium term, large scale penetration is far from assured, unless there are further policies to address a number of barriers. In the short term to around 2020-2025, EVs will remain more expensive to purchase and run than equivalent internal combustion engine (ICE) vehicles. In the medium term beyond 2020-2025, EVs are likely to become competitive on a lifetime cost basis. However, they may still confront other financing challenges, such as higher upfront purchase costs (as opposed to lifetime costs). This barrier may be particularly important if consumers are myopic and discount future fuel savings, or if they are credit constrained. In the longer run, EVs will create other challenges for governments to deal with, such as fuel tax revenue erosion. EV support policy should therefore be designed with a dynamic, at least decadal perspective. In this paper, we consider a three-phase financing strategy corresponding to the above described challenges. A range of fiscal policy tools are likely to be needed as part of any feasible regulatory framework for supporting massive EV roll out. But this raises the critical issue of the distributional impacts of the transition to EVs. The upfront financing challenge may be particularly relevant for lower income households, while at the same time, massive roll-out of EVs will require that middle and lower income households start to purchase electric

Magnetohydrodynamics: Parallel computation of the dynamics of thermonuclear and astrophysical plasmas. 1. Annual report of massively parallel computing pilot project 93MPR05

International Nuclear Information System (INIS)

1994-08-01

This is the first annual report of the MPP pilot project 93MPR05. In this pilot project four research groups with different, complementary backgrounds collaborate with the aim to develop new algorithms and codes to simulate the magnetohydrodynamics of thermonuclear and astrophysical plasmas on massively parallel machines. The expected speed-up is required to simulate the dynamics of the hot plasmas of interest which are characterized by very large magnetic Reynolds numbers and, hence, require high spatial and temporal resolutions (for details see section 1). The four research groups that collaborated to produce the results reported here are: The MHD group of Prof. Dr. J.P. Goedbloed at the FOM-Institute for Plasma Physics 'Rijnhuizen' in Nieuwegein, the group of Prof. Dr. H. van der Vorst at the Mathematics Institute of Utrecht University, the group of Prof. Dr. A.G. Hearn at the Astronomical Institute of Utrecht University, and the group of Dr. Ir. H.J.J. te Riele at the CWI in Amsterdam. The full project team met frequently during this first project year to discuss progress reports, current problems, etc. (see section 2). The main results of the first project year are: - Proof of the scalability of typical linear and nonlinear MHD codes - development and testing of a parallel version of the Arnoldi algorithm - development and testing of alternative methods for solving large non-Hermitian eigenvalue problems - porting of the 3D nonlinear semi-implicit time evolution code HERA to an MPP system. The steps that were scheduled to reach these intended results are given in section 3. (orig./WL)

Magnetohydrodynamics: Parallel computation of the dynamics of thermonuclear and astrophysical plasmas. 1. Annual report of massively parallel computing pilot project 93MPR05

Energy Technology Data Exchange (ETDEWEB)

NONE

1994-08-01

This is the first annual report of the MPP pilot project 93MPR05. In this pilot project four research groups with different, complementary backgrounds collaborate with the aim to develop new algorithms and codes to simulate the magnetohydrodynamics of thermonuclear and astrophysical plasmas on massively parallel machines. The expected speed-up is required to simulate the dynamics of the hot plasmas of interest which are characterized by very large magnetic Reynolds numbers and, hence, require high spatial and temporal resolutions (for details see section 1). The four research groups that collaborated to produce the results reported here are: The MHD group of Prof. Dr. J.P. Goedbloed at the FOM-Institute for Plasma Physics `Rijnhuizen` in Nieuwegein, the group of Prof. Dr. H. van der Vorst at the Mathematics Institute of Utrecht University, the group of Prof. Dr. A.G. Hearn at the Astronomical Institute of Utrecht University, and the group of Dr. Ir. H.J.J. te Riele at the CWI in Amsterdam. The full project team met frequently during this first project year to discuss progress reports, current problems, etc. (see section 2). The main results of the first project year are: - Proof of the scalability of typical linear and nonlinear MHD codes - development and testing of a parallel version of the Arnoldi algorithm - development and testing of alternative methods for solving large non-Hermitian eigenvalue problems - porting of the 3D nonlinear semi-implicit time evolution code HERA to an MPP system. The steps that were scheduled to reach these intended results are given in section 3. (orig./WL).

Optimisation of a parallel ocean general circulation model

OpenAIRE

M. I. Beare; D. P. Stevens

1997-01-01

International audience; This paper presents the development of a general-purpose parallel ocean circulation model, for use on a wide range of computer platforms, from traditional scalar machines to workstation clusters and massively parallel processors. Parallelism is provided, as a modular option, via high-level message-passing routines, thus hiding the technical intricacies from the user. An initial implementation highlights that the parallel efficiency of the model is adversely affected by...

Genotypic tropism testing by massively parallel sequencing: qualitative and quantitative analysis

Directory of Open Access Journals (Sweden)

Thiele Bernhard

2011-05-01

Full Text Available Abstract Background Inferring viral tropism from genotype is a fast and inexpensive alternative to phenotypic testing. While being highly predictive when performed on clonal samples, sensitivity of predicting CXCR4-using (X4 variants drops substantially in clinical isolates. This is mainly attributed to minor variants not detected by standard bulk-sequencing. Massively parallel sequencing (MPS detects single clones thereby being much more sensitive. Using this technology we wanted to improve genotypic prediction of coreceptor usage. Methods Plasma samples from 55 antiretroviral-treated patients tested for coreceptor usage with the Monogram Trofile Assay were sequenced with standard population-based approaches. Fourteen of these samples were selected for further analysis with MPS. Tropism was predicted from each sequence with geno2pheno[coreceptor]. Results Prediction based on bulk-sequencing yielded 59.1% sensitivity and 90.9% specificity compared to the trofile assay. With MPS, 7600 reads were generated on average per isolate. Minorities of sequences with high confidence in CXCR4-usage were found in all samples, irrespective of phenotype. When using the default false-positive-rate of geno2pheno[coreceptor] (10%, and defining a minority cutoff of 5%, the results were concordant in all but one isolate. Conclusions The combination of MPS and coreceptor usage prediction results in a fast and accurate alternative to phenotypic assays. The detection of X4-viruses in all isolates suggests that coreceptor usage as well as fitness of minorities is important for therapy outcome. The high sensitivity of this technology in combination with a quantitative description of the viral population may allow implementing meaningful cutoffs for predicting response to CCR5-antagonists in the presence of X4-minorities.

Genotypic tropism testing by massively parallel sequencing: qualitative and quantitative analysis.

Science.gov (United States)

Däumer, Martin; Kaiser, Rolf; Klein, Rolf; Lengauer, Thomas; Thiele, Bernhard; Thielen, Alexander

2011-05-13

Inferring viral tropism from genotype is a fast and inexpensive alternative to phenotypic testing. While being highly predictive when performed on clonal samples, sensitivity of predicting CXCR4-using (X4) variants drops substantially in clinical isolates. This is mainly attributed to minor variants not detected by standard bulk-sequencing. Massively parallel sequencing (MPS) detects single clones thereby being much more sensitive. Using this technology we wanted to improve genotypic prediction of coreceptor usage. Plasma samples from 55 antiretroviral-treated patients tested for coreceptor usage with the Monogram Trofile Assay were sequenced with standard population-based approaches. Fourteen of these samples were selected for further analysis with MPS. Tropism was predicted from each sequence with geno2pheno[coreceptor]. Prediction based on bulk-sequencing yielded 59.1% sensitivity and 90.9% specificity compared to the trofile assay. With MPS, 7600 reads were generated on average per isolate. Minorities of sequences with high confidence in CXCR4-usage were found in all samples, irrespective of phenotype. When using the default false-positive-rate of geno2pheno[coreceptor] (10%), and defining a minority cutoff of 5%, the results were concordant in all but one isolate. The combination of MPS and coreceptor usage prediction results in a fast and accurate alternative to phenotypic assays. The detection of X4-viruses in all isolates suggests that coreceptor usage as well as fitness of minorities is important for therapy outcome. The high sensitivity of this technology in combination with a quantitative description of the viral population may allow implementing meaningful cutoffs for predicting response to CCR5-antagonists in the presence of X4-minorities.

GRay: A MASSIVELY PARALLEL GPU-BASED CODE FOR RAY TRACING IN RELATIVISTIC SPACETIMES

Energy Technology Data Exchange (ETDEWEB)

Chan, Chi-kwan; Psaltis, Dimitrios; Özel, Feryal [Department of Astronomy, University of Arizona, 933 N. Cherry Ave., Tucson, AZ 85721 (United States)

2013-11-01

We introduce GRay, a massively parallel integrator designed to trace the trajectories of billions of photons in a curved spacetime. This graphics-processing-unit (GPU)-based integrator employs the stream processing paradigm, is implemented in CUDA C/C++, and runs on nVidia graphics cards. The peak performance of GRay using single-precision floating-point arithmetic on a single GPU exceeds 300 GFLOP (or 1 ns per photon per time step). For a realistic problem, where the peak performance cannot be reached, GRay is two orders of magnitude faster than existing central-processing-unit-based ray-tracing codes. This performance enhancement allows more effective searches of large parameter spaces when comparing theoretical predictions of images, spectra, and light curves from the vicinities of compact objects to observations. GRay can also perform on-the-fly ray tracing within general relativistic magnetohydrodynamic algorithms that simulate accretion flows around compact objects. Making use of this algorithm, we calculate the properties of the shadows of Kerr black holes and the photon rings that surround them. We also provide accurate fitting formulae of their dependencies on black hole spin and observer inclination, which can be used to interpret upcoming observations of the black holes at the center of the Milky Way, as well as M87, with the Event Horizon Telescope.

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.

Hybrid massively parallel fast sweeping method for static Hamilton–Jacobi equations

Energy Technology Data Exchange (ETDEWEB)

Detrixhe, Miles, E-mail: mdetrixhe@engineering.ucsb.edu [Department of Mechanical Engineering (United States); University of California Santa Barbara, Santa Barbara, CA, 93106 (United States); Gibou, Frédéric, E-mail: fgibou@engineering.ucsb.edu [Department of Mechanical Engineering (United States); University of California Santa Barbara, Santa Barbara, CA, 93106 (United States); Department of Computer Science (United States); Department of Mathematics (United States)

2016-10-01

The fast sweeping method is a popular algorithm for solving a variety of static Hamilton–Jacobi equations. Fast sweeping algorithms for parallel computing have been developed, but are severely limited. In this work, we present a multilevel, hybrid parallel algorithm that combines the desirable traits of two distinct parallel methods. The fine and coarse grained components of the algorithm take advantage of heterogeneous computer architecture common in high performance computing facilities. We present the algorithm and demonstrate its effectiveness on a set of example problems including optimal control, dynamic games, and seismic wave propagation. We give results for convergence, parallel scaling, and show state-of-the-art speedup values for the fast sweeping method.

Hybrid massively parallel fast sweeping method for static Hamilton–Jacobi equations

International Nuclear Information System (INIS)

Detrixhe, Miles; Gibou, Frédéric

2016-01-01

The fast sweeping method is a popular algorithm for solving a variety of static Hamilton–Jacobi equations. Fast sweeping algorithms for parallel computing have been developed, but are severely limited. In this work, we present a multilevel, hybrid parallel algorithm that combines the desirable traits of two distinct parallel methods. The fine and coarse grained components of the algorithm take advantage of heterogeneous computer architecture common in high performance computing facilities. We present the algorithm and demonstrate its effectiveness on a set of example problems including optimal control, dynamic games, and seismic wave propagation. We give results for convergence, parallel scaling, and show state-of-the-art speedup values for the fast sweeping method.

A Scalable Parallel PWTD-Accelerated SIE Solver for Analyzing Transient Scattering from Electrically Large Objects

KAUST Repository

Liu, Yang

2015-12-17

A scalable parallel plane-wave time-domain (PWTD) algorithm for efficient and accurate analysis of transient scattering from electrically large objects is presented. The algorithm produces scalable communication patterns on very large numbers of processors by leveraging two mechanisms: (i) a hierarchical parallelization strategy to evenly distribute the computation and memory loads at all levels of the PWTD tree among processors, and (ii) a novel asynchronous communication scheme to reduce the cost and memory requirement of the communications between the processors. The efficiency and accuracy of the algorithm are demonstrated through its applications to the analysis of transient scattering from a perfect electrically conducting (PEC) sphere with a diameter of 70 wavelengths and a PEC square plate with a dimension of 160 wavelengths. Furthermore, the proposed algorithm is used to analyze transient fields scattered from realistic airplane and helicopter models under high frequency excitation.

Electromagnetic form factors of a massive neutrino

International Nuclear Information System (INIS)

Dvornikov, M.S.; Studenikin, A.I.

2004-01-01

Electromagnetic form factors of a massive neutrino are studied in a minimally extended standard model in an arbitrary R ξ gauge and taking into account the dependence on the masses of all interacting particles. The contribution from all Feynman diagrams to the electric, magnetic, and anapole form factors, in which the dependence of the masses of all particles as well as on gauge parameters is accounted for exactly, are obtained for the first time in explicit form. The asymptotic behavior of the magnetic form factor for large negative squares of the momentum of an external photon is analyzed and the expression for the anapole moment of a massive neutrino is derived. The results are generalized to the case of mixing between various flavors of the neutrino. Explicit expressions are obtained for the electric, magnetic, and electric dipole and anapole transitional form factors as well as for the transitional electric dipole moment

Three pillars for achieving quantum mechanical molecular dynamics simulations of huge systems: Divide-and-conquer, density-functional tight-binding, and massively parallel computation.

Science.gov (United States)

Nishizawa, Hiroaki; Nishimura, Yoshifumi; Kobayashi, Masato; Irle, Stephan; Nakai, Hiromi

2016-08-05

The linear-scaling divide-and-conquer (DC) quantum chemical methodology is applied to the density-functional tight-binding (DFTB) theory to develop a massively parallel program that achieves on-the-fly molecular reaction dynamics simulations of huge systems from scratch. The functions to perform large scale geometry optimization and molecular dynamics with DC-DFTB potential energy surface are implemented to the program called DC-DFTB-K. A novel interpolation-based algorithm is developed for parallelizing the determination of the Fermi level in the DC method. The performance of the DC-DFTB-K program is assessed using a laboratory computer and the K computer. Numerical tests show the high efficiency of the DC-DFTB-K program, a single-point energy gradient calculation of a one-million-atom system is completed within 60 s using 7290 nodes of the K computer. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Frequency of Usher syndrome type 1 in deaf children by massively parallel DNA sequencing.

Science.gov (United States)

Yoshimura, Hidekane; Miyagawa, Maiko; Kumakawa, Kozo; Nishio, Shin-Ya; Usami, Shin-Ichi

2016-05-01

Usher syndrome type 1 (USH1) is the most severe of the three USH subtypes due to its profound hearing loss, absent vestibular response and retinitis pigmentosa appearing at a prepubescent age. Six causative genes have been identified for USH1, making early diagnosis and therapy possible through DNA testing. Targeted exon sequencing of selected genes using massively parallel DNA sequencing (MPS) technology enables clinicians to systematically tackle previously intractable monogenic disorders and improve molecular diagnosis. Using MPS along with direct sequence analysis, we screened 227 unrelated non-syndromic deaf children and detected recessive mutations in USH1 causative genes in five patients (2.2%): three patients harbored MYO7A mutations and one each carried CDH23 or PCDH15 mutations. As indicated by an earlier genotype-phenotype correlation study of the CDH23 and PCDH15 genes, we considered the latter two patients to have USH1. Based on clinical findings, it was also highly likely that one patient with MYO7A mutations possessed USH1 due to a late onset age of walking. This first report describing the frequency (1.3-2.2%) of USH1 among non-syndromic deaf children highlights the importance of comprehensive genetic testing for early disease diagnosis.

The control of a parallel hybrid-electric propulsion system for a small unmanned aerial vehicle using a CMAC neural network.

Science.gov (United States)

Harmon, Frederick G; Frank, Andrew A; Joshi, Sanjay S

2005-01-01

A Simulink model, a propulsion energy optimization algorithm, and a CMAC controller were developed for a small parallel hybrid-electric unmanned aerial vehicle (UAV). The hybrid-electric UAV is intended for military, homeland security, and disaster-monitoring missions involving intelligence, surveillance, and reconnaissance (ISR). The Simulink model is a forward-facing simulation program used to test different control strategies. The flexible energy optimization algorithm for the propulsion system allows relative importance to be assigned between the use of gasoline, electricity, and recharging. A cerebellar model arithmetic computer (CMAC) neural network approximates the energy optimization results and is used to control the parallel hybrid-electric propulsion system. The hybrid-electric UAV with the CMAC controller uses 67.3% less energy than a two-stroke gasoline-powered UAV during a 1-h ISR mission and 37.8% less energy during a longer 3-h ISR mission.

Optimizing a massive parallel sequencing workflow for quantitative miRNA expression analysis.

Directory of Open Access Journals (Sweden)

Francesca Cordero

Full Text Available BACKGROUND: Massive Parallel Sequencing methods (MPS can extend and improve the knowledge obtained by conventional microarray technology, both for mRNAs and short non-coding RNAs, e.g. miRNAs. The processing methods used to extract and interpret the information are an important aspect of dealing with the vast amounts of data generated from short read sequencing. Although the number of computational tools for MPS data analysis is constantly growing, their strengths and weaknesses as part of a complex analytical pipe-line have not yet been well investigated. PRIMARY FINDINGS: A benchmark MPS miRNA dataset, resembling a situation in which miRNAs are spiked in biological replication experiments was assembled by merging a publicly available MPS spike-in miRNAs data set with MPS data derived from healthy donor peripheral blood mononuclear cells. Using this data set we observed that short reads counts estimation is strongly under estimated in case of duplicates miRNAs, if whole genome is used as reference. Furthermore, the sensitivity of miRNAs detection is strongly dependent by the primary tool used in the analysis. Within the six aligners tested, specifically devoted to miRNA detection, SHRiMP and MicroRazerS show the highest sensitivity. Differential expression estimation is quite efficient. Within the five tools investigated, two of them (DESseq, baySeq show a very good specificity and sensitivity in the detection of differential expression. CONCLUSIONS: The results provided by our analysis allow the definition of a clear and simple analytical optimized workflow for miRNAs digital quantitative analysis.

Optimizing a massive parallel sequencing workflow for quantitative miRNA expression analysis.

Science.gov (United States)

Cordero, Francesca; Beccuti, Marco; Arigoni, Maddalena; Donatelli, Susanna; Calogero, Raffaele A

2012-01-01

Massive Parallel Sequencing methods (MPS) can extend and improve the knowledge obtained by conventional microarray technology, both for mRNAs and short non-coding RNAs, e.g. miRNAs. The processing methods used to extract and interpret the information are an important aspect of dealing with the vast amounts of data generated from short read sequencing. Although the number of computational tools for MPS data analysis is constantly growing, their strengths and weaknesses as part of a complex analytical pipe-line have not yet been well investigated. A benchmark MPS miRNA dataset, resembling a situation in which miRNAs are spiked in biological replication experiments was assembled by merging a publicly available MPS spike-in miRNAs data set with MPS data derived from healthy donor peripheral blood mononuclear cells. Using this data set we observed that short reads counts estimation is strongly under estimated in case of duplicates miRNAs, if whole genome is used as reference. Furthermore, the sensitivity of miRNAs detection is strongly dependent by the primary tool used in the analysis. Within the six aligners tested, specifically devoted to miRNA detection, SHRiMP and MicroRazerS show the highest sensitivity. Differential expression estimation is quite efficient. Within the five tools investigated, two of them (DESseq, baySeq) show a very good specificity and sensitivity in the detection of differential expression. The results provided by our analysis allow the definition of a clear and simple analytical optimized workflow for miRNAs digital quantitative analysis.

Parallel thermal radiation transport in two dimensions

International Nuclear Information System (INIS)

Smedley-Stevenson, R.P.; Ball, S.R.

2003-01-01

This paper describes the distributed memory parallel implementation of a deterministic thermal radiation transport algorithm in a 2-dimensional ALE hydrodynamics code. The parallel algorithm consists of a variety of components which are combined in order to produce a state of the art computational capability, capable of solving large thermal radiation transport problems using Blue-Oak, the 3 Tera-Flop MPP (massive parallel processors) computing facility at AWE (United Kingdom). Particular aspects of the parallel algorithm are described together with examples of the performance on some challenging applications. (author)

Parallel thermal radiation transport in two dimensions

Energy Technology Data Exchange (ETDEWEB)

Smedley-Stevenson, R.P.; Ball, S.R. [AWE Aldermaston (United Kingdom)

2003-07-01

This paper describes the distributed memory parallel implementation of a deterministic thermal radiation transport algorithm in a 2-dimensional ALE hydrodynamics code. The parallel algorithm consists of a variety of components which are combined in order to produce a state of the art computational capability, capable of solving large thermal radiation transport problems using Blue-Oak, the 3 Tera-Flop MPP (massive parallel processors) computing facility at AWE (United Kingdom). Particular aspects of the parallel algorithm are described together with examples of the performance on some challenging applications. (author)

Identification of the bovine Arachnomelia mutation by massively parallel sequencing implicates sulfite oxidase (SUOX in bone development.

Directory of Open Access Journals (Sweden)

Cord Drögemüller

2010-08-01

Full Text Available Arachnomelia is a monogenic recessive defect of skeletal development in cattle. The causative mutation was previously mapped to a ∼7 Mb interval on chromosome 5. Here we show that array-based sequence capture and massively parallel sequencing technology, combined with the typical family structure in livestock populations, facilitates the identification of the causative mutation. We re-sequenced the entire critical interval in a healthy partially inbred cow carrying one copy of the critical chromosome segment in its ancestral state and one copy of the same segment with the arachnomelia mutation, and we detected a single heterozygous position. The genetic makeup of several partially inbred cattle provides extremely strong support for the causality of this mutation. The mutation represents a single base insertion leading to a premature stop codon in the coding sequence of the SUOX gene and is perfectly associated with the arachnomelia phenotype. Our findings suggest an important role for sulfite oxidase in bone development.

Identification of the Bovine Arachnomelia Mutation by Massively Parallel Sequencing Implicates Sulfite Oxidase (SUOX) in Bone Development

Science.gov (United States)

Drögemüller, Cord; Tetens, Jens; Sigurdsson, Snaevar; Gentile, Arcangelo; Testoni, Stefania; Lindblad-Toh, Kerstin; Leeb, Tosso

2010-01-01

Arachnomelia is a monogenic recessive defect of skeletal development in cattle. The causative mutation was previously mapped to a ∼7 Mb interval on chromosome 5. Here we show that array-based sequence capture and massively parallel sequencing technology, combined with the typical family structure in livestock populations, facilitates the identification of the causative mutation. We re-sequenced the entire critical interval in a healthy partially inbred cow carrying one copy of the critical chromosome segment in its ancestral state and one copy of the same segment with the arachnomelia mutation, and we detected a single heterozygous position. The genetic makeup of several partially inbred cattle provides extremely strong support for the causality of this mutation. The mutation represents a single base insertion leading to a premature stop codon in the coding sequence of the SUOX gene and is perfectly associated with the arachnomelia phenotype. Our findings suggest an important role for sulfite oxidase in bone development. PMID:20865119

Dissecting Cell-Type Composition and Activity-Dependent Transcriptional State in Mammalian Brains by Massively Parallel Single-Nucleus RNA-Seq.

Science.gov (United States)

Hu, Peng; Fabyanic, Emily; Kwon, Deborah Y; Tang, Sheng; Zhou, Zhaolan; Wu, Hao

2017-12-07

Massively parallel single-cell RNA sequencing can precisely resolve cellular diversity in a high-throughput manner at low cost, but unbiased isolation of intact single cells from complex tissues such as adult mammalian brains is challenging. Here, we integrate sucrose-gradient-assisted purification of nuclei with droplet microfluidics to develop a highly scalable single-nucleus RNA-seq approach (sNucDrop-seq), which is free of enzymatic dissociation and nucleus sorting. By profiling ∼18,000 nuclei isolated from cortical tissues of adult mice, we demonstrate that sNucDrop-seq not only accurately reveals neuronal and non-neuronal subtype composition with high sensitivity but also enables in-depth analysis of transient transcriptional states driven by neuronal activity, at single-cell resolution, in vivo. Copyright © 2017 Elsevier Inc. All rights reserved.

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)

Parallelization of quantum molecular dynamics simulation code

International Nuclear Information System (INIS)

Kato, Kaori; Kunugi, Tomoaki; Shibahara, Masahiko; Kotake, Susumu

1998-02-01

A quantum molecular dynamics simulation code has been developed for the analysis of the thermalization of photon energies in the molecule or materials in Kansai Research Establishment. The simulation code is parallelized for both Scalar massively parallel computer (Intel Paragon XP/S75) and Vector parallel computer (Fujitsu VPP300/12). Scalable speed-up has been obtained with a distribution to processor units by division of particle group in both parallel computers. As a result of distribution to processor units not only by particle group but also by the particles calculation that is constructed with fine calculations, highly parallelization performance is achieved in Intel Paragon XP/S75. (author)

Parallel Tensor Compression for Large-Scale Scientific Data.

Energy Technology Data Exchange (ETDEWEB)

Kolda, Tamara G. [Sandia National Lab. (SNL-CA), Livermore, CA (United States); Ballard, Grey [Sandia National Lab. (SNL-CA), Livermore, CA (United States); Austin, Woody Nathan [Univ. of Texas, Austin, TX (United States)

2015-10-01

As parallel computing trends towards the exascale, scientific data produced by high-fidelity simulations are growing increasingly massive. For instance, a simulation on a three-dimensional spatial grid with 512 points per dimension that tracks 64 variables per grid point for 128 time steps yields 8 TB of data. By viewing the data as a dense five way tensor, we can compute a Tucker decomposition to find inherent low-dimensional multilinear structure, achieving compression ratios of up to 10000 on real-world data sets with negligible loss in accuracy. So that we can operate on such massive data, we present the first-ever distributed memory parallel implementation for the Tucker decomposition, whose key computations correspond to parallel linear algebra operations, albeit with nonstandard data layouts. Our approach specifies a data distribution for tensors that avoids any tensor data redistribution, either locally or in parallel. We provide accompanying analysis of the computation and communication costs of the algorithms. To demonstrate the compression and accuracy of the method, we apply our approach to real-world data sets from combustion science simulations. We also provide detailed performance results, including parallel performance in both weak and strong scaling experiments.

Image reconstruction method for electrical capacitance tomography based on the combined series and parallel normalization model

International Nuclear Information System (INIS)

Dong, Xiangyuan; Guo, Shuqing

2008-01-01

In this paper, a novel image reconstruction method for electrical capacitance tomography (ECT) based on the combined series and parallel model is presented. A regularization technique is used to obtain a stabilized solution of the inverse problem. Also, the adaptive coefficient of the combined model is deduced by numerical optimization. Simulation results indicate that it can produce higher quality images when compared to the algorithm based on the parallel or series models for the cases tested in this paper. It provides a new algorithm for ECT application

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.

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...

A Parallel Adaboost-Backpropagation Neural Network for Massive Image Dataset Classification

Science.gov (United States)

Cao, Jianfang; Chen, Lichao; Wang, Min; Shi, Hao; Tian, Yun

2016-01-01

Image classification uses computers to simulate human understanding and cognition of images by automatically categorizing images. This study proposes a faster image classification approach that parallelizes the traditional Adaboost-Backpropagation (BP) neural network using the MapReduce parallel programming model. First, we construct a strong classifier by assembling the outputs of 15 BP neural networks (which are individually regarded as weak classifiers) based on the Adaboost algorithm. Second, we design Map and Reduce tasks for both the parallel Adaboost-BP neural network and the feature extraction algorithm. Finally, we establish an automated classification model by building a Hadoop cluster. We use the Pascal VOC2007 and Caltech256 datasets to train and test the classification model. The results are superior to those obtained using traditional Adaboost-BP neural network or parallel BP neural network approaches. Our approach increased the average classification accuracy rate by approximately 14.5% and 26.0% compared to the traditional Adaboost-BP neural network and parallel BP neural network, respectively. Furthermore, the proposed approach requires less computation time and scales very well as evaluated by speedup, sizeup and scaleup. The proposed approach may provide a foundation for automated large-scale image classification and demonstrates practical value. PMID:27905520

Investigation and experimental validation of the contribution of optical interconnects in the SYMPHONIE massively parallel computer

International Nuclear Information System (INIS)

Scheer, Patrick

1998-01-01

Progress in microelectronics lead to electronic circuits which are increasingly integrated, with an operating frequency and an inputs/outputs count larger than the ones supported by printed circuit board and back-plane technologies. As a result, distributed systems with several boards cannot fully exploit the performance of integrated circuits. In synchronous parallel computers, the situation is worsen since the overall system performances rely on the efficiency of electrical interconnects between the integrated circuits which include the processing elements (PE). The study of a real parallel computer named SYMPHONIE shows for instance that the system operating frequency is far smaller than the capabilities of the microelectronics technology used for the PE implementation. Optical interconnections may cancel these limitations by providing more efficient connections between the PE. Especially, free-space optical interconnections based on vertical-cavity surface-emitting lasers (VCSEL), micro-lens and PIN photodiodes are compatible with the required features of the PE communications. Zero bias modulation of VCSEL with CMOS-compatible digital signals is studied and experimentally demonstrated. A model of the propagation of truncated gaussian beams through micro-lenses is developed. It is then used to optimise the geometry of the detection areas. A dedicated mechanical system is also proposed and implemented for integrating free-space optical interconnects in a standard electronic environment, representative of the one of parallel computer systems. A specially designed demonstrator provides the experimental validation of the above physical concepts. (author) [fr

Experimentally attainable example of chaotic tunneling: The hydrogen atom in parallel static electric and magnetic fields

International Nuclear Information System (INIS)

Delande, Dominique; Zakrzewski, Jakub

2003-01-01

Statistics of tunneling rates in the presence of chaotic classical dynamics is discussed on a realistic example: a hydrogen atom placed in parallel, uniform, static electric, and magnetic fields, where tunneling is followed by ionization along the fields direction. Depending on the magnetic quantum number, one may observe either a standard Porter-Thomas distribution of tunneling rates or, for strong scarring by a periodic orbit parallel to the external fields, strong deviations from it. For the latter case, a simple model based on random matrix theory gives the correct distribution

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

Pair-breaking effects by parallel magnetic field in electric-field-induced surface superconductivity

International Nuclear Information System (INIS)

Nabeta, Masahiro; Tanaka, Kenta K.; Onari, Seiichiro; Ichioka, Masanori

2016-01-01

Highlights: • Zeeman effect shifts superconducting gaps of sub-band system, towards pair-breaking. • Higher-level sub-bands become normal-state-like electronic states by magnetic fields. • Magnetic field dependence of zero-energy DOS reflects multi-gap superconductivity. - Abstract: We study paramagnetic pair-breaking in electric-field-induced surface superconductivity, when magnetic field is applied parallel to the surface. The calculation is performed by Bogoliubov-de Gennes theory with s-wave pairing, including the screening effect of electric fields by the induced carriers near the surface. Due to the Zeeman shift by applied fields, electronic states at higher-level sub-bands become normal-state-like. Therefore, the magnetic field dependence of Fermi-energy density of states reflects the multi-gap structure in the surface superconductivity.

Cellular automata a parallel model

CERN Document Server

Mazoyer, J

1999-01-01

Cellular automata can be viewed both as computational models and modelling systems of real processes. This volume emphasises the first aspect. In articles written by leading researchers, sophisticated massive parallel algorithms (firing squad, life, Fischer's primes recognition) are treated. Their computational power and the specific complexity classes they determine are surveyed, while some recent results in relation to chaos from a new dynamic systems point of view are also presented. Audience: This book will be of interest to specialists of theoretical computer science and the parallelism challenge.

Massively parallel sequencing and the emergence of forensic genomics: Defining the policy and legal issues for law enforcement.

Science.gov (United States)

Scudder, Nathan; McNevin, Dennis; Kelty, Sally F; Walsh, Simon J; Robertson, James

2018-03-01

Use of DNA in forensic science will be significantly influenced by new technology in coming years. Massively parallel sequencing and forensic genomics will hasten the broadening of forensic DNA analysis beyond short tandem repeats for identity towards a wider array of genetic markers, in applications as diverse as predictive phenotyping, ancestry assignment, and full mitochondrial genome analysis. With these new applications come a range of legal and policy implications, as forensic science touches on areas as diverse as 'big data', privacy and protected health information. Although these applications have the potential to make a more immediate and decisive forensic intelligence contribution to criminal investigations, they raise policy issues that will require detailed consideration if this potential is to be realised. The purpose of this paper is to identify the scope of the issues that will confront forensic and user communities. Copyright © 2017 The Chartered Society of Forensic Sciences. All rights reserved.

Practical tools to implement massive parallel pyrosequencing of PCR products in next generation molecular diagnostics.

Directory of Open Access Journals (Sweden)

Kim De Leeneer

Full Text Available Despite improvements in terms of sequence quality and price per basepair, Sanger sequencing remains restricted to screening of individual disease genes. The development of massively parallel sequencing (MPS technologies heralded an era in which molecular diagnostics for multigenic disorders becomes reality. Here, we outline different PCR amplification based strategies for the screening of a multitude of genes in a patient cohort. We performed a thorough evaluation in terms of set-up, coverage and sequencing variants on the data of 10 GS-FLX experiments (over 200 patients. Crucially, we determined the actual coverage that is required for reliable diagnostic results using MPS, and provide a tool to calculate the number of patients that can be screened in a single run. Finally, we provide an overview of factors contributing to false negative or false positive mutation calls and suggest ways to maximize sensitivity and specificity, both important in a routine setting. By describing practical strategies for screening of multigenic disorders in a multitude of samples and providing answers to questions about minimum required coverage, the number of patients that can be screened in a single run and the factors that may affect sensitivity and specificity we hope to facilitate the implementation of MPS technology in molecular diagnostics.

Torque Split Strategy for Parallel Hybrid Electric Vehicles with an Integrated Starter Generator

OpenAIRE

Fu, Zhumu; Gao, Aiyun; Wang, Xiaohong; Song, Xiaona

2014-01-01

This paper presents a torque split strategy for parallel hybrid electric vehicles with an integrated starter generator (ISG-PHEV) by using fuzzy logic control. By combining the efficiency map and the optimum torque curve of the internal combustion engine (ICE) with the state of charge (SOC) of the batteries, the torque split strategy is designed, which manages the ICE within its peak efficiency region. Taking the quantified ICE torque, the quantified SOC of the batteries, and the quantified I...

A bumpy ride on the diagnostic bench of massive parallel sequencing, the case of the mitochondrial genome.

Directory of Open Access Journals (Sweden)

Kim Vancampenhout

Full Text Available The advent of massive parallel sequencing (MPS has revolutionized the field of human molecular genetics, including the diagnostic study of mitochondrial (mt DNA dysfunction. The analysis of the complete mitochondrial genome using MPS platforms is now common and will soon outrun conventional sequencing. However, the development of a robust and reliable protocol is rather challenging. A previous pilot study for the re-sequencing of human mtDNA revealed an uneven coverage, affecting predominantly part of the plus strand. In an attempt to address this problem, we undertook a comparative study of standard and modified protocols for the Ion Torrent PGM system. We could not improve strand representation by altering the recommended shearing methodology of the standard workflow or omitting the DNA polymerase amplification step from the library construction process. However, we were able to associate coverage bias of the plus strand with a specific sequence motif. Additionally, we compared coverage and variant calling across technologies. The same samples were also sequenced on a MiSeq device which showed that coverage and heteroplasmic variant calling were much improved.

A safe an easy method for building consensus HIV sequences from 454 massively parallel sequencing data.

Science.gov (United States)

Fernández-Caballero Rico, Jose Ángel; Chueca Porcuna, Natalia; Álvarez Estévez, Marta; Mosquera Gutiérrez, María Del Mar; Marcos Maeso, María Ángeles; García, Federico

2018-02-01

To show how to generate a consensus sequence from the information of massive parallel sequences data obtained from routine HIV anti-retroviral resistance studies, and that may be suitable for molecular epidemiology studies. Paired Sanger (Trugene-Siemens) and next-generation sequencing (NGS) (454 GSJunior-Roche) HIV RT and protease sequences from 62 patients were studied. NGS consensus sequences were generated using Mesquite, using 10%, 15%, and 20% thresholds. Molecular evolutionary genetics analysis (MEGA) was used for phylogenetic studies. At a 10% threshold, NGS-Sanger sequences from 17/62 patients were phylogenetically related, with a median bootstrap-value of 88% (IQR83.5-95.5). Association increased to 36/62 sequences, median bootstrap 94% (IQR85.5-98)], using a 15% threshold. Maximum association was at the 20% threshold, with 61/62 sequences associated, and a median bootstrap value of 99% (IQR98-100). A safe method is presented to generate consensus sequences from HIV-NGS data at 20% threshold, which will prove useful for molecular epidemiological studies. Copyright © 2016 Elsevier España, S.L.U. and Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica. All rights reserved.

Detection and Evaluation of Spatio-Temporal Spike Patterns in Massively Parallel Spike Train Data with SPADE

Directory of Open Access Journals (Sweden)

Pietro Quaglio

2017-05-01

Full Text Available Repeated, precise sequences of spikes are largely considered a signature of activation of cell assemblies. These repeated sequences are commonly known under the name of spatio-temporal patterns (STPs. STPs are hypothesized to play a role in the communication of information in the computational process operated by the cerebral cortex. A variety of statistical methods for the detection of STPs have been developed and applied to electrophysiological recordings, but such methods scale poorly with the current size of available parallel spike train recordings (more than 100 neurons. In this work, we introduce a novel method capable of overcoming the computational and statistical limits of existing analysis techniques in detecting repeating STPs within massively parallel spike trains (MPST. We employ advanced data mining techniques to efficiently extract repeating sequences of spikes from the data. Then, we introduce and compare two alternative approaches to distinguish statistically significant patterns from chance sequences. The first approach uses a measure known as conceptual stability, of which we investigate a computationally cheap approximation for applications to such large data sets. The second approach is based on the evaluation of pattern statistical significance. In particular, we provide an extension to STPs of a method we recently introduced for the evaluation of statistical significance of synchronous spike patterns. The performance of the two approaches is evaluated in terms of computational load and statistical power on a variety of artificial data sets that replicate specific features of experimental data. Both methods provide an effective and robust procedure for detection of STPs in MPST data. The method based on significance evaluation shows the best overall performance, although at a higher computational cost. We name the novel procedure the spatio-temporal Spike PAttern Detection and Evaluation (SPADE analysis.

Massive coordination of residential embedded electricity generation and demand response using the PowerMatcher approach

International Nuclear Information System (INIS)

Kamphuis, I.G.; Hommelberg, M.P.F.; Warmer, C.J.; Kok, J.K.

2007-01-01

Different driving forces push the electricity production towards decentralization. The projected increase of distributed power generation on the residential level with an increasing proportion of intermittent renewable energy resources poses problems for continuously matching the energy balance when coordination takes place centrally. On the other hand, new opportunities arise by intelligent clustering of generators and demand in so-called Virtual Power Plants. Part of the responsibility for new coordination mechanisms, then, has to be laid locally. To achieve this, the current electricity infrastructure is expected to evolve into a network of networks (including ICT (Information and Communication Technology)-networks), in which all system parts communicate with one another, are aware of each other's context and may influence each other. In this paper, a multi-agent systems approach, using price signal-vectors from an electronic market is presented as an appropriate technology needed for massive control and coordination tasks in these future electricity networks. The PowerMatcher, a market-based control concept for supply and demand matching (SDM) in electricity networks, is discussed. The results within a simulation study show the ability to raise the simultaneousness of electricity production and consumption within (local) control clusters with cogeneration and heat-pumps by exchanging price signals and coordinated allocation using market algorithms. The control concept, however, can also be applied in other business cases like reduction of imbalance cost in commercial portfolios or virtual power plant operators, utilizing distributed generators. Furthermore, a PowerMatcher-based field test configuration with 15 Stirling-engine powered micro-CHP's is described, which is currently in operation within a field test in the Netherlands

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

Scalable Strategies for Computing with Massive Data

Directory of Open Access Journals (Sweden)

Michael Kane

2013-11-01

Full Text Available This paper presents two complementary statistical computing frameworks that address challenges in parallel processing and the analysis of massive data. First, the foreach package allows users of the R programming environment to define parallel loops that may be run sequentially on a single machine, in parallel on a symmetric multiprocessing (SMP machine, or in cluster environments without platform-specific code. Second, the bigmemory package implements memory- and file-mapped data structures that provide (a access to arbitrarily large data while retaining a look and feel that is familiar to R users and (b data structures that are shared across processor cores in order to support efficient parallel computing techniques. Although these packages may be used independently, this paper shows how they can be used in combination to address challenges that have effectively been beyond the reach of researchers who lack specialized software development skills or expensive hardware.

Magnetospheric Multiscale Satellites Observations of Parallel Electric Fields Associated with Magnetic Reconnection

Science.gov (United States)

Ergun, R. E.; Goodrich, K. A.; Wilder, F. D.; Holmes, J. C.; Stawarz, J. E.; Eriksson, S.; Sturner, A. P.; Malaspina, D. M.; Usanova, M. E.; Torbert, R. B.; Lindqvist, P.-A.; Khotyaintsev, Y.; Burch, J. L.; Strangeway, R. J.; Russell, C. T.; Pollock, C. J.; Giles, B. L.; Hesse, M.; Chen, L. J.; Lapenta, G.; Goldman, M. V.; Newman, D. L.; Schwartz, S. J.; Eastwood, J. P.; Phan, T. D.; Mozer, F. S.; Drake, J.; Shay, M. A.; Cassak, P. A.; Nakamura, R.; Marklund, G.

2016-06-01

We report observations from the Magnetospheric Multiscale satellites of parallel electric fields (E∥ ) associated with magnetic reconnection in the subsolar region of the Earth's magnetopause. E∥ events near the electron diffusion region have amplitudes on the order of 100 mV /m , which are significantly larger than those predicted for an antiparallel reconnection electric field. This Letter addresses specific types of E∥ events, which appear as large-amplitude, near unipolar spikes that are associated with tangled, reconnected magnetic fields. These E∥ events are primarily in or near a current layer near the separatrix and are interpreted to be double layers that may be responsible for secondary reconnection in tangled magnetic fields or flux ropes. These results are telling of the three-dimensional nature of magnetopause reconnection and indicate that magnetopause reconnection may be often patchy and/or drive turbulence along the separatrix that results in flux ropes and/or tangled magnetic fields.

Electromagnetic ion-cyclotron instability in the presence of a parallel electric field with general loss-cone distribution function - particle aspect analysis

Directory of Open Access Journals (Sweden)

G. Ahirwar

2006-08-01

Full Text Available The effect of parallel electric field on the growth rate, parallel and perpendicular resonant energy and marginal stability of the electromagnetic ion-cyclotron (EMIC wave with general loss-cone distribution function in a low β homogeneous plasma is investigated by particle aspect approach. The effect of the steepness of the loss-cone distribution is investigated on the electromagnetic ion-cyclotron wave. The whole plasma is considered to consist of resonant and non-resonant particles. It is assumed that resonant particles participate in the energy exchange with the wave, whereas non-resonant particles support the oscillatory motion of the wave. The wave is assumed to propagate parallel to the static magnetic field. The effect of the parallel electric field with the general distribution function is to control the growth rate of the EMIC waves, whereas the effect of steep loss-cone distribution is to enhance the growth rate and perpendicular heating of the ions. This study is relevant to the analysis of ion conics in the presence of an EMIC wave in the auroral acceleration region of the Earth's magnetoplasma.

Electrical properties of the 8-12th September, 2015 massive dust outbreak over the Levant

Science.gov (United States)

Katz, Shai; Yair, Yoav; Price, Colin; Yaniv, Roy; Silber, Israel; Lynn, Barry; Ziv, Baruch

2018-03-01

We report new electrical measurements conducted during the massive dust outbreak that occurred over the Levant in September 08-12, 2015. That event was one of the strongest dust storms on record and engulfed the entire region for 5 consecutive days, over Iraq through Syria, Jordan, Israel, Lebanon, Cyprus and Egypt. At its peak, Aerosol Optical Thickness of 4.0 was measured in southern Israel. Ground-based measurements of the electrical field (Ez) and current density (J) were conducted at the Wise Observatory (WO) in Mizpe-Ramon (30°35‧N, 34°45‧E) and near the top of Mt. Hermon (30°24‧N, 35°51‧E). During the dust outbreak very large fluctuations in the electrical parameters were measured at both stations, with remarkable differences between the two locations. While at the Mt. Hermon station we registered positive values of the electric field and total current density, the values registered at the Wise Observatory were significantly smaller and more negative. The Mt. Hermon site showed Ez and J values fluctuating between - 460 and + 570 V m- 1 and - 14.5 and + 18 pA m- 2 respectively. In contrast, the Ez values registered at WO varied between - 430 and + 10 V m- 1, and the current density fluctuated between - 6 and + 3 pA m- 2. We show that the unique generation and evolution of this dust outbreak gave rise to a significantly different charge structure compared with that observed in short lived convective events, and suggest a tentative explanation for the obtained results.

A parallel solution for high resolution histological image analysis.

Science.gov (United States)

Bueno, G; González, R; Déniz, O; García-Rojo, M; González-García, J; Fernández-Carrobles, M M; Vállez, N; Salido, J

2012-10-01

This paper describes a general methodology for developing parallel image processing algorithms based on message passing for high resolution images (on the order of several Gigabytes). These algorithms have been applied to histological images and must be executed on massively parallel processing architectures. Advances in new technologies for complete slide digitalization in pathology have been combined with developments in biomedical informatics. However, the efficient use of these digital slide systems is still a challenge. The image processing that these slides are subject to is still limited both in terms of data processed and processing methods. The work presented here focuses on the need to design and develop parallel image processing tools capable of obtaining and analyzing the entire gamut of information included in digital slides. Tools have been developed to assist pathologists in image analysis and diagnosis, and they cover low and high-level image processing methods applied to histological images. Code portability, reusability and scalability have been tested by using the following parallel computing architectures: distributed memory with massive parallel processors and two networks, INFINIBAND and Myrinet, composed of 17 and 1024 nodes respectively. The parallel framework proposed is flexible, high performance solution and it shows that the efficient processing of digital microscopic images is possible and may offer important benefits to pathology laboratories. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

System design and energetic characterization of a four-wheel-driven series–parallel hybrid electric powertrain for heavy-duty applications

International Nuclear Information System (INIS)

Wang, Enhua; Guo, Di; Yang, Fuyuan

2015-01-01

Highlights: • A novel four-wheel-driven series–parallel hybrid powertrain is proposed. • A system model and a rule-based control strategy are designed. • Energetic performance is compared to a rear-wheel-driven hybrid powertrain. • Less torsional oscillation and more robust regenerative braking are achieved. - Abstract: Powertrain topology design is vital for system performance of a hybrid electric vehicle. In this paper, a novel four-wheel-driven series–parallel hybrid electric powertrain is proposed. A motor is connected to the differential of the rear axle. An auxiliary power unit is linked to the differential of the front axle via a clutch. First, a mathematical model was established to evaluate the fuel-saving potential. A rule-based energy management algorithm was subsequently designed, and its working parameters were optimized. The hybrid powertrain system was applied to a transit bus, and the system characteristics were analyzed. Compared to an existing coaxial power-split hybrid powertrain, the fuel economy of the four-wheel-driven series–parallel hybrid powertrain can be at the same level under normal road conditions. However, the proposed four-wheel-driven series–parallel hybrid powertrain can recover braking energy more efficiently under road conditions with a low adhesive coefficient and can alleviate the torsional oscillation occurring at the existing coaxial power-split hybrid powertrain. Therefore, the four-wheel-driven series–parallel hybrid powertrain is a good solution for transit buses toward more robust performance.

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

Optimisation of a parallel ocean general circulation model

Science.gov (United States)

Beare, M. I.; Stevens, D. P.

1997-10-01

This paper presents the development of a general-purpose parallel ocean circulation model, for use on a wide range of computer platforms, from traditional scalar machines to workstation clusters and massively parallel processors. Parallelism is provided, as a modular option, via high-level message-passing routines, thus hiding the technical intricacies from the user. An initial implementation highlights that the parallel efficiency of the model is adversely affected by a number of factors, for which optimisations are discussed and implemented. The resulting ocean code is portable and, in particular, allows science to be achieved on local workstations that could otherwise only be undertaken on state-of-the-art supercomputers.

Layout design and energetic analysis of a complex diesel parallel hybrid electric vehicle

International Nuclear Information System (INIS)

Finesso, Roberto; Spessa, Ezio; Venditti, Mattia

2014-01-01

Highlights: • Layout design, energetic and cost analysis of complex parallel hybrid vehicles. • Development of global and real-time optimizers for control strategy identification. • Rule-based control strategies to minimize fuel consumption and NO x . • Energy share across each working mode for battery and thermal engine. - Abstract: The present paper is focused on the design, optimization and analysis of a complex parallel hybrid electric vehicle, equipped with two electric machines on both the front and rear axles, and on the evaluation of its potential to reduce fuel consumption and NO x emissions over several driving missions. The vehicle has been compared with two conventional parallel hybrid vehicles, equipped with a single electric machine on the front axle or on the rear axle, as well as with a conventional vehicle. All the vehicles have been equipped with compression ignition engines. The optimal layout of each vehicle was identified on the basis of the minimization of the overall powertrain costs during the whole vehicle life. These costs include the initial investment due to the production of the components as well as the operating costs related to fuel consumption and to battery depletion. Identification of the optimal powertrain control strategy, in terms of the management of the power flows of the engine and electric machines, and of gear selection, is necessary in order to be able to fully exploit the potential of the hybrid architecture. To this end, two global optimizers, one of a deterministic nature and another of a stochastic type, and two real-time optimizers have been developed, applied and compared. A new mathematical technique has been developed and applied to the vehicle simulation model in order to decrease the computational time of the optimizers. First, the vehicle model equations were written in order to allow a coarse time grid to be used, then, the control variables (i.e., power flow and gear number) were discretized, and the

Regional-scale calculation of the LS factor using parallel processing

Science.gov (United States)

Liu, Kai; Tang, Guoan; Jiang, Ling; Zhu, A.-Xing; Yang, Jianyi; Song, Xiaodong

2015-05-01

With the increase of data resolution and the increasing application of USLE over large areas, the existing serial implementation of algorithms for computing the LS factor is becoming a bottleneck. In this paper, a parallel processing model based on message passing interface (MPI) is presented for the calculation of the LS factor, so that massive datasets at a regional scale can be processed efficiently. The parallel model contains algorithms for calculating flow direction, flow accumulation, drainage network, slope, slope length and the LS factor. According to the existence of data dependence, the algorithms are divided into local algorithms and global algorithms. Parallel strategy are designed according to the algorithm characters including the decomposition method for maintaining the integrity of the results, optimized workflow for reducing the time taken for exporting the unnecessary intermediate data and a buffer-communication-computation strategy for improving the communication efficiency. Experiments on a multi-node system show that the proposed parallel model allows efficient calculation of the LS factor at a regional scale with a massive dataset.

The Confidence-Accuracy Relationship in Diagnostic Assessment: The Case of the Potential Difference in Parallel Electric Circuits

Science.gov (United States)

Saglam, Murat

2015-01-01

This study explored the relationship between accuracy of and confidence in performance of 114 prospective primary school teachers in answering diagnostic questions on potential difference in parallel electric circuits. The participants were required to indicate their confidence in their answers for each question. Bias and calibration indices were…

AMIDST: Analysis of MassIve Data STreams

DEFF Research Database (Denmark)

Masegosa, Andres; Martinez, Ana Maria; Borchani, Hanen

2015-01-01

The Analysis of MassIve Data STreams (AMIDST) Java toolbox provides a collection of scalable and parallel algorithms for inference and learning of hybrid Bayesian networks from data streams. The toolbox, available at http://amidst.github.io/toolbox/ under the Apache Software License version 2.......0, also efficiently leverages existing functionalities and algorithms by interfacing to software tools such as HUGIN and MOA....

Massively parallel sequencing and genome-wide copy number analysis revealed a clonal relationship in benign metastasizing leiomyoma

Science.gov (United States)

Lee, Li-Yu; Lin, Gigin; Chen, Shu-Jen; Lu, Yen-Jung; Huang, Huei-Jean; Yen, Chi-Feng; Han, Chien Min; Lee, Yun-Shien; Wang, Tzu-Hao; Chao, Angel

2017-01-01

Benign metastasizing leiomyoma (BML) is a rare disease entity typically presenting as multiple extrauterine leiomyomas associated with a uterine leiomyoma. It has been hypothesized that the extrauterine leiomyomata represent distant metastasis of the uterine leiomyoma. To date, the only molecular evidence supporting this hypothesis was derived from clonality analyses based on X-chromosome inactivation assays. Here, we sought to address this issue by examining paired specimens of synchronous pulmonary and uterine leiomyomata from three patients using targeted massively parallel sequencing and molecular inversion probe array analysis for detecting somatic mutations and copy number aberrations. We detected identical non-hot-spot somatic mutations and similar patterns of copy number aberrations (CNAs) in paired pulmonary and uterine leiomyomata from two patients, indicating the clonal relationship between pulmonary and uterine leiomyomata. In addition to loss of chromosome 22q found in the literature, we identified additional recurrent CNAs including losses of chromosome 3q and 11q. In conclusion, our findings of the clonal relationship between synchronous pulmonary and uterine leiomyomas support the hypothesis that BML represents a condition wherein a uterine leiomyoma disseminates to distant extrauterine locations. PMID:28533481

Massively parallel sequencing and genome-wide copy number analysis revealed a clonal relationship in benign metastasizing leiomyoma.

Science.gov (United States)

Wu, Ren-Chin; Chao, An-Shine; Lee, Li-Yu; Lin, Gigin; Chen, Shu-Jen; Lu, Yen-Jung; Huang, Huei-Jean; Yen, Chi-Feng; Han, Chien Min; Lee, Yun-Shien; Wang, Tzu-Hao; Chao, Angel

2017-07-18

Benign metastasizing leiomyoma (BML) is a rare disease entity typically presenting as multiple extrauterine leiomyomas associated with a uterine leiomyoma. It has been hypothesized that the extrauterine leiomyomata represent distant metastasis of the uterine leiomyoma. To date, the only molecular evidence supporting this hypothesis was derived from clonality analyses based on X-chromosome inactivation assays. Here, we sought to address this issue by examining paired specimens of synchronous pulmonary and uterine leiomyomata from three patients using targeted massively parallel sequencing and molecular inversion probe array analysis for detecting somatic mutations and copy number aberrations. We detected identical non-hot-spot somatic mutations and similar patterns of copy number aberrations (CNAs) in paired pulmonary and uterine leiomyomata from two patients, indicating the clonal relationship between pulmonary and uterine leiomyomata. In addition to loss of chromosome 22q found in the literature, we identified additional recurrent CNAs including losses of chromosome 3q and 11q. In conclusion, our findings of the clonal relationship between synchronous pulmonary and uterine leiomyomas support the hypothesis that BML represents a condition wherein a uterine leiomyoma disseminates to distant extrauterine locations.

Parallel adaptive simulations on unstructured meshes

International Nuclear Information System (INIS)

Shephard, M S; Jansen, K E; Sahni, O; Diachin, L A

2007-01-01

This paper discusses methods being developed by the ITAPS center to support the execution of parallel adaptive simulations on unstructured meshes. The paper first outlines the ITAPS approach to the development of interoperable mesh, geometry and field services to support the needs of SciDAC application in these areas. The paper then demonstrates the ability of unstructured adaptive meshing methods built on such interoperable services to effectively solve important physics problems. Attention is then focused on ITAPs' developing ability to solve adaptive unstructured mesh problems on massively parallel computers

Parallel inversion of a massive ERT data set to characterize deep vadose zone contamination beneath former nuclear waste infiltration galleries at the Hanford Site B-Complex (Invited)

Science.gov (United States)

Johnson, T.; Rucker, D. F.; Wellman, D.

2013-12-01

The Hanford Site, located in south-central Washington, USA, originated in the early 1940's as part of the Manhattan Project and produced plutonium used to build the United States nuclear weapons stockpile. In accordance with accepted industrial practice of that time, a substantial portion of relatively low-activity liquid radioactive waste was disposed of by direct discharge to either surface soil or into near-surface infiltration galleries such as cribs and trenches. This practice was supported by early investigations beginning in the 1940s, including studies by Geological Survey (USGS) experts, whose investigations found vadose zone soils at the site suitable for retaining radionuclides to the extent necessary to protect workers and members of the general public based on the standards of that time. That general disposal practice has long since been discontinued, and the US Department of Energy (USDOE) is now investigating residual contamination at former infiltration galleries as part of its overall environmental management and remediation program. Most of the liquid wastes released into the subsurface were highly ionic and electrically conductive, and therefore present an excellent target for imaging by Electrical Resistivity Tomography (ERT) within the low-conductivity sands and gravels comprising Hanford's vadose zone. In 2006, USDOE commissioned a large scale surface ERT survey to characterize vadose zone contamination beneath the Hanford Site B-Complex, which contained 8 infiltration trenches, 12 cribs, and one tile field. The ERT data were collected in a pole-pole configuration with 18 north-south trending lines, and 18 east-west trending lines ranging from 417m to 816m in length. The final data set consisted of 208,411 measurements collected on 4859 electrodes, covering an area of 600m x 600m. Given the computational demands of inverting this massive data set as a whole, the data were initially inverted in parts with a shared memory inversion code, which

Tinker-HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields.

Science.gov (United States)

Lagardère, Louis; Jolly, Luc-Henri; Lipparini, Filippo; Aviat, Félix; Stamm, Benjamin; Jing, Zhifeng F; Harger, Matthew; Torabifard, Hedieh; Cisneros, G Andrés; Schnieders, Michael J; Gresh, Nohad; Maday, Yvon; Ren, Pengyu Y; Ponder, Jay W; Piquemal, Jean-Philip

2018-01-28

We present Tinker-HP, a massively MPI parallel package dedicated to classical molecular dynamics (MD) and to multiscale simulations, using advanced polarizable force fields (PFF) encompassing distributed multipoles electrostatics. Tinker-HP is an evolution of the popular Tinker package code that conserves its simplicity of use and its reference double precision implementation for CPUs. Grounded on interdisciplinary efforts with applied mathematics, Tinker-HP allows for long polarizable MD simulations on large systems up to millions of atoms. We detail in the paper the newly developed extension of massively parallel 3D spatial decomposition to point dipole polarizable models as well as their coupling to efficient Krylov iterative and non-iterative polarization solvers. The design of the code allows the use of various computer systems ranging from laboratory workstations to modern petascale supercomputers with thousands of cores. Tinker-HP proposes therefore the first high-performance scalable CPU computing environment for the development of next generation point dipole PFFs and for production simulations. Strategies linking Tinker-HP to Quantum Mechanics (QM) in the framework of multiscale polarizable self-consistent QM/MD simulations are also provided. The possibilities, performances and scalability of the software are demonstrated via benchmarks calculations using the polarizable AMOEBA force field on systems ranging from large water boxes of increasing size and ionic liquids to (very) large biosystems encompassing several proteins as well as the complete satellite tobacco mosaic virus and ribosome structures. For small systems, Tinker-HP appears to be competitive with the Tinker-OpenMM GPU implementation of Tinker. As the system size grows, Tinker-HP remains operational thanks to its access to distributed memory and takes advantage of its new algorithmic enabling for stable long timescale polarizable simulations. Overall, a several thousand-fold acceleration over

Parallel Computation of RCS of Electrically Large Platform with Coatings Modeled with NURBS Surfaces

Directory of Open Access Journals (Sweden)

Ying Yan

2012-01-01

Full Text Available The significance of Radar Cross Section (RCS in the military applications makes its prediction an important problem. This paper uses large-scale parallel Physical Optics (PO to realize the fast computation of RCS to electrically large targets, which are modeled by Non-Uniform Rational B-Spline (NURBS surfaces and coated with dielectric materials. Some numerical examples are presented to validate this paper’s method. In addition, 1024 CPUs are used in Shanghai Supercomputer Center (SSC to perform the simulation of a model with the maximum electrical size 1966.7 λ for the first time in China. From which, it can be found that this paper’s method can greatly speed the calculation and is capable of solving the real-life problem of RCS prediction.

Smoldyn on graphics processing units: massively parallel Brownian dynamics simulations.

Science.gov (United States)

Dematté, Lorenzo

2012-01-01

Space is a very important aspect in the simulation of biochemical systems; recently, the need for simulation algorithms able to cope with space is becoming more and more compelling. Complex and detailed models of biochemical systems need to deal with the movement of single molecules and particles, taking into consideration localized fluctuations, transportation phenomena, and diffusion. A common drawback of spatial models lies in their complexity: models can become very large, and their simulation could be time consuming, especially if we want to capture the systems behavior in a reliable way using stochastic methods in conjunction with a high spatial resolution. In order to deliver the promise done by systems biology to be able to understand a system as whole, we need to scale up the size of models we are able to simulate, moving from sequential to parallel simulation algorithms. In this paper, we analyze Smoldyn, a widely diffused algorithm for stochastic simulation of chemical reactions with spatial resolution and single molecule detail, and we propose an alternative, innovative implementation that exploits the parallelism of Graphics Processing Units (GPUs). The implementation executes the most computational demanding steps (computation of diffusion, unimolecular, and bimolecular reaction, as well as the most common cases of molecule-surface interaction) on the GPU, computing them in parallel on each molecule of the system. The implementation offers good speed-ups and real time, high quality graphics output

Optimisation of a parallel ocean general circulation model

Directory of Open Access Journals (Sweden)

M. I. Beare

1997-10-01

Full Text Available This paper presents the development of a general-purpose parallel ocean circulation model, for use on a wide range of computer platforms, from traditional scalar machines to workstation clusters and massively parallel processors. Parallelism is provided, as a modular option, via high-level message-passing routines, thus hiding the technical intricacies from the user. An initial implementation highlights that the parallel efficiency of the model is adversely affected by a number of factors, for which optimisations are discussed and implemented. The resulting ocean code is portable and, in particular, allows science to be achieved on local workstations that could otherwise only be undertaken on state-of-the-art supercomputers.

Optimisation of a parallel ocean general circulation model

Directory of Open Access Journals (Sweden)

M. I. Beare

Full Text Available This paper presents the development of a general-purpose parallel ocean circulation model, for use on a wide range of computer platforms, from traditional scalar machines to workstation clusters and massively parallel processors. Parallelism is provided, as a modular option, via high-level message-passing routines, thus hiding the technical intricacies from the user. An initial implementation highlights that the parallel efficiency of the model is adversely affected by a number of factors, for which optimisations are discussed and implemented. The resulting ocean code is portable and, in particular, allows science to be achieved on local workstations that could otherwise only be undertaken on state-of-the-art supercomputers.

QuASAR-MPRA: accurate allele-specific analysis for massively parallel reporter assays.

Science.gov (United States)

Kalita, Cynthia A; Moyerbrailean, Gregory A; Brown, Christopher; Wen, Xiaoquan; Luca, Francesca; Pique-Regi, Roger

2018-03-01

The majority of the human genome is composed of non-coding regions containing regulatory elements such as enhancers, which are crucial for controlling gene expression. Many variants associated with complex traits are in these regions, and may disrupt gene regulatory sequences. Consequently, it is important to not only identify true enhancers but also to test if a variant within an enhancer affects gene regulation. Recently, allele-specific analysis in high-throughput reporter assays, such as massively parallel reporter assays (MPRAs), have been used to functionally validate non-coding variants. However, we are still missing high-quality and robust data analysis tools for these datasets. We have further developed our method for allele-specific analysis QuASAR (quantitative allele-specific analysis of reads) to analyze allele-specific signals in barcoded read counts data from MPRA. Using this approach, we can take into account the uncertainty on the original plasmid proportions, over-dispersion, and sequencing errors. The provided allelic skew estimate and its standard error also simplifies meta-analysis of replicate experiments. Additionally, we show that a beta-binomial distribution better models the variability present in the allelic imbalance of these synthetic reporters and results in a test that is statistically well calibrated under the null. Applying this approach to the MPRA data, we found 602 SNPs with significant (false discovery rate 10%) allele-specific regulatory function in LCLs. We also show that we can combine MPRA with QuASAR estimates to validate existing experimental and computational annotations of regulatory variants. Our study shows that with appropriate data analysis tools, we can improve the power to detect allelic effects in high-throughput reporter assays. http://github.com/piquelab/QuASAR/tree/master/mpra. fluca@wayne.edu or rpique@wayne.edu. Supplementary data are available online at Bioinformatics. © The Author (2017). Published by

Enabling inspection solutions for future mask technologies through the development of massively parallel E-Beam inspection

Science.gov (United States)

Malloy, Matt; Thiel, Brad; Bunday, Benjamin D.; Wurm, Stefan; Jindal, Vibhu; Mukhtar, Maseeh; Quoi, Kathy; Kemen, Thomas; Zeidler, Dirk; Eberle, Anna Lena; Garbowski, Tomasz; Dellemann, Gregor; Peters, Jan Hendrik

2015-09-01

The new device architectures and materials being introduced for sub-10nm manufacturing, combined with the complexity of multiple patterning and the need for improved hotspot detection strategies, have pushed current wafer inspection technologies to their limits. In parallel, gaps in mask inspection capability are growing as new generations of mask technologies are developed to support these sub-10nm wafer manufacturing requirements. In particular, the challenges associated with nanoimprint and extreme ultraviolet (EUV) mask inspection require new strategies that enable fast inspection at high sensitivity. The tradeoffs between sensitivity and throughput for optical and e-beam inspection are well understood. Optical inspection offers the highest throughput and is the current workhorse of the industry for both wafer and mask inspection. E-beam inspection offers the highest sensitivity but has historically lacked the throughput required for widespread adoption in the manufacturing environment. It is unlikely that continued incremental improvements to either technology will meet tomorrow's requirements, and therefore a new inspection technology approach is required; one that combines the high-throughput performance of optical with the high-sensitivity capabilities of e-beam inspection. To support the industry in meeting these challenges SUNY Poly SEMATECH has evaluated disruptive technologies that can meet the requirements for high volume manufacturing (HVM), for both the wafer fab [1] and the mask shop. Highspeed massively parallel e-beam defect inspection has been identified as the leading candidate for addressing the key gaps limiting today's patterned defect inspection techniques. As of late 2014 SUNY Poly SEMATECH completed a review, system analysis, and proof of concept evaluation of multiple e-beam technologies for defect inspection. A champion approach has been identified based on a multibeam technology from Carl Zeiss. This paper includes a discussion on the

CELLS v1.0: updated and parallelized version of an electrical scheme to simulate multiple electrified clouds and flashes over large domains

Directory of Open Access Journals (Sweden)

C. Barthe

2012-01-01

Full Text Available The paper describes the fully parallelized electrical scheme CELLS which is suitable to simulate explicitly electrified storm systems on parallel computers. Our motivation here is to show that a cloud electricity scheme can be developed for use on large grids with complex terrain. Large computational domains are needed to perform real case meteorological simulations with many independent convective cells.

The scheme computes the bulk electric charge attached to each cloud particle and hydrometeor. Positive and negative ions are also taken into account. Several parametrizations of the dominant non-inductive charging process are included and an inductive charging process as well. The electric field is obtained by inverting the Gauss equation with an extension to terrain-following coordinates. The new feature concerns the lightning flash scheme which is a simplified version of an older detailed sequential scheme. Flashes are composed of a bidirectional leader phase (vertical extension from the triggering point and a phase obeying a fractal law (with horizontal extension on electrically charged zones. The originality of the scheme lies in the way the branching phase is treated to get a parallel code.

The complete electrification scheme is tested for the 10 July 1996 STERAO case and for the 21 July 1998 EULINOX case. Flash characteristics are analysed in detail and additional sensitivity experiments are performed for the STERAO case. Although the simulations were run for flat terrain conditions, they show that the model behaves well on multiprocessor computers. This opens a wide area of application for this electrical scheme with the next objective of running real meterological case on large domains.

Optimal Battery Utilization Over Lifetime for Parallel Hybrid Electric Vehicle to Maximize Fuel Economy

Energy Technology Data Exchange (ETDEWEB)

Patil, Chinmaya; Naghshtabrizi, Payam; Verma, Rajeev; Tang, Zhijun; Smith, Kandler; Shi, Ying

2016-08-01

This paper presents a control strategy to maximize fuel economy of a parallel hybrid electric vehicle over a target life of the battery. Many approaches to maximizing fuel economy of parallel hybrid electric vehicle do not consider the effect of control strategy on the life of the battery. This leads to an oversized and underutilized battery. There is a trade-off between how aggressively to use and 'consume' the battery versus to use the engine and consume fuel. The proposed approach addresses this trade-off by exploiting the differences in the fast dynamics of vehicle power management and slow dynamics of battery aging. The control strategy is separated into two parts, (1) Predictive Battery Management (PBM), and (2) Predictive Power Management (PPM). PBM is the higher level control with slow update rate, e.g. once per month, responsible for generating optimal set points for PPM. The considered set points in this paper are the battery power limits and State Of Charge (SOC). The problem of finding the optimal set points over the target battery life that minimize engine fuel consumption is solved using dynamic programming. PPM is the lower level control with high update rate, e.g. a second, responsible for generating the optimal HEV energy management controls and is implemented using model predictive control approach. The PPM objective is to find the engine and battery power commands to achieve the best fuel economy given the battery power and SOC constraints imposed by PBM. Simulation results with a medium duty commercial hybrid electric vehicle and the proposed two-level hierarchical control strategy show that the HEV fuel economy is maximized while meeting a specified target battery life. On the other hand, the optimal unconstrained control strategy achieves marginally higher fuel economy, but fails to meet the target battery life.

Resistor Combinations for Parallel Circuits.

Science.gov (United States)

McTernan, James P.

1978-01-01

To help simplify both teaching and learning of parallel circuits, a high school electricity/electronics teacher presents and illustrates the use of tables of values for parallel resistive circuits in which total resistances are whole numbers. (MF)

Parallel algorithms for interactive manipulation of digital terrain models

Science.gov (United States)

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

1988-01-01

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

Parallel processing architecture for H.264 deblocking filter on multi-core platforms

Science.gov (United States)

Prasad, Durga P.; Sonachalam, Sekar; Kunchamwar, Mangesh K.; Gunupudi, Nageswara Rao

2012-03-01

Massively parallel computing (multi-core) chips offer outstanding new solutions that satisfy the increasing demand for high resolution and high quality video compression technologies such as H.264. Such solutions not only provide exceptional quality but also efficiency, low power, and low latency, previously unattainable in software based designs. While custom hardware and Application Specific Integrated Circuit (ASIC) technologies may achieve lowlatency, low power, and real-time performance in some consumer devices, many applications require a flexible and scalable software-defined solution. The deblocking filter in H.264 encoder/decoder poses difficult implementation challenges because of heavy data dependencies and the conditional nature of the computations. Deblocking filter implementations tend to be fixed and difficult to reconfigure for different needs. The ability to scale up for higher quality requirements such as 10-bit pixel depth or a 4:2:2 chroma format often reduces the throughput of a parallel architecture designed for lower feature set. A scalable architecture for deblocking filtering, created with a massively parallel processor based solution, means that the same encoder or decoder will be deployed in a variety of applications, at different video resolutions, for different power requirements, and at higher bit-depths and better color sub sampling patterns like YUV, 4:2:2, or 4:4:4 formats. Low power, software-defined encoders/decoders may be implemented using a massively parallel processor array, like that found in HyperX technology, with 100 or more cores and distributed memory. The large number of processor elements allows the silicon device to operate more efficiently than conventional DSP or CPU technology. This software programing model for massively parallel processors offers a flexible implementation and a power efficiency close to that of ASIC solutions. This work describes a scalable parallel architecture for an H.264 compliant deblocking

Massively parallel algorithms for trace-driven cache simulations

Science.gov (United States)

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

1991-01-01

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

Massively parallel implementations of coupled-cluster methods for electron spin resonance spectra. I. Isotropic hyperfine coupling tensors in large radicals

Energy Technology Data Exchange (ETDEWEB)

Verma, Prakash; Morales, Jorge A., E-mail: jorge.morales@ttu.edu [Department of Chemistry and Biochemistry, Texas Tech University, P.O. Box 41061, Lubbock, Texas 79409-1061 (United States); Perera, Ajith [Department of Chemistry and Biochemistry, Texas Tech University, P.O. Box 41061, Lubbock, Texas 79409-1061 (United States); Department of Chemistry, Quantum Theory Project, University of Florida, Gainesville, Florida 32611 (United States)

2013-11-07

Coupled cluster (CC) methods provide highly accurate predictions of molecular properties, but their high computational cost has precluded their routine application to large systems. Fortunately, recent computational developments in the ACES III program by the Bartlett group [the OED/ERD atomic integral package, the super instruction processor, and the super instruction architecture language] permit overcoming that limitation by providing a framework for massively parallel CC implementations. In that scheme, we are further extending those parallel CC efforts to systematically predict the three main electron spin resonance (ESR) tensors (A-, g-, and D-tensors) to be reported in a series of papers. In this paper inaugurating that series, we report our new ACES III parallel capabilities that calculate isotropic hyperfine coupling constants in 38 neutral, cationic, and anionic radicals that include the {sup 11}B, {sup 17}O, {sup 9}Be, {sup 19}F, {sup 1}H, {sup 13}C, {sup 35}Cl, {sup 33}S,{sup 14}N, {sup 31}P, and {sup 67}Zn nuclei. Present parallel calculations are conducted at the Hartree-Fock (HF), second-order many-body perturbation theory [MBPT(2)], CC singles and doubles (CCSD), and CCSD with perturbative triples [CCSD(T)] levels using Roos augmented double- and triple-zeta atomic natural orbitals basis sets. HF results consistently overestimate isotropic hyperfine coupling constants. However, inclusion of electron correlation effects in the simplest way via MBPT(2) provides significant improvements in the predictions, but not without occasional failures. In contrast, CCSD results are consistently in very good agreement with experimental results. Inclusion of perturbative triples to CCSD via CCSD(T) leads to small improvements in the predictions, which might not compensate for the extra computational effort at a non-iterative N{sup 7}-scaling in CCSD(T). The importance of these accurate computations of isotropic hyperfine coupling constants to elucidate

Resolution of the neutron transport equation by massively parallel computer in the Cronos code

International Nuclear Information System (INIS)

Zardini, D.M.

1996-01-01

The feasibility of neutron transport problems parallel resolution by CRONOS code's SN module is here studied. In this report we give the first data about the parallel resolution by angular variable decomposition of the transport equation. Problems about parallel resolution by spatial variable decomposition and memory stage limits are also explained here. (author)

Massively parallel E-beam inspection: enabling next-generation patterned defect inspection for wafer and mask manufacturing

Science.gov (United States)

Malloy, Matt; Thiel, Brad; Bunday, Benjamin D.; Wurm, Stefan; Mukhtar, Maseeh; Quoi, Kathy; Kemen, Thomas; Zeidler, Dirk; Eberle, Anna Lena; Garbowski, Tomasz; Dellemann, Gregor; Peters, Jan Hendrik

2015-03-01

SEMATECH aims to identify and enable disruptive technologies to meet the ever-increasing demands of semiconductor high volume manufacturing (HVM). As such, a program was initiated in 2012 focused on high-speed e-beam defect inspection as a complement, and eventual successor, to bright field optical patterned defect inspection [1]. The primary goal is to enable a new technology to overcome the key gaps that are limiting modern day inspection in the fab; primarily, throughput and sensitivity to detect ultra-small critical defects. The program specifically targets revolutionary solutions based on massively parallel e-beam technologies, as opposed to incremental improvements to existing e-beam and optical inspection platforms. Wafer inspection is the primary target, but attention is also being paid to next generation mask inspection. During the first phase of the multi-year program multiple technologies were reviewed, a down-selection was made to the top candidates, and evaluations began on proof of concept systems. A champion technology has been selected and as of late 2014 the program has begun to move into the core technology maturation phase in order to enable eventual commercialization of an HVM system. Performance data from early proof of concept systems will be shown along with roadmaps to achieving HVM performance. SEMATECH's vision for moving from early-stage development to commercialization will be shown, including plans for development with industry leading technology providers.

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.

An efficient implementation of a backpropagation learning algorithm on quadrics parallel supercomputer

International Nuclear Information System (INIS)

Taraglio, S.; Massaioli, F.

1995-08-01

A parallel implementation of a library to build and train Multi Layer Perceptrons via the Back Propagation algorithm is presented. The target machine is the SIMD massively parallel supercomputer Quadrics. Performance measures are provided on three different machines with different number of processors, for two network examples. A sample source code is given

Radial electric field and ion parallel flow in the quasi-symmetric and Mirror configurations of HSX

Science.gov (United States)

Kumar, S. T. A.; Dobbins, T. J.; Talmadge, J. N.; Wilcox, R. S.; Anderson, D. T.

2018-05-01

The radial electric field and the ion mean parallel flow are obtained in the helically symmetric experiment stellarator from toroidal flow measurements of C+6 ion at two locations on a flux surface, using the Pfirsch–Schlüter effect. Results from the standard quasi-helically symmetric magnetic configuration are compared with those from the Mirror configuration where the quasi-symmetry is deliberately degraded using auxiliary coils. For similar injected power, the quasi-symmetric configuration is observed to have significantly lower flows while the experimental observations from the Mirror geometry are in better agreement with neoclassical calculations. Indications are that the radial electric field near the core of the quasi-symmetric configuration may be governed by non-neoclassical processes.

Massively parallel read mapping on GPUs with the q-group index and PEANUT

NARCIS (Netherlands)

J. Köster (Johannes); S. Rahmann (Sven)

2014-01-01

textabstractWe present the q-group index, a novel data structure for read mapping tailored towards graphics processing units (GPUs) with a small memory footprint and efficient parallel algorithms for querying and building. On top of the q-group index we introduce PEANUT, a highly parallel GPU-based

Parallel implementation of the PHOENIX generalized stellar atmosphere program. II. Wavelength parallelization

International Nuclear Information System (INIS)

Baron, E.; Hauschildt, Peter H.

1998-01-01

We describe an important addition to the parallel implementation of our generalized nonlocal thermodynamic equilibrium (NLTE) stellar atmosphere and radiative transfer computer program PHOENIX. In a previous paper in this series we described data and task parallel algorithms we have developed for radiative transfer, spectral line opacity, and NLTE opacity and rate calculations. These algorithms divided the work spatially or by spectral lines, that is, distributing the radial zones, individual spectral lines, or characteristic rays among different processors and employ, in addition, task parallelism for logically independent functions (such as atomic and molecular line opacities). For finite, monotonic velocity fields, the radiative transfer equation is an initial value problem in wavelength, and hence each wavelength point depends upon the previous one. However, for sophisticated NLTE models of both static and moving atmospheres needed to accurately describe, e.g., novae and supernovae, the number of wavelength points is very large (200,000 - 300,000) and hence parallelization over wavelength can lead both to considerable speedup in calculation time and the ability to make use of the aggregate memory available on massively parallel supercomputers. Here, we describe an implementation of a pipelined design for the wavelength parallelization of PHOENIX, where the necessary data from the processor working on a previous wavelength point is sent to the processor working on the succeeding wavelength point as soon as it is known. Our implementation uses a MIMD design based on a relatively small number of standard message passing interface (MPI) library calls and is fully portable between serial and parallel computers. copyright 1998 The American Astronomical Society

A visualization of null geodesics for the bonnor massive dipole

Directory of Open Access Journals (Sweden)

G. Andree Oliva Mercado

2015-08-01

Full Text Available In this work we simulate null geodesics for the Bonnor massive dipole metric by implementing a symbolic-numerical algorithm in Sage and Python. This program is also capable of visualizing in 3D, in principle, the geodesics for any given metric. Geodesics are launched from a common point, collectively forming a cone of light beams, simulating a solid-angle section of a point source in front of a massive object with a magnetic field. Parallel light beams also were considered, and their bending due to the curvature of the space-time was simulated.

Utilizing borehole electrical images to interpret lithofacies of fan-delta: A case study of Lower Triassic Baikouquan Formation in Mahu Depression, Junggar Basin, China

Directory of Open Access Journals (Sweden)

Yuan Rui

2017-11-01

Full Text Available Large-scale conglomerate fan-delta aprons were typical deposits on the slope of Mahu Depression during the Early Triassic. Without outcrops, it is difficult to study the lithofacies only by examining the limited cores from the main oil-bearing interval of the Baikouquan Formation. Borehole electrical imaging log provides abundant high-resolution geologic information that is obtainable only from real rocks previously. Referring to the lithology and sedimentary structure of cores, a case study of fan-deltas in the Lower Triassic Baikouquan Formation of the Mahu Depression presents a methodology for interpreting the complicated lithofacies utilizing borehole electrical images. Eleven types of lithologies and five types of sedimentary structures are summarized in borehole electrical images. The sediments are fining upward from gravel to silt and clay in the Baikouquan Formation. Fine-pebbles and granules are the main deposits in T1b1 and T1b2, but sandstones, siltstones and mudstones are more developed in T1b3. The main sedimentary textures are massive beddings, cross beddings and scour-and-fill structures. Parallel and horizontal beddings are more developed in T1b3 relatively. On integrated analysis of the lithology and sedimentary structure, eight lithofacies from electrical images, referred to as image lithofacies, is established for the fan-deltas. Granules to coarse-pebbles within massive beddings, granules to coarse-pebbles within cross and parallel beddings, siltstones within horizontal and massive beddings are the most developed lithofacies respectively in T1b1, T1b2 and T1b3. It indicates a gradual rise of the lake level of Mahu depression during the Early Triassic, with the fan-delta aprons retrograding towards to the margin of the basin. Therefore, the borehole electrical imaging log compensate for the limitation of cores of the Baikouquan Formation, providing an effective new approach to interpret the lithofacies of fan-delta.

Utilizing borehole electrical images to interpret lithofacies of fan-delta: A case study of Lower Triassic Baikouquan Formation in Mahu Depression, Junggar Basin, China

Science.gov (United States)

Yuan, Rui; Zhang, Changmin; Tang, Yong; Qu, Jianhua; Guo, Xudong; Sun, Yuqiu; Zhu, Rui; Zhou, Yuanquan (Nancy)

2017-11-01

Large-scale conglomerate fan-delta aprons were typical deposits on the slope of Mahu Depression during the Early Triassic. Without outcrops, it is difficult to study the lithofacies only by examining the limited cores from the main oil-bearing interval of the Baikouquan Formation. Borehole electrical imaging log provides abundant high-resolution geologic information that is obtainable only from real rocks previously. Referring to the lithology and sedimentary structure of cores, a case study of fan-deltas in the Lower Triassic Baikouquan Formation of the Mahu Depression presents a methodology for interpreting the complicated lithofacies utilizing borehole electrical images. Eleven types of lithologies and five types of sedimentary structures are summarized in borehole electrical images. The sediments are fining upward from gravel to silt and clay in the Baikouquan Formation. Fine-pebbles and granules are the main deposits in T1b1 and T1b2, but sandstones, siltstones and mudstones are more developed in T1b3. The main sedimentary textures are massive beddings, cross beddings and scour-and-fill structures. Parallel and horizontal beddings are more developed in T1b3 relatively. On integrated analysis of the lithology and sedimentary structure, eight lithofacies from electrical images, referred to as image lithofacies, is established for the fan-deltas. Granules to coarse-pebbles within massive beddings, granules to coarse-pebbles within cross and parallel beddings, siltstones within horizontal and massive beddings are the most developed lithofacies respectively in T1b1, T1b2 and T1b3. It indicates a gradual rise of the lake level of Mahu depression during the Early Triassic, with the fan-delta aprons retrograding towards to the margin of the basin. Therefore, the borehole electrical imaging log compensate for the limitation of cores of the Baikouquan Formation, providing an effective new approach to interpret the lithofacies of fan-delta.

Advanced computer techniques for inverse modeling of electric current in cardiac tissue

Energy Technology Data Exchange (ETDEWEB)

Hutchinson, S.A.; Romero, L.A.; Diegert, C.F.

1996-08-01

For many years, ECG`s and vector cardiograms have been the tools of choice for non-invasive diagnosis of cardiac conduction problems, such as found in reentrant tachycardia or Wolff-Parkinson-White (WPW) syndrome. Through skillful analysis of these skin-surface measurements of cardiac generated electric currents, a physician can deduce the general location of heart conduction irregularities. Using a combination of high-fidelity geometry modeling, advanced mathematical algorithms and massively parallel computing, Sandia`s approach would provide much more accurate information and thus allow the physician to pinpoint the source of an arrhythmia or abnormal conduction pathway.

A task parallel implementation of fast multipole methods

KAUST Repository

Taura, Kenjiro

2012-11-01

This paper describes a task parallel implementation of ExaFMM, an open source implementation of fast multipole methods (FMM), using a lightweight task parallel library MassiveThreads. Although there have been many attempts on parallelizing FMM, experiences have almost exclusively been limited to formulation based on flat homogeneous parallel loops. FMM in fact contains operations that cannot be readily expressed in such conventional but restrictive models. We show that task parallelism, or parallel recursions in particular, allows us to parallelize all operations of FMM naturally and scalably. Moreover it allows us to parallelize a \\'\\'mutual interaction\\'\\' for force/potential evaluation, which is roughly twice as efficient as a more conventional, unidirectional force/potential evaluation. The net result is an open source FMM that is clearly among the fastest single node implementations, including those on GPUs; with a million particles on a 32 cores Sandy Bridge 2.20GHz node, it completes a single time step including tree construction and force/potential evaluation in 65 milliseconds. The study clearly showcases both programmability and performance benefits of flexible parallel constructs over more monolithic parallel loops. © 2012 IEEE.

Torque Split Strategy for Parallel Hybrid Electric Vehicles with an Integrated Starter Generator

Directory of Open Access Journals (Sweden)

Zhumu Fu

2014-01-01

Full Text Available This paper presents a torque split strategy for parallel hybrid electric vehicles with an integrated starter generator (ISG-PHEV by using fuzzy logic control. By combining the efficiency map and the optimum torque curve of the internal combustion engine (ICE with the state of charge (SOC of the batteries, the torque split strategy is designed, which manages the ICE within its peak efficiency region. Taking the quantified ICE torque, the quantified SOC of the batteries, and the quantified ICE speed as inputs, and regarding the output torque demanded on the ICE as an output, a fuzzy logic controller (FLC with relevant fuzzy rules has been developed to determine the optimal torque distribution among the ICE, the ISG, and the electric motor/generator (EMG effectively. The simulation results reveal that, compared with the conventional torque control strategy which uses rule-based controller (RBC in different driving cycles, the proposed FLC improves the fuel economy of the ISG-PHEV, increases the efficiency of the ICE, and maintains batteries SOC within its operation range more availably.

Feasibility studies for a high energy physics MC program on massive parallel platforms

International Nuclear Information System (INIS)

Bertolotto, L.M.; Peach, K.J.; Apostolakis, J.; Bruschini, C.E.; Calafiura, P.; Gagliardi, F.; Metcalf, M.; Norton, A.; Panzer-Steindel, B.

1994-01-01

The parallelization of a Monte Carlo program for the NA48 experiment is presented. As a first step, a task farming structure was realized. Based on this, a further step, making use of a distributed database for showers in the electro-magnetic calorimeter, was implemented. Further possibilities for using parallel processing for a quasi-real time calibration of the calorimeter are described

Molecular diagnosis of glycogen storage disease and disorders with overlapping clinical symptoms by massive parallel sequencing.

Science.gov (United States)

Vega, Ana I; Medrano, Celia; Navarrete, Rosa; Desviat, Lourdes R; Merinero, Begoña; Rodríguez-Pombo, Pilar; Vitoria, Isidro; Ugarte, Magdalena; Pérez-Cerdá, Celia; Pérez, Belen

2016-10-01

Glycogen storage disease (GSD) is an umbrella term for a group of genetic disorders that involve the abnormal metabolism of glycogen; to date, 23 types of GSD have been identified. The nonspecific clinical presentation of GSD and the lack of specific biomarkers mean that Sanger sequencing is now widely relied on for making a diagnosis. However, this gene-by-gene sequencing technique is both laborious and costly, which is a consequence of the number of genes to be sequenced and the large size of some genes. This work reports the use of massive parallel sequencing to diagnose patients at our laboratory in Spain using either a customized gene panel (targeted exome sequencing) or the Illumina Clinical-Exome TruSight One Gene Panel (clinical exome sequencing (CES)). Sequence variants were matched against biochemical and clinical hallmarks. Pathogenic mutations were detected in 23 patients. Twenty-two mutations were recognized (mostly loss-of-function mutations), including 11 that were novel in GSD-associated genes. In addition, CES detected five patients with mutations in ALDOB, LIPA, NKX2-5, CPT2, or ANO5. Although these genes are not involved in GSD, they are associated with overlapping phenotypic characteristics such as hepatic, muscular, and cardiac dysfunction. These results show that next-generation sequencing, in combination with the detection of biochemical and clinical hallmarks, provides an accurate, high-throughput means of making genetic diagnoses of GSD and related diseases.Genet Med 18 10, 1037-1043.

Comprehensive microRNA profiling in B-cells of human centenarians by massively parallel sequencing

Directory of Open Access Journals (Sweden)

Gombar Saurabh

2012-07-01

Full Text Available Abstract Background MicroRNAs (miRNAs are small, non-coding RNAs that regulate gene expression and play a critical role in development, homeostasis, and disease. Despite their demonstrated roles in age-associated pathologies, little is known about the role of miRNAs in human aging and longevity. Results We employed massively parallel sequencing technology to identify miRNAs expressed in B-cells from Ashkenazi Jewish centenarians, i.e., those living to a hundred and a human model of exceptional longevity, and younger controls without a family history of longevity. With data from 26.7 million reads comprising 9.4 × 108 bp from 3 centenarian and 3 control individuals, we discovered a total of 276 known miRNAs and 8 unknown miRNAs ranging several orders of magnitude in expression levels, a typical characteristics of saturated miRNA-sequencing. A total of 22 miRNAs were found to be significantly upregulated, with only 2 miRNAs downregulated, in centenarians as compared to controls. Gene Ontology analysis of the predicted and validated targets of the 24 differentially expressed miRNAs indicated enrichment of functional pathways involved in cell metabolism, cell cycle, cell signaling, and cell differentiation. A cross sectional expression analysis of the differentially expressed miRNAs in B-cells from Ashkenazi Jewish individuals between the 50th and 100th years of age indicated that expression levels of miR-363* declined significantly with age. Centenarians, however, maintained the youthful expression level. This result suggests that miR-363* may be a candidate longevity-associated miRNA. Conclusion Our comprehensive miRNA data provide a resource for further studies to identify genetic pathways associated with aging and longevity in humans.

Towards Interactive Visual Exploration of Parallel Programs using a Domain-Specific Language

KAUST Repository

Klein, Tobias; Bruckner, Stefan; Grö ller, M. Eduard; Hadwiger, Markus; Rautek, Peter

2016-01-01

The use of GPUs and the massively parallel computing paradigm have become wide-spread. We describe a framework for the interactive visualization and visual analysis of the run-time behavior of massively parallel programs, especially OpenCL kernels. This facilitates understanding a program's function and structure, finding the causes of possible slowdowns, locating program bugs, and interactively exploring and visually comparing different code variants in order to improve performance and correctness. Our approach enables very specific, user-centered analysis, both in terms of the recording of the run-time behavior and the visualization itself. Instead of having to manually write instrumented code to record data, simple code annotations tell the source-to-source compiler which code instrumentation to generate automatically. The visualization part of our framework then enables the interactive analysis of kernel run-time behavior in a way that can be very specific to a particular problem or optimization goal, such as analyzing the causes of memory bank conflicts or understanding an entire parallel algorithm.

Towards Interactive Visual Exploration of Parallel Programs using a Domain-Specific Language

KAUST Repository

Klein, Tobias

2016-04-19

The use of GPUs and the massively parallel computing paradigm have become wide-spread. We describe a framework for the interactive visualization and visual analysis of the run-time behavior of massively parallel programs, especially OpenCL kernels. This facilitates understanding a program\\'s function and structure, finding the causes of possible slowdowns, locating program bugs, and interactively exploring and visually comparing different code variants in order to improve performance and correctness. Our approach enables very specific, user-centered analysis, both in terms of the recording of the run-time behavior and the visualization itself. Instead of having to manually write instrumented code to record data, simple code annotations tell the source-to-source compiler which code instrumentation to generate automatically. The visualization part of our framework then enables the interactive analysis of kernel run-time behavior in a way that can be very specific to a particular problem or optimization goal, such as analyzing the causes of memory bank conflicts or understanding an entire parallel algorithm.

Ultrascalable petaflop parallel supercomputer

Science.gov (United States)

Blumrich, Matthias A [Ridgefield, CT; Chen, Dong [Croton On Hudson, NY; Chiu, George [Cross River, NY; Cipolla, Thomas M [Katonah, NY; Coteus, Paul W [Yorktown Heights, NY; Gara, Alan G [Mount Kisco, NY; Giampapa, Mark E [Irvington, NY; Hall, Shawn [Pleasantville, NY; Haring, Rudolf A [Cortlandt Manor, NY; Heidelberger, Philip [Cortlandt Manor, NY; Kopcsay, Gerard V [Yorktown Heights, NY; Ohmacht, Martin [Yorktown Heights, NY; Salapura, Valentina [Chappaqua, NY; Sugavanam, Krishnan [Mahopac, NY; Takken, Todd [Brewster, NY

2010-07-20

A massively parallel supercomputer of petaOPS-scale includes node architectures based upon System-On-a-Chip technology, where each processing node comprises a single Application Specific Integrated Circuit (ASIC) having up to four processing elements. The ASIC nodes are interconnected by multiple independent networks that optimally maximize the throughput of packet communications between nodes with minimal latency. The multiple networks may include three high-speed networks for parallel algorithm message passing including a Torus, collective network, and a Global Asynchronous network that provides global barrier and notification functions. These multiple independent networks may be collaboratively or independently utilized according to the needs or phases of an algorithm for optimizing algorithm processing performance. The use of a DMA engine is provided to facilitate message passing among the nodes without the expenditure of processing resources at the node.

A Generic Mesh Data Structure with Parallel Applications

Science.gov (United States)

Cochran, William Kenneth, Jr.

2009-01-01

High performance, massively-parallel multi-physics simulations are built on efficient mesh data structures. Most data structures are designed from the bottom up, focusing on the implementation of linear algebra routines. In this thesis, we explore a top-down approach to design, evaluating the various needs of many aspects of simulation, not just…

Parallel finite elements with domain decomposition and its pre-processing

International Nuclear Information System (INIS)

Yoshida, A.; Yagawa, G.; Hamada, S.

1993-01-01

This paper describes a parallel finite element analysis using a domain decomposition method, and the pre-processing for the parallel calculation. Computer simulations are about to replace experiments in various fields, and the scale of model to be simulated tends to be extremely large. On the other hand, computational environment has drastically changed in these years. Especially, parallel processing on massively parallel computers or computer networks is considered to be promising techniques. In order to achieve high efficiency on such parallel computation environment, large granularity of tasks, a well-balanced workload distribution are key issues. It is also important to reduce the cost of pre-processing in such parallel FEM. From the point of view, the authors developed the domain decomposition FEM with the automatic and dynamic task-allocation mechanism and the automatic mesh generation/domain subdivision system for it. (author)

Solution of the within-group multidimensional discrete ordinates transport equations on massively parallel architectures

Science.gov (United States)

Zerr, Robert Joseph

2011-12-01

The integral transport matrix method (ITMM) has been used as the kernel of new parallel solution methods for the discrete ordinates approximation of the within-group neutron transport equation. The ITMM abandons the repetitive mesh sweeps of the traditional source iterations (SI) scheme in favor of constructing stored operators that account for the direct coupling factors among all the cells and between the cells and boundary surfaces. The main goals of this work were to develop the algorithms that construct these operators and employ them in the solution process, determine the most suitable way to parallelize the entire procedure, and evaluate the behavior and performance of the developed methods for increasing number of processes. This project compares the effectiveness of the ITMM with the SI scheme parallelized with the Koch-Baker-Alcouffe (KBA) method. The primary parallel solution method involves a decomposition of the domain into smaller spatial sub-domains, each with their own transport matrices, and coupled together via interface boundary angular fluxes. Each sub-domain has its own set of ITMM operators and represents an independent transport problem. Multiple iterative parallel solution methods have investigated, including parallel block Jacobi (PBJ), parallel red/black Gauss-Seidel (PGS), and parallel GMRES (PGMRES). The fastest observed parallel solution method, PGS, was used in a weak scaling comparison with the PARTISN code. Compared to the state-of-the-art SI-KBA with diffusion synthetic acceleration (DSA), this new method without acceleration/preconditioning is not competitive for any problem parameters considered. The best comparisons occur for problems that are difficult for SI DSA, namely highly scattering and optically thick. SI DSA execution time curves are generally steeper than the PGS ones. However, until further testing is performed it cannot be concluded that SI DSA does not outperform the ITMM with PGS even on several thousand or tens of

An efficient parallel algorithm for matrix-vector multiplication

Energy Technology Data Exchange (ETDEWEB)

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

1993-03-01

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

Efficient numerical methods for fluid- and electrodynamics on massively parallel systems

Energy Technology Data Exchange (ETDEWEB)

Zudrop, Jens

2016-07-01

In the last decade, computer technology has evolved rapidly. Modern high performance computing systems offer a tremendous amount of computing power in the range of a few peta floating point operations per second. In contrast, numerical software development is much slower and most existing simulation codes cannot exploit the full computing power of these systems. Partially, this is due to the numerical methods themselves and partially it is related to bottlenecks within the parallelization concept and its data structures. The goal of the thesis is the development of numerical algorithms and corresponding data structures to remedy both kinds of parallelization bottlenecks. The approach is based on a co-design of the numerical schemes (including numerical analysis) and their realizations in algorithms and software. Various kinds of applications, from multicomponent flows (Lattice Boltzmann Method) to electrodynamics (Discontinuous Galerkin Method) to embedded geometries (Octree), are considered and efficiency of the developed approaches is demonstrated for large scale simulations.

Parallelized event chain algorithm for dense hard sphere and polymer systems

International Nuclear Information System (INIS)

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

2015-01-01

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

Facilitating arrhythmia simulation: the method of quantitative cellular automata modeling and parallel running

Directory of Open Access Journals (Sweden)

Mondry Adrian

2004-08-01

Full Text Available Abstract Background Many arrhythmias are triggered by abnormal electrical activity at the ionic channel and cell level, and then evolve spatio-temporally within the heart. To understand arrhythmias better and to diagnose them more precisely by their ECG waveforms, a whole-heart model is required to explore the association between the massively parallel activities at the channel/cell level and the integrative electrophysiological phenomena at organ level. Methods We have developed a method to build large-scale electrophysiological models by using extended cellular automata, and to run such models on a cluster of shared memory machines. We describe here the method, including the extension of a language-based cellular automaton to implement quantitative computing, the building of a whole-heart model with Visible Human Project data, the parallelization of the model on a cluster of shared memory computers with OpenMP and MPI hybrid programming, and a simulation algorithm that links cellular activity with the ECG. Results We demonstrate that electrical activities at channel, cell, and organ levels can be traced and captured conveniently in our extended cellular automaton system. Examples of some ECG waveforms simulated with a 2-D slice are given to support the ECG simulation algorithm. A performance evaluation of the 3-D model on a four-node cluster is also given. Conclusions Quantitative multicellular modeling with extended cellular automata is a highly efficient and widely applicable method to weave experimental data at different levels into computational models. This process can be used to investigate complex and collective biological activities that can be described neither by their governing differentiation equations nor by discrete parallel computation. Transparent cluster computing is a convenient and effective method to make time-consuming simulation feasible. Arrhythmias, as a typical case, can be effectively simulated with the methods

Distributed Parallel Endmember Extraction of Hyperspectral Data Based on Spark

Directory of Open Access Journals (Sweden)

Zebin Wu

2016-01-01

Full Text Available Due to the increasing dimensionality and volume of remotely sensed hyperspectral data, the development of acceleration techniques for massive hyperspectral image analysis approaches is a very important challenge. Cloud computing offers many possibilities of distributed processing of hyperspectral datasets. This paper proposes a novel distributed parallel endmember extraction method based on iterative error analysis that utilizes cloud computing principles to efficiently process massive hyperspectral data. The proposed method takes advantage of technologies including MapReduce programming model, Hadoop Distributed File System (HDFS, and Apache Spark to realize distributed parallel implementation for hyperspectral endmember extraction, which significantly accelerates the computation of hyperspectral processing and provides high throughput access to large hyperspectral data. The experimental results, which are obtained by extracting endmembers of hyperspectral datasets on a cloud computing platform built on a cluster, demonstrate the effectiveness and computational efficiency of the proposed method.

ESPRIT-Forest: Parallel clustering of massive amplicon sequence data in subquadratic time.

Science.gov (United States)

Cai, Yunpeng; Zheng, Wei; Yao, Jin; Yang, Yujie; Mai, Volker; Mao, Qi; Sun, Yijun

2017-04-01

The rapid development of sequencing technology has led to an explosive accumulation of genomic sequence data. Clustering is often the first step to perform in sequence analysis, and hierarchical clustering is one of the most commonly used approaches for this purpose. However, it is currently computationally expensive to perform hierarchical clustering of extremely large sequence datasets due to its quadratic time and space complexities. In this paper we developed a new algorithm called ESPRIT-Forest for parallel hierarchical clustering of sequences. The algorithm achieves subquadratic time and space complexity and maintains a high clustering accuracy comparable to the standard method. The basic idea is to organize sequences into a pseudo-metric based partitioning tree for sub-linear time searching of nearest neighbors, and then use a new multiple-pair merging criterion to construct clusters in parallel using multiple threads. The new algorithm was tested on the human microbiome project (HMP) dataset, currently one of the largest published microbial 16S rRNA sequence dataset. Our experiment demonstrated that with the power of parallel computing it is now compu- tationally feasible to perform hierarchical clustering analysis of tens of millions of sequences. The software is available at http://www.acsu.buffalo.edu/∼yijunsun/lab/ESPRIT-Forest.html.

Parallel preconditioning techniques for sparse CG solvers

Energy Technology Data Exchange (ETDEWEB)

Basermann, A.; Reichel, B.; Schelthoff, C. [Central Institute for Applied Mathematics, Juelich (Germany)

1996-12-31

Conjugate gradient (CG) methods to solve sparse systems of linear equations play an important role in numerical methods for solving discretized partial differential equations. The large size and the condition of many technical or physical applications in this area result in the need for efficient parallelization and preconditioning techniques of the CG method. In particular for very ill-conditioned matrices, sophisticated preconditioner are necessary to obtain both acceptable convergence and accuracy of CG. Here, we investigate variants of polynomial and incomplete Cholesky preconditioners that markedly reduce the iterations of the simply diagonally scaled CG and are shown to be well suited for massively parallel machines.

Massively parallel sequencing and targeted exomes in familial kidney disease can diagnose underlying genetic disorders.

Science.gov (United States)

Mallett, Andrew J; McCarthy, Hugh J; Ho, Gladys; Holman, Katherine; Farnsworth, Elizabeth; Patel, Chirag; Fletcher, Jeffery T; Mallawaarachchi, Amali; Quinlan, Catherine; Bennetts, Bruce; Alexander, Stephen I

2017-12-01

Inherited kidney disease encompasses a broad range of disorders, with both multiple genes contributing to specific phenotypes and single gene defects having multiple clinical presentations. Advances in sequencing capacity may allow a genetic diagnosis for familial renal disease, by testing the increasing number of known causative genes. However, there has been limited translation of research findings of causative genes into clinical settings. Here, we report the results of a national accredited diagnostic genetic service for familial renal disease. An expert multidisciplinary team developed a targeted exomic sequencing approach with ten curated multigene panels (207 genes) and variant assessment individualized to the patient's phenotype. A genetic diagnosis (pathogenic genetic variant[s]) was identified in 58 of 135 families referred in two years. The genetic diagnosis rate was similar between families with a pediatric versus adult proband (46% vs 40%), although significant differences were found in certain panels such as atypical hemolytic uremic syndrome (88% vs 17%). High diagnostic rates were found for Alport syndrome (22 of 27) and tubular disorders (8 of 10), whereas the monogenic diagnostic rate for congenital anomalies of the kidney and urinary tract was one of 13. Quality reporting was aided by a strong clinical renal and genetic multidisciplinary committee review. Importantly, for a diagnostic service, few variants of uncertain significance were found with this targeted, phenotype-based approach. Thus, use of targeted massively parallel sequencing approaches in inherited kidney disease has a significant capacity to diagnose the underlying genetic disorder across most renal phenotypes. Copyright © 2017 International Society of Nephrology. Published by Elsevier Inc. All rights reserved.

Genomic Characterization of Non–Small-Cell Lung Cancer in African Americans by Targeted Massively Parallel Sequencing

Science.gov (United States)

Araujo, Luiz H.; Timmers, Cynthia; Bell, Erica Hlavin; Shilo, Konstantin; Lammers, Philip E.; Zhao, Weiqiang; Natarajan, Thanemozhi G.; Miller, Clinton J.; Zhang, Jianying; Yilmaz, Ayse S.; Liu, Tom; Coombes, Kevin; Amann, Joseph; Carbone, David P.

2015-01-01

Purpose Technologic advances have enabled the comprehensive analysis of genetic perturbations in non–small-cell lung cancer (NSCLC); however, African Americans have often been underrepresented in these studies. This ethnic group has higher lung cancer incidence and mortality rates, and some studies have suggested a lower incidence of epidermal growth factor receptor mutations. Herein, we report the most in-depth molecular profile of NSCLC in African Americans to date. Methods A custom panel was designed to cover the coding regions of 81 NSCLC-related genes and 40 ancestry-informative markers. Clinical samples were sequenced on a massively parallel sequencing instrument, and anaplastic lymphoma kinase translocation was evaluated by fluorescent in situ hybridization. Results The study cohort included 99 patients (61% males, 94% smokers) comprising 31 squamous and 68 nonsquamous cell carcinomas. We detected 227 nonsilent variants in the coding sequence, including 24 samples with nonoverlapping, classic driver alterations. The frequency of driver mutations was not significantly different from that of whites, and no association was found between genetic ancestry and the presence of somatic mutations. Copy number alteration analysis disclosed distinguishable amplifications in the 3q chromosome arm in squamous cell carcinomas and pointed toward a handful of targetable alterations. We also found frequent SMARCA4 mutations and protein loss, mostly in driver-negative tumors. Conclusion Our data suggest that African American ancestry may not be significantly different from European/white background for the presence of somatic driver mutations in NSCLC. Furthermore, we demonstrated that using a comprehensive genotyping approach could identify numerous targetable alterations, with potential impact on therapeutic decisions. PMID:25918285

A massively parallel sequencing approach uncovers ancient origins and high genetic variability of endangered Przewalski's horses.

Science.gov (United States)

Goto, Hiroki; Ryder, Oliver A; Fisher, Allison R; Schultz, Bryant; Kosakovsky Pond, Sergei L; Nekrutenko, Anton; Makova, Kateryna D

2011-01-01

The endangered Przewalski's horse is the closest relative of the domestic horse and is the only true wild horse species surviving today. The question of whether Przewalski's horse is the direct progenitor of domestic horse has been hotly debated. Studies of DNA diversity within Przewalski's horses have been sparse but are urgently needed to ensure their successful reintroduction to the wild. In an attempt to resolve the controversy surrounding the phylogenetic position and genetic diversity of Przewalski's horses, we used massively parallel sequencing technology to decipher the complete mitochondrial and partial nuclear genomes for all four surviving maternal lineages of Przewalski's horses. Unlike single-nucleotide polymorphism (SNP) typing usually affected by ascertainment bias, the present method is expected to be largely unbiased. Three mitochondrial haplotypes were discovered-two similar ones, haplotypes I/II, and one substantially divergent from the other two, haplotype III. Haplotypes I/II versus III did not cluster together on a phylogenetic tree, rejecting the monophyly of Przewalski's horse maternal lineages, and were estimated to split 0.117-0.186 Ma, significantly preceding horse domestication. In the phylogeny based on autosomal sequences, Przewalski's horses formed a monophyletic clade, separate from the Thoroughbred domestic horse lineage. Our results suggest that Przewalski's horses have ancient origins and are not the direct progenitors of domestic horses. The analysis of the vast amount of sequence data presented here suggests that Przewalski's and domestic horse lineages diverged at least 0.117 Ma but since then have retained ancestral genetic polymorphism and/or experienced gene flow.

Parameters Design for a Parallel Hybrid Electric Bus Using Regenerative Brake Model

Directory of Open Access Journals (Sweden)

Zilin Ma

2014-01-01

Full Text Available A design methodology which uses the regenerative brake model is introduced to determine the major system parameters of a parallel electric hybrid bus drive train. Hybrid system parameters mainly include the power rating of internal combustion engine (ICE, gear ratios of transmission, power rating, and maximal torque of motor, power, and capacity of battery. The regenerative model is built in the vehicle model to estimate the regenerative energy in the real road conditions. The design target is to ensure that the vehicle meets the specified vehicle performance, such as speed and acceleration, and at the same time, operates the ICE within an expected speed range. Several pairs of parameters are selected from the result analysis, and the fuel saving result in the road test shows that a 25% reduction is achieved in fuel consumption.

Mapping robust parallel multigrid algorithms to scalable memory architectures

Science.gov (United States)

Overman, Andrea; Vanrosendale, John

1993-01-01

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

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.

A Novel Algorithm for Solving the Multidimensional Neutron Transport Equation on Massively Parallel Architectures

Energy Technology Data Exchange (ETDEWEB)

Azmy, Yousry

2014-06-10

We employ the Integral Transport Matrix Method (ITMM) as the kernel of new parallel solution methods for the discrete ordinates approximation of the within-group neutron transport equation. The ITMM abandons the repetitive mesh sweeps of the traditional source iterations (SI) scheme in favor of constructing stored operators that account for the direct coupling factors among all the cells' fluxes and between the cells' and boundary surfaces' fluxes. The main goals of this work are to develop the algorithms that construct these operators and employ them in the solution process, determine the most suitable way to parallelize the entire procedure, and evaluate the behavior and parallel performance of the developed methods with increasing number of processes, P. The fastest observed parallel solution method, Parallel Gauss-Seidel (PGS), was used in a weak scaling comparison with the PARTISN transport code, which uses the source iteration (SI) scheme parallelized with the Koch-baker-Alcouffe (KBA) method. Compared to the state-of-the-art SI-KBA with diffusion synthetic acceleration (DSA), this new method- even without acceleration/preconditioning-is completitive for optically thick problems as P is increased to the tens of thousands range. For the most optically thick cells tested, PGS reduced execution time by an approximate factor of three for problems with more than 130 million computational cells on P = 32,768. Moreover, the SI-DSA execution times's trend rises generally more steeply with increasing P than the PGS trend. Furthermore, the PGS method outperforms SI for the periodic heterogeneous layers (PHL) configuration problems. The PGS method outperforms SI and SI-DSA on as few as P = 16 for PHL problems and reduces execution time by a factor of ten or more for all problems considered with more than 2 million computational cells on P = 4.096.

Tiling as a Durable Abstraction for Parallelism and Data Locality

Energy Technology Data Exchange (ETDEWEB)

Unat, Didem [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Chan, Cy P. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Zhang, Weiqun [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Bell, John [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Shalf, John [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

2013-11-18

Tiling is a useful loop transformation for expressing parallelism and data locality. Automated tiling transformations that preserve data-locality are increasingly important due to hardware trends towards massive parallelism and the increasing costs of data movement relative to the cost of computing. We propose TiDA as a durable tiling abstraction that centralizes parameterized tiling information within array data types with minimal changes to the source code. The data layout information can be used by the compiler and runtime to automatically manage parallelism, optimize data locality, and schedule tasks intelligently. In this study, we present the design features and early interface of TiDA along with some preliminary results.

Parallel Implicit Algorithms for CFD

Science.gov (United States)

Keyes, David E.

1998-01-01

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

Recent progress in 3D EM/EM-PIC simulation with ARGUS and parallel ARGUS

International Nuclear Information System (INIS)

Mankofsky, A.; Petillo, J.; Krueger, W.; Mondelli, A.; McNamara, B.; Philp, R.

1994-01-01

ARGUS is an integrated, 3-D, volumetric simulation model for systems involving electric and magnetic fields and charged particles, including materials embedded in the simulation region. The code offers the capability to carry out time domain and frequency domain electromagnetic simulations of complex physical systems. ARGUS offers a boolean solid model structure input capability that can include essentially arbitrary structures on the computational domain, and a modular architecture that allows multiple physics packages to access the same data structure and to share common code utilities. Physics modules are in place to compute electrostatic and electromagnetic fields, the normal modes of RF structures, and self-consistent particle-in-cell (PIC) simulation in either a time dependent mode or a steady state mode. The PIC modules include multiple particle species, the Lorentz equations of motion, and algorithms for the creation of particles by emission from material surfaces, injection onto the grid, and ionization. In this paper, we present an updated overview of ARGUS, with particular emphasis given in recent algorithmic and computational advances. These include a completely rewritten frequency domain solver which efficiently treats lossy materials and periodic structures, a parallel version of ARGUS with support for both shared memory parallel vector (i.e. CRAY) machines and distributed memory massively parallel MIMD systems, and numerous new applications of the code

Map-Based Power-Split Strategy Design with Predictive Performance Optimization for Parallel Hybrid Electric Vehicles

Directory of Open Access Journals (Sweden)

Jixiang Fan

2015-09-01

Full Text Available In this paper, a map-based optimal energy management strategy is proposed to improve the consumption economy of a plug-in parallel hybrid electric vehicle. In the design of the maps, which provide both the torque split between engine and motor and the gear shift, not only the current vehicle speed and power demand, but also the optimality based on the predicted trajectory of vehicle dynamics are considered. To seek the optimality, the equivalent consumption, which trades off the fuel and electricity usages, is chosen as the cost function. Moreover, in order to decrease the model errors in the process of optimization conducted in the discrete time domain, the variational integrator is employed to calculate the evolution of the vehicle dynamics. To evaluate the proposed energy management strategy, the simulation results performed on a professional GT-Suit simulator are demonstrated and the comparison to a real-time optimization method is also given to show the advantage of the proposed off-line optimization approach.

Big Data GPU-Driven Parallel Processing Spatial and Spatio-Temporal Clustering Algorithms

Science.gov (United States)

Konstantaras, Antonios; Skounakis, Emmanouil; Kilty, James-Alexander; Frantzeskakis, Theofanis; Maravelakis, Emmanuel

2016-04-01

Advances in graphics processing units' technology towards encompassing parallel architectures [1], comprised of thousands of cores and multiples of parallel threads, provide the foundation in terms of hardware for the rapid processing of various parallel applications regarding seismic big data analysis. Seismic data are normally stored as collections of vectors in massive matrices, growing rapidly in size as wider areas are covered, denser recording networks are being established and decades of data are being compiled together [2]. Yet, many processes regarding seismic data analysis are performed on each seismic event independently or as distinct tiles [3] of specific grouped seismic events within a much larger data set. Such processes, independent of one another can be performed in parallel narrowing down processing times drastically [1,3]. This research work presents the development and implementation of three parallel processing algorithms using Cuda C [4] for the investigation of potentially distinct seismic regions [5,6] present in the vicinity of the southern Hellenic seismic arc. The algorithms, programmed and executed in parallel comparatively, are the: fuzzy k-means clustering with expert knowledge [7] in assigning overall clusters' number; density-based clustering [8]; and a selves-developed spatio-temporal clustering algorithm encompassing expert [9] and empirical knowledge [10] for the specific area under investigation. Indexing terms: GPU parallel programming, Cuda C, heterogeneous processing, distinct seismic regions, parallel clustering algorithms, spatio-temporal clustering References [1] Kirk, D. and Hwu, W.: 'Programming massively parallel processors - A hands-on approach', 2nd Edition, Morgan Kaufman Publisher, 2013 [2] Konstantaras, A., Valianatos, F., Varley, M.R. and Makris, J.P.: 'Soft-Computing Modelling of Seismicity in the Southern Hellenic Arc', Geoscience and Remote Sensing Letters, vol. 5 (3), pp. 323-327, 2008 [3] Papadakis, S. and

Gene discovery using massively parallel pyrosequencing to develop ESTs for the flesh fly Sarcophaga crassipalpis

Directory of Open Access Journals (Sweden)

Hahn Daniel A

2009-05-01

Full Text Available Abstract Background Flesh flies in the genus Sarcophaga are important models for investigating endocrinology, diapause, cold hardiness, reproduction, and immunity. Despite the prominence of Sarcophaga flesh flies as models for insect physiology and biochemistry, and in forensic studies, little genomic or transcriptomic data are available for members of this genus. We used massively parallel pyrosequencing on the Roche 454-FLX platform to produce a substantial EST dataset for the flesh fly Sarcophaga crassipalpis. To maximize sequence diversity, we pooled RNA extracted from whole bodies of all life stages and normalized the cDNA pool after reverse transcription. Results We obtained 207,110 ESTs with an average read length of 241 bp. These reads assembled into 20,995 contigs and 31,056 singletons. Using BLAST searches of the NR and NT databases we were able to identify 11,757 unique gene elements (ES. crassipalpis unigenes among GO Biological Process functional groups with that of the Drosophila melanogaster transcriptome suggests that our ESTs are broadly representative of the flesh fly transcriptome. Insertion and deletion errors in 454 sequencing present a serious hurdle to comparative transcriptome analysis. Aided by a new approach to correcting for these errors, we performed a comparative analysis of genetic divergence across GO categories among S. crassipalpis, D. melanogaster, and Anopheles gambiae. The results suggest that non-synonymous substitutions occur at similar rates across categories, although genes related to response to stimuli may evolve slightly faster. In addition, we identified over 500 potential microsatellite loci and more than 12,000 SNPs among our ESTs. Conclusion Our data provides the first large-scale EST-project for flesh flies, a much-needed resource for exploring this model species. In addition, we identified a large number of potential microsatellite and SNP markers that could be used in population and systematic

Sampling the Denatured State of Polypeptides in Water, Urea, and Guanidine Chloride to Strict Equilibrium Conditions with the Help of Massively Parallel Computers.

Science.gov (United States)

Meloni, Roberto; Camilloni, Carlo; Tiana, Guido

2014-02-11

The denatured state of polypeptides and proteins, stabilized by chemical denaturants like urea and guanidine chloride, displays residual secondary structure when studied by nuclear-magnetic-resonance spectroscopy. However, these experimental techniques are weakly sensitive, and thus molecular-dynamics simulations can be useful to complement the experimental findings. To sample the denatured state, we made use of massively-parallel computers and of a variant of the replica exchange algorithm, in which the different branches, connected with unbiased replicas, favor the formation and disruption of local secondary structure. The algorithm is applied to the second hairpin of GB1 in water, in urea, and in guanidine chloride. We show with the help of different criteria that the simulations converge to equilibrium. It results that urea and guanidine chloride, besides inducing some polyproline-II structure, have different effect on the hairpin. Urea disrupts completely the native region and stabilizes a state which resembles a random coil, while guanidine chloride has a milder effect.

New adaptive differencing strategy in the PENTRAN 3-d parallel Sn code

International Nuclear Information System (INIS)

Sjoden, G.E.; Haghighat, A.

1996-01-01

It is known that three-dimensional (3-D) discrete ordinates (S n ) transport problems require an immense amount of storage and computational effort to solve. For this reason, parallel codes that offer a capability to completely decompose the angular, energy, and spatial domains among a distributed network of processors are required. One such code recently developed is PENTRAN, which iteratively solves 3-D multi-group, anisotropic S n problems on distributed-memory platforms, such as the IBM-SP2. Because large problems typically contain several different material zones with various properties, available differencing schemes should automatically adapt to the transport physics in each material zone. To minimize the memory and message-passing overhead required for massively parallel S n applications, available differencing schemes in an adaptive strategy should also offer reasonable accuracy and positivity, yet require only the zeroth spatial moment of the transport equation; differencing schemes based on higher spatial moments, in spite of their greater accuracy, require at least twice the amount of storage and communication cost for implementation in a massively parallel transport code. This paper discusses a new adaptive differencing strategy that uses increasingly accurate schemes with low parallel memory and communication overhead. This strategy, implemented in PENTRAN, includes a new scheme, exponential directional averaged (EDA) differencing

GPU Parallel Bundle Block Adjustment

Directory of Open Access Journals (Sweden)

ZHENG Maoteng

2017-09-01

Full Text Available To deal with massive data in photogrammetry, we introduce the GPU parallel computing technology. The preconditioned conjugate gradient and inexact Newton method are also applied to decrease the iteration times while solving the normal equation. A brand new workflow of bundle adjustment is developed to utilize GPU parallel computing technology. Our method can avoid the storage and inversion of the big normal matrix, and compute the normal matrix in real time. The proposed method can not only largely decrease the memory requirement of normal matrix, but also largely improve the efficiency of bundle adjustment. It also achieves the same accuracy as the conventional method. Preliminary experiment results show that the bundle adjustment of a dataset with about 4500 images and 9 million image points can be done in only 1.5 minutes while achieving sub-pixel accuracy.

Xyce parallel electronic simulator : users' guide.

Energy Technology Data Exchange (ETDEWEB)

Mei, Ting; Rankin, Eric Lamont; Thornquist, Heidi K.; Santarelli, Keith R.; Fixel, Deborah A.; Coffey, Todd Stirling; Russo, Thomas V.; Schiek, Richard Louis; Warrender, Christina E.; Keiter, Eric Richard; Pawlowski, Roger Patrick

2011-05-01

This manual describes the use of the Xyce Parallel Electronic Simulator. Xyce has been designed as a SPICE-compatible, high-performance analog circuit simulator, and has been written to support the simulation needs of the Sandia National Laboratories electrical designers. This development has focused on improving capability over the current state-of-the-art in the following areas: (1) Capability to solve extremely large circuit problems by supporting large-scale parallel computing platforms (up to thousands of processors). Note that this includes support for most popular parallel and serial computers; (2) Improved performance for all numerical kernels (e.g., time integrator, nonlinear and linear solvers) through state-of-the-art algorithms and novel techniques. (3) Device models which are specifically tailored to meet Sandia's needs, including some radiation-aware devices (for Sandia users only); and (4) Object-oriented code design and implementation using modern coding practices that ensure that the Xyce Parallel Electronic Simulator will be maintainable and extensible far into the future. Xyce is a parallel code in the most general sense of the phrase - a message passing parallel implementation - which allows it to run efficiently on the widest possible number of computing platforms. These include serial, shared-memory and distributed-memory parallel as well as heterogeneous platforms. Careful attention has been paid to the specific nature of circuit-simulation problems to ensure that optimal parallel efficiency is achieved as the number of processors grows. The development of Xyce provides a platform for computational research and development aimed specifically at the needs of the Laboratory. With Xyce, Sandia has an 'in-house' capability with which both new electrical (e.g., device model development) and algorithmic (e.g., faster time-integration methods, parallel solver algorithms) research and development can be performed. As a result, Xyce is

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

Application of massively parallel sequencing to genetic diagnosis in multiplex families with idiopathic sensorineural hearing impairment.

Directory of Open Access Journals (Sweden)

Chen-Chi Wu

Full Text Available Despite the clinical utility of genetic diagnosis to address idiopathic sensorineural hearing impairment (SNHI, the current strategy for screening mutations via Sanger sequencing suffers from the limitation that only a limited number of DNA fragments associated with common deafness mutations can be genotyped. Consequently, a definitive genetic diagnosis cannot be achieved in many families with discernible family history. To investigate the diagnostic utility of massively parallel sequencing (MPS, we applied the MPS technique to 12 multiplex families with idiopathic SNHI in which common deafness mutations had previously been ruled out. NimbleGen sequence capture array was designed to target all protein coding sequences (CDSs and 100 bp of the flanking sequence of 80 common deafness genes. We performed MPS on the Illumina HiSeq2000, and applied BWA, SAMtools, Picard, GATK, Variant Tools, ANNOVAR, and IGV for bioinformatics analyses. Initial data filtering with allele frequencies (0.95 prioritized 5 indels (insertions/deletions and 36 missense variants in the 12 multiplex families. After further validation by Sanger sequencing, segregation pattern, and evolutionary conservation of amino acid residues, we identified 4 variants in 4 different genes, which might lead to SNHI in 4 families compatible with autosomal dominant inheritance. These included GJB2 p.R75Q, MYO7A p.T381M, KCNQ4 p.S680F, and MYH9 p.E1256K. Among them, KCNQ4 p.S680F and MYH9 p.E1256K were novel. In conclusion, MPS allows genetic diagnosis in multiplex families with idiopathic SNHI by detecting mutations in relatively uncommon deafness genes.

Parallel k-means++ for Multiple Shared-Memory Architectures

Energy Technology Data Exchange (ETDEWEB)

Mackey, Patrick S.; Lewis, Robert R.

2016-09-22

In recent years k-means++ has become a popular initialization technique for improved k-means clustering. To date, most of the work done to improve its performance has involved parallelizing algorithms that are only approximations of k-means++. In this paper we present a parallelization of the exact k-means++ algorithm, with a proof of its correctness. We develop implementations for three distinct shared-memory architectures: multicore CPU, high performance GPU, and the massively multithreaded Cray XMT platform. We demonstrate the scalability of the algorithm on each platform. In addition we present a visual approach for showing which platform performed k-means++ the fastest for varying data sizes.

Parallel processing is good for your scientific codes...But massively parallel processing is so much better

International Nuclear Information System (INIS)

Thomas, B.; Domain, Ch.; Souffez, Y.; Eon-Duval, P.

1998-01-01

Harnessing the power of many computers, to solve concurrently difficult scientific problems, is one of the most innovative trend in High Performance Computing. At EDF, we have invested in parallel computing and have achieved significant results. First we improved the processing speed of strategic codes, in order to extend their scope. Then we turned to numerical simulations at the atomic scale. These computations, we never dreamt of before, provided us with a better understanding of metallurgic phenomena. More precisely we were able to trace defects in alloys that are used in nuclear power plants. (author)

Thermal Casimir effect in Kerr spacetime with quintessence and massive gravitons

Energy Technology Data Exchange (ETDEWEB)

Bezerra, V.B. [Universidade Federal da Paraiba, Departamento de Fisica, Joao Pessoa, PB (Brazil); Christiansen, H.R. [Ciencia e Tecnologia do Ceara (IFCE), Departamento de Fisica, Instituto Federal de Educacao, Sobral, CE (Brazil); Cunha, M.S. [Universidade Estadual do Ceara, Grupo de Fisica Teorica (GFT), Fortaleza, CE (Brazil); Muniz, C.R.; Tahim, M.O. [Universidade Estadual do Ceara, Faculdade de Educacao, Ciencias e Letras do Sertao Central, Quixada, CE (Brazil)

2017-11-15

Starting from an analytical expression for the Helmholtz free energy we calculate the thermal corrections to the Casimir energy density and entropy within nearby ideal parallel plates in the vacuum of a massless scalar field. Our framework is the Kerr spacetime in the presence of quintessence and massive gravitons. The high and low temperature regimes are especially analyzed in order to distinguish the main contributions. For instance, in the high temperature regime, we show that the force between the plates is repulsive and grows with both the quintessence and the massive gravitons. Regarding the Casimir entropy, our results are in agreement with the Nernst heat theorem and therefore confirm the third law of thermodynamics in the present scenario. (orig.)

"Feeling" Series and Parallel Resistances.

Science.gov (United States)

Morse, Robert A.

1993-01-01

Equipped with drinking straws and stirring straws, a teacher can help students understand how resistances in electric circuits combine in series and in parallel. Follow-up suggestions are provided. (ZWH)

Parallel Harmony Search Based Distributed Energy Resource Optimization

Energy Technology Data Exchange (ETDEWEB)

Ceylan, Oguzhan [ORNL; Liu, Guodong [ORNL; Tomsovic, Kevin [University of Tennessee, Knoxville (UTK)

2015-01-01

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

AdiosStMan: Parallelizing Casacore Table Data System using Adaptive IO System

Science.gov (United States)

Wang, R.; Harris, C.; Wicenec, A.

2016-07-01

In this paper, we investigate the Casacore Table Data System (CTDS) used in the casacore and CASA libraries, and methods to parallelize it. CTDS provides a storage manager plugin mechanism for third-party developers to design and implement their own CTDS storage managers. Having this in mind, we looked into various storage backend techniques that can possibly enable parallel I/O for CTDS by implementing new storage managers. After carrying on benchmarks showing the excellent parallel I/O throughput of the Adaptive IO System (ADIOS), we implemented an ADIOS based parallel CTDS storage manager. We then applied the CASA MSTransform frequency split task to verify the ADIOS Storage Manager. We also ran a series of performance tests to examine the I/O throughput in a massively parallel scenario.

Electrical Impedance Tomography Reconstruction Through Simulated Annealing using a New Outside-in Heuristic and GPU Parallelization

International Nuclear Information System (INIS)

Tavares, R S; Tsuzuki, M S G; Martins, T C

2012-01-01

Electrical Impedance Tomography (EIT) is an imaging technique that attempts to reconstruct the conductivity distribution inside an object from electrical currents and potentials applied and measured at its surface. The EIT reconstruction problem is approached as an optimization problem, where the difference between the simulated and measured distributions must be minimized. This optimization problem can be solved using Simulated Annealing (SA), but at a high computational cost. To reduce the computational load, it is possible to use an incomplete evaluation of the objective function. This algorithm showed to present an outside-in behavior, determining the impedance of the external elements first, similar to a layer striping algorithm. A new outside-in heuristic to make use of this property is proposed. It also presents the impact of using GPU for parallelizing matrix-vector multiplication and triangular solvers. Results with experimental data are presented. The outside-in heuristic showed to be faster when compared to the conventional SA algorithm.

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...

The electrical MHD and Hall current impact on micropolar nanofluid flow between rotating parallel plates

Science.gov (United States)

Shah, Zahir; Islam, Saeed; Gul, Taza; Bonyah, Ebenezer; Altaf Khan, Muhammad

2018-06-01

The current research aims to examine the combined effect of magnetic and electric field on micropolar nanofluid between two parallel plates in a rotating system. The nanofluid flow between two parallel plates is taken under the influence of Hall current. The flow of micropolar nanofluid has been assumed in steady state. The rudimentary governing equations have been changed to a set of differential nonlinear and coupled equations using suitable similarity variables. An optimal approach has been used to acquire the solution of the modelled problems. The convergence of the method has been shown numerically. The impact of the Skin friction on velocity profile, Nusslet number on temperature profile and Sherwood number on concentration profile have been studied. The influences of the Hall currents, rotation, Brownian motion and thermophoresis analysis of micropolar nanofluid have been mainly focused in this work. Moreover, for comprehension the physical presentation of the embedded parameters that is, coupling parameter N1 , viscosity parameter Re , spin gradient viscosity parameter N2 , rotating parameter Kr , Micropolar fluid constant N3 , magnetic parameter M , Prandtl number Pr , Thermophoretic parameter Nt , Brownian motion parameter Nb , and Schmidt number Sc have been plotted and deliberated graphically.

Effects of electric field and Coriolis force on electrohydrodynamic stability of poorly conducting couple stress parallel fluid flow in a channel

International Nuclear Information System (INIS)

Shankar, B.M.; Rudraiah, N.

2013-01-01

The linear stability of electrohydrodynamic poorly conducting couple stress viscous parallel fluid flow in a channel is studied in the presence of a non-uniform transverse electric field and Coriolis force using energy method and supplemented with Galerkin Technique. The sufficient condition for stability is obtained for sufficiently small values of the Reynolds number, R e . From this condition we show that strengthening or weakening of the stability criterion is dictated by the values of the strength of electric field, the coefficient of couple stress fluid and independent of Taylor number. In particular, it is shown that the interaction of electric field with couple stress is more effective in stabilizing the poorly conducting couple stress fluid compared to that in an ordinary Newtonian viscous fluid. (author)

Scalable parallel prefix solvers for discrete ordinates transport

International Nuclear Information System (INIS)

Pautz, S.; Pandya, T.; Adams, M.

2009-01-01

The well-known 'sweep' algorithm for inverting the streaming-plus-collision term in first-order deterministic radiation transport calculations has some desirable numerical properties. However, it suffers from parallel scaling issues caused by a lack of concurrency. The maximum degree of concurrency, and thus the maximum parallelism, grows more slowly than the problem size for sweeps-based solvers. We investigate a new class of parallel algorithms that involves recasting the streaming-plus-collision problem in prefix form and solving via cyclic reduction. This method, although computationally more expensive at low levels of parallelism than the sweep algorithm, offers better theoretical scalability properties. Previous work has demonstrated this approach for one-dimensional calculations; we show how to extend it to multidimensional calculations. Notably, for multiple dimensions it appears that this approach is limited to long-characteristics discretizations; other discretizations cannot be cast in prefix form. We implement two variants of the algorithm within the radlib/SCEPTRE transport code library at Sandia National Laboratories and show results on two different massively parallel systems. Both the 'forward' and 'symmetric' solvers behave similarly, scaling well to larger degrees of parallelism then sweeps-based solvers. We do observe some issues at the highest levels of parallelism (relative to the system size) and discuss possible causes. We conclude that this approach shows good potential for future parallel systems, but the parallel scalability will depend heavily on the architecture of the communication networks of these systems. (authors)

Streaming Parallel GPU Acceleration of Large-Scale filter-based Spiking Neural Networks

NARCIS (Netherlands)

L.P. Slazynski (Leszek); S.M. Bohte (Sander)

2012-01-01

htmlabstractThe arrival of graphics processing (GPU) cards suitable for massively parallel computing promises a↵ordable large-scale neural network simulation previously only available at supercomputing facil- ities. While the raw numbers suggest that GPUs may outperform CPUs by at least an order of

Development of parallel Fokker-Planck code ALLAp

International Nuclear Information System (INIS)

Batishcheva, A.A.; Sigmar, D.J.; Koniges, A.E.

1996-01-01

We report on our ongoing development of the 3D Fokker-Planck code ALLA for a highly collisional scrape-off-layer (SOL) plasma. A SOL with strong gradients of density and temperature in the spatial dimension is modeled. Our method is based on a 3-D adaptive grid (in space, magnitude of the velocity, and cosine of the pitch angle) and a second order conservative scheme. Note that the grid size is typically 100 x 257 x 65 nodes. It was shown in our previous work that only these capabilities make it possible to benchmark a 3D code against a spatially-dependent self-similar solution of a kinetic equation with the Landau collision term. In the present work we show results of a more precise benchmarking against the exact solutions of the kinetic equation using a new parallel code ALLAp with an improved method of parallelization and a modified boundary condition at the plasma edge. We also report first results from the code parallelization using Message Passing Interface for a Massively Parallel CRI T3D platform. We evaluate the ALLAp code performance versus the number of T3D processors used and compare its efficiency against a Work/Data Sharing parallelization scheme and a workstation version

Ion and electron injection in ionosphere and magnetosphere. Application to the parallel electric field measurement in auroral zones

International Nuclear Information System (INIS)

Pirre, M.

1982-11-01

New methods of measuring parallel electric field in auroral zones are investigated in this thesis. In the studied methods, artificial injection of ions Li + and electrons from a spacecraf is used. Measurements obtained during the ARAKS experiment are also presented. The behaviour of the ionospheric plasma located few hundred meters from a 0,5A electron beam injected in ionosphere from a rocket is studied, together with the behaviour of a Cs plasma artificially injected from the same spacecraft [fr

Beam dynamics simulations using a parallel version of PARMILA

International Nuclear Information System (INIS)

Ryne, R.D.

1996-01-01

The computer code PARMILA has been the primary tool for the design of proton and ion linacs in the United States for nearly three decades. Previously it was sufficient to perform simulations with of order 10000 particles, but recently the need to perform high resolution halo studies for next-generation, high intensity linacs has made it necessary to perform simulations with of order 100 million particles. With the advent of massively parallel computers such simulations are now within reach. Parallel computers already make it possible, for example, to perform beam dynamics calculations with tens of millions of particles, requiring over 10 GByte of core memory, in just a few hours. Also, parallel computers are becoming easier to use thanks to the availability of mature, Fortran-like languages such as Connection Machine Fortran and High Performance Fortran. We will describe our experience developing a parallel version of PARMILA and the performance of the new code

Beam dynamics simulations using a parallel version of PARMILA

International Nuclear Information System (INIS)

Ryne, Robert

1996-01-01

The computer code PARMILA has been the primary tool for the design of proton and ion linacs in the United States for nearly three decades. Previously it was sufficient to perform simulations with of order 10000 particles, but recently the need to perform high resolution halo studies for next-generation, high intensity linacs has made it necessary to perform simulations with of order 100 million particles. With the advent of massively parallel computers such simulations are now within reach. Parallel computers already make it possible, for example, to perform beam dynamics calculations with tens of millions of particles, requiring over 10 GByte of core memory, in just a few hours. Also, parallel computers are becoming easier to use thanks to the availability of mature, Fortran-like languages such as Connection Machine Fortran and High Performance Fortran. We will describe our experience developing a parallel version of PARMILA and the performance of the new code. (author)

Measurements of electron drift and diffusion properties in a large cylindrical drift chamber (TPC) with parallel electric and magnetic fields

International Nuclear Information System (INIS)

Richstein, J.

1986-01-01

This work describes measurements on the drift of electrons in gases, using the TPC90, the prototype of the ALEPH Time Projection Chamber. Tracks which were created by UV-Laser ionization have been drifted over distances of up to 1.3 m in parallel electric and magnetic fields. Electron drift properties have been systematically measured as a function of these, in several gas mixtures. (orig./HSI)

'Iconic' tracking algorithms for high energy physics using the TRAX-I massively parallel processor

International Nuclear Information System (INIS)

Vesztergombi, G.

1989-01-01

TRAX-I, a cost-effective parallel microcomputer, applying associative string processor (ASP) architecture with 16 K parallel processing elements, is being built by Aspex Microsystems Ltd. (UK). When applied to the tracking problem of very complex events with several hundred tracks, the large number of processors allows one to dedicate one or more processors to each wire (in MWPC), each pixel (in digitized images from streamer chambers or other visual detectors), or each pad (in TPC) to perform very efficient pattern recognition. Some linear tracking algorithms based on this ''ionic'' representation are presented. (orig.)

'Iconic' tracking algorithms for high energy physics using the TRAX-I massively parallel processor

International Nuclear Information System (INIS)

Vestergombi, G.

1989-11-01

TRAX-I, a cost-effective parallel microcomputer, applying Associative String Processor (ASP) architecture with 16 K parallel processing elements, is being built by Aspex Microsystems Ltd. (UK). When applied to the tracking problem of very complex events with several hundred tracks, the large number of processors allows one to dedicate one or more processors to each wire (in MWPC), each pixel (in digitized images from streamer chambers or other visual detectors), or each pad (in TPC) to perform very efficient pattern recognition. Some linear tracking algorithms based on this 'iconic' representation are presented. (orig.)

MASSIVELY PARALLEL LATENT SEMANTIC ANALYSES USING A GRAPHICS PROCESSING UNIT

Energy Technology Data Exchange (ETDEWEB)

Cavanagh, J.; Cui, S.

2009-01-01

Latent Semantic Analysis (LSA) aims to reduce the dimensions of large term-document datasets using Singular Value Decomposition. However, with the ever-expanding size of datasets, current implementations are not fast enough to quickly and easily compute the results on a standard PC. A graphics processing unit (GPU) can solve some highly parallel problems much faster than a traditional sequential processor or central processing unit (CPU). Thus, a deployable system using a GPU to speed up large-scale LSA processes would be a much more effective choice (in terms of cost/performance ratio) than using a PC cluster. Due to the GPU’s application-specifi c architecture, harnessing the GPU’s computational prowess for LSA is a great challenge. We presented a parallel LSA implementation on the GPU, using NVIDIA® Compute Unifi ed Device Architecture and Compute Unifi ed Basic Linear Algebra Subprograms software. The performance of this implementation is compared to traditional LSA implementation on a CPU using an optimized Basic Linear Algebra Subprograms library. After implementation, we discovered that the GPU version of the algorithm was twice as fast for large matrices (1 000x1 000 and above) that had dimensions not divisible by 16. For large matrices that did have dimensions divisible by 16, the GPU algorithm ran fi ve to six times faster than the CPU version. The large variation is due to architectural benefi ts of the GPU for matrices divisible by 16. It should be noted that the overall speeds for the CPU version did not vary from relative normal when the matrix dimensions were divisible by 16. Further research is needed in order to produce a fully implementable version of LSA. With that in mind, the research we presented shows that the GPU is a viable option for increasing the speed of LSA, in terms of cost/performance ratio.

Massive branes

International Nuclear Information System (INIS)

Bergshoeff, E.; Ortin, T.

1998-01-01

We investigate the effective world-volume theories of branes in a background given by (the bosonic sector of) 10-dimensional massive IIA supergravity (''''massive branes'''') and their M-theoretic origin. In the case of the solitonic 5-brane of type IIA superstring theory the construction of the Wess-Zumino term in the world-volume action requires a dualization of the massive Neveu-Schwarz/Neveu-Schwarz target space 2-form field. We find that, in general, the effective world-volume theory of massive branes contains new world-volume fields that are absent in the massless case, i.e. when the mass parameter m of massive IIA supergravity is set to zero. We show how these new world-volume fields can be introduced in a systematic way. (orig.)

Mn-silicide nanostructures aligned on massively parallel silicon nano-ribbons

International Nuclear Information System (INIS)

De Padova, Paola; Ottaviani, Carlo; Ronci, Fabio; Colonna, Stefano; Quaresima, Claudio; Cricenti, Antonio; Olivieri, Bruno; Dávila, Maria E; Hennies, Franz; Pietzsch, Annette; Shariati, Nina; Le Lay, Guy

2013-01-01

The growth of Mn nanostructures on a 1D grating of silicon nano-ribbons is investigated at atomic scale by means of scanning tunneling microscopy, low energy electron diffraction and core level photoelectron spectroscopy. The grating of silicon nano-ribbons represents an atomic scale template that can be used in a surface-driven route to control the combination of Si with Mn in the development of novel materials for spintronics devices. The Mn atoms show a preferential adsorption site on silicon atoms, forming one-dimensional nanostructures. They are parallel oriented with respect to the surface Si array, which probably predetermines the diffusion pathways of the Mn atoms during the process of nanostructure formation.

Parallel Algorithms for Switching Edges in Heterogeneous Graphs.

Science.gov (United States)

Bhuiyan, Hasanuzzaman; Khan, Maleq; Chen, Jiangzhuo; Marathe, Madhav

2017-06-01

An edge switch is an operation on a graph (or network) where two edges are selected randomly and one of their end vertices are swapped with each other. Edge switch operations have important applications in graph theory and network analysis, such as in generating random networks with a given degree sequence, modeling and analyzing dynamic networks, and in studying various dynamic phenomena over a network. The recent growth of real-world networks motivates the need for efficient parallel algorithms. The dependencies among successive edge switch operations and the requirement to keep the graph simple (i.e., no self-loops or parallel edges) as the edges are switched lead to significant challenges in designing a parallel algorithm. Addressing these challenges requires complex synchronization and communication among the processors leading to difficulties in achieving a good speedup by parallelization. In this paper, we present distributed memory parallel algorithms for switching edges in massive networks. These algorithms provide good speedup and scale well to a large number of processors. A harmonic mean speedup of 73.25 is achieved on eight different networks with 1024 processors. One of the steps in our edge switch algorithms requires the computation of multinomial random variables in parallel. This paper presents the first non-trivial parallel algorithm for the problem, achieving a speedup of 925 using 1024 processors.

A massively parallel method of characteristic neutral particle transport code for GPUs

International Nuclear Information System (INIS)

Boyd, W. R.; Smith, K.; Forget, B.

2013-01-01

Over the past 20 years, parallel computing has enabled computers to grow ever larger and more powerful while scientific applications have advanced in sophistication and resolution. This trend is being challenged, however, as the power consumption for conventional parallel computing architectures has risen to unsustainable levels and memory limitations have come to dominate compute performance. Heterogeneous computing platforms, such as Graphics Processing Units (GPUs), are an increasingly popular paradigm for solving these issues. This paper explores the applicability of GPUs for deterministic neutron transport. A 2D method of characteristics (MOC) code - OpenMOC - has been developed with solvers for both shared memory multi-core platforms as well as GPUs. The multi-threading and memory locality methodologies for the GPU solver are presented. Performance results for the 2D C5G7 benchmark demonstrate 25-35 x speedup for MOC on the GPU. The lessons learned from this case study will provide the basis for further exploration of MOC on GPUs as well as design decisions for hardware vendors exploring technologies for the next generation of machines for scientific computing. (authors)

Global transcriptional profiling of the toxic dinoflagellate Alexandrium fundyense using Massively Parallel Signature Sequencing

Directory of Open Access Journals (Sweden)

Anderson Donald M

2006-04-01

Full Text Available Abstract Background Dinoflagellates are one of the most important classes of marine and freshwater algae, notable both for their functional diversity and ecological significance. They occur naturally as free-living cells, as endosymbionts of marine invertebrates and are well known for their involvement in "red tides". Dinoflagellates are also notable for their unusual genome content and structure, which suggests that the organization and regulation of dinoflagellate genes may be very different from that of most eukaryotes. To investigate the content and regulation of the dinoflagellate genome, we performed a global analysis of the transcriptome of the toxic dinoflagellate Alexandrium fundyense under nitrate- and phosphate-limited conditions using Massively Parallel Signature Sequencing (MPSS. Results Data from the two MPSS libraries showed that the number of unique signatures found in A. fundyense cells is similar to that of humans and Arabidopsis thaliana, two eukaryotes that have been extensively analyzed using this method. The general distribution, abundance and expression patterns of the A. fundyense signatures were also quite similar to other eukaryotes, and at least 10% of the A. fundyense signatures were differentially expressed between the two conditions. RACE amplification and sequencing of a subset of signatures showed that multiple signatures arose from sequence variants of a single gene. Single signatures also mapped to different sequence variants of the same gene. Conclusion The MPSS data presented here provide a quantitative view of the transcriptome and its regulation in these unusual single-celled eukaryotes. The observed signature abundance and distribution in Alexandrium is similar to that of other eukaryotes that have been analyzed using MPSS. Results of signature mapping via RACE indicate that many signatures result from sequence variants of individual genes. These data add to the growing body of evidence for widespread gene

Massively Parallel Polar Decomposition on Distributed-Memory Systems

KAUST Repository

Ltaief, Hatem

2018-01-01

We present a high-performance implementation of the Polar Decomposition (PD) on distributed-memory systems. Building upon on the QR-based Dynamically Weighted Halley (QDWH) algorithm, the key idea lies in finding the best rational approximation for the scalar sign function, which also corresponds to the polar factor for symmetric matrices, to further accelerate the QDWH convergence. Based on the Zolotarev rational functions—introduced by Zolotarev (ZOLO) in 1877— this new PD algorithm ZOLO-PD converges within two iterations even for ill-conditioned matrices, instead of the original six iterations needed for QDWH. ZOLO-PD uses the property of Zolotarev functions that optimality is maintained when two functions are composed in an appropriate manner. The resulting ZOLO-PD has a convergence rate up to seventeen, in contrast to the cubic convergence rate for QDWH. This comes at the price of higher arithmetic costs and memory footprint. These extra floating-point operations can, however, be processed in an embarrassingly parallel fashion. We demonstrate performance using up to 102, 400 cores on two supercomputers. We demonstrate that, in the presence of a large number of processing units, ZOLO-PD is able to outperform QDWH by up to 2.3X speedup, especially in situations where QDWH runs out of work, for instance, in the strong scaling mode of operation.

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.

Unified Lambert Tool for Massively Parallel Applications in Space Situational Awareness

Science.gov (United States)

Woollands, Robyn M.; Read, Julie; Hernandez, Kevin; Probe, Austin; Junkins, John L.

2018-03-01

This paper introduces a parallel-compiled tool that combines several of our recently developed methods for solving the perturbed Lambert problem using modified Chebyshev-Picard iteration. This tool (unified Lambert tool) consists of four individual algorithms, each of which is unique and better suited for solving a particular type of orbit transfer. The first is a Keplerian Lambert solver, which is used to provide a good initial guess (warm start) for solving the perturbed problem. It is also used to determine the appropriate algorithm to call for solving the perturbed problem. The arc length or true anomaly angle spanned by the transfer trajectory is the parameter that governs the automated selection of the appropriate perturbed algorithm, and is based on the respective algorithm convergence characteristics. The second algorithm solves the perturbed Lambert problem using the modified Chebyshev-Picard iteration two-point boundary value solver. This algorithm does not require a Newton-like shooting method and is the most efficient of the perturbed solvers presented herein, however the domain of convergence is limited to about a third of an orbit and is dependent on eccentricity. The third algorithm extends the domain of convergence of the modified Chebyshev-Picard iteration two-point boundary value solver to about 90% of an orbit, through regularization with the Kustaanheimo-Stiefel transformation. This is the second most efficient of the perturbed set of algorithms. The fourth algorithm uses the method of particular solutions and the modified Chebyshev-Picard iteration initial value solver for solving multiple revolution perturbed transfers. This method does require "shooting" but differs from Newton-like shooting methods in that it does not require propagation of a state transition matrix. The unified Lambert tool makes use of the General Mission Analysis Tool and we use it to compute thousands of perturbed Lambert trajectories in parallel on the Space Situational

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.

Tryton Supercomputer Capabilities for Analysis of Massive Data Streams

Directory of Open Access Journals (Sweden)

Krawczyk Henryk

2015-09-01

Full Text Available The recently deployed supercomputer Tryton, located in the Academic Computer Center of Gdansk University of Technology, provides great means for massive parallel processing. Moreover, the status of the Center as one of the main network nodes in the PIONIER network enables the fast and reliable transfer of data produced by miscellaneous devices scattered in the area of the whole country. The typical examples of such data are streams containing radio-telescope and satellite observations. Their analysis, especially with real-time constraints, can be challenging and requires the usage of dedicated software components. We propose a solution for such parallel analysis using the supercomputer, supervised by the KASKADA platform, which with the conjunction with immerse 3D visualization techniques can be used to solve problems such as pulsar detection and chronometric or oil-spill simulation on the sea surface.

Lifshitz black branes and DC transport coefficients in massive Einstein-Maxwell-dilaton gravity

Science.gov (United States)

Kuang, Xiao-Mei; Papantonopoulos, Eleftherios; Wu, Jian-Pin; Zhou, Zhenhua

2018-03-01

We construct analytical Lifshitz massive black brane solutions in massive Einstein-Maxwell-dilaton gravity theory. We also study the thermodynamics of these black brane solutions and obtain the thermodynamical stability conditions. On the dual nonrelativistic boundary field theory with Lifshitz symmetry, we analytically compute the DC transport coefficients, including the electric conductivity, thermoelectric conductivity, and thermal conductivity. The novel property of our model is that the massive term supports the Lifshitz black brane solutions with z ≠1 in such a way that the DC transport coefficients in the dual field theory are finite. We also find that the Wiedemann-Franz law in this dual boundary field theory is violated, which indicates that it may involve strong interactions.

Effects of electric field and Coriolis force on electrohydrodynamic stability of poorly conducting couple stress parallel fluid flow in a channel

International Nuclear Information System (INIS)

Shankar, B.M.; Rudraiah, N.

2013-01-01

The effective functioning of microfluidic devices in chemical, electrical and mechanical engineering involving fluidics particularly those having vibrations and petroleum products containing organic, inorganic and other microfluidics require understanding and control of stability of poorly conducting parallel fluid flows. The electrical conductivity, σ, of a poorly conducting fluidics, increases with the temperature and the concentration of freely suspended particles like RBC, WBC and so on in the blood, the hylauronic acid (HA) and nutrients of synovial fluid in synovial joints will spin producing microrotation, forming micropolar fluid of Eringen. The presence of Deuterium - Tritium (DT) in inertial fusion target (IFT) may also be modeled using micropolar fluid theory of Eringen. A particular case of micropolar fluid theory when microrotation balances with the natural vorticity of a poorly conducting fluidics in the presence of an electric field is called ‘electrohydrodynamic couple stress fluid’ (EHDCF). These EHDCFs exhibit a variation of electrical conductivity, ∇ σ, increasing with temperature and concentration of freely suspended particles, releases the charges from the nuclei forming distribution of charge density, ρ e . These charges induce an electric field, 1 E i . If need be, we can apply an electric field, 1 E a , by embedding electrodes of different potentials at the boundaries. The total electric field, 1 E = 1 E i + 1 E a , produces a current density, 1 J = ρ σ 1 E, according to Ohm’s law and also produces an electric force, 1 F σ = σ 1 E. This current 1 J acts as sensing and the force, 1 F σ acts as actuation. These two properties make the poorly conducting couple stress fluid to act as a smart material. The objective of this paper is to show that EHDCV in presence of coriolis force plays a significant role in controlling the stability of parallel flows which is essential for an effective functioning of machineries that occur in

Electric field and dielectrophoretic force on a dielectric particle chain in a parallel-plate electrode system

International Nuclear Information System (INIS)

Techaumnat, B; Eua-arporn, B; Takuma, T

2004-01-01

This paper presents results of calculations of the electric field and dielectrophoretic force on a dielectric particle chain suspended in a host liquid lying between parallel-plate electrodes. The method of calculation is based on the method of multipole images using the multipole re-expansion technique. We have investigated the effect of the particle permittivity, the tilt angle (between the chain and the applied field) and the chain arrangement on the electric field and force. The results show that the electric field intensification rises in accordance with the increase in the ratio of the particle-to-liquid permittivity, Γ ε . The electric field at the contact point between the particles decreases with increasing tilt angle, while the maximal field at the contact point between the particles and the plate electrodes is almost unchanged. The maximal field can be approximated by a simple formula, which is a quadratic function of Γ ε . The dielectrophoretic force depends significantly on the distance from other particles or an electrode. However, for the tilt angles in this paper, the horizontal force on the upper particle of the chain always has the direction opposite to the shear direction. The maximal horizontal force of a chain varies proportional to (Γ ε - 1) 1.7 if the particles in the chain are still in contact with each other. The approximated force, based on the force on an isolated chain, has been compared with our calculation results. The comparison shows that no approximation model agrees well with our results throughout the range of permittivity ratios

Electrical principles 3 checkbook

CERN Document Server

Bird, J O

2013-01-01

Electrical Principles 3 Checkbook aims to introduce students to the basic electrical principles needed by technicians in electrical engineering, electronics, and telecommunications.The book first tackles circuit theorems, single-phase series A.C. circuits, and single-phase parallel A.C. circuits. Discussions focus on worked problems on parallel A.C. circuits, worked problems on series A.C. circuits, main points concerned with D.C. circuit analysis, worked problems on circuit theorems, and further problems on circuit theorems. The manuscript then examines three-phase systems and D.C. transients

The Destructive Birth of Massive Stars and Massive Star Clusters

Science.gov (United States)

Rosen, Anna; Krumholz, Mark; McKee, Christopher F.; Klein, Richard I.; Ramirez-Ruiz, Enrico

2017-01-01

Massive stars play an essential role in the Universe. They are rare, yet the energy and momentum they inject into the interstellar medium with their intense radiation fields dwarfs the contribution by their vastly more numerous low-mass cousins. Previous theoretical and observational studies have concluded that the feedback associated with massive stars' radiation fields is the dominant mechanism regulating massive star and massive star cluster (MSC) formation. Therefore detailed simulation of the formation of massive stars and MSCs, which host hundreds to thousands of massive stars, requires an accurate treatment of radiation. For this purpose, we have developed a new, highly accurate hybrid radiation algorithm that properly treats the absorption of the direct radiation field from stars and the re-emission and processing by interstellar dust. We use our new tool to perform a suite of three-dimensional radiation-hydrodynamic simulations of the formation of massive stars and MSCs. For individual massive stellar systems, we simulate the collapse of massive pre-stellar cores with laminar and turbulent initial conditions and properly resolve regions where we expect instabilities to grow. We find that mass is channeled to the massive stellar system via gravitational and Rayleigh-Taylor (RT) instabilities. For laminar initial conditions, proper treatment of the direct radiation field produces later onset of RT instability, but does not suppress it entirely provided the edges of the radiation-dominated bubbles are adequately resolved. RT instabilities arise immediately for turbulent pre-stellar cores because the initial turbulence seeds the instabilities. To model MSC formation, we simulate the collapse of a dense, turbulent, magnetized Mcl = 106 M⊙ molecular cloud. We find that the influence of the magnetic pressure and radiative feedback slows down star formation. Furthermore, we find that star formation is suppressed along dense filaments where the magnetic field is

Application of parallel computing techniques to a large-scale reservoir simulation

International Nuclear Information System (INIS)

Zhang, Keni; Wu, Yu-Shu; Ding, Chris; Pruess, Karsten

2001-01-01

Even with the continual advances made in both computational algorithms and computer hardware used in reservoir modeling studies, large-scale simulation of fluid and heat flow in heterogeneous reservoirs remains a challenge. The problem commonly arises from intensive computational requirement for detailed modeling investigations of real-world reservoirs. This paper presents the application of a massive parallel-computing version of the TOUGH2 code developed for performing large-scale field simulations. As an application example, the parallelized TOUGH2 code is applied to develop a three-dimensional unsaturated-zone numerical model simulating flow of moisture, gas, and heat in the unsaturated zone of Yucca Mountain, Nevada, a potential repository for high-level radioactive waste. The modeling approach employs refined spatial discretization to represent the heterogeneous fractured tuffs of the system, using more than a million 3-D gridblocks. The problem of two-phase flow and heat transfer within the model domain leads to a total of 3,226,566 linear equations to be solved per Newton iteration. The simulation is conducted on a Cray T3E-900, a distributed-memory massively parallel computer. Simulation results indicate that the parallel computing technique, as implemented in the TOUGH2 code, is very efficient. The reliability and accuracy of the model results have been demonstrated by comparing them to those of small-scale (coarse-grid) models. These comparisons show that simulation results obtained with the refined grid provide more detailed predictions of the future flow conditions at the site, aiding in the assessment of proposed repository performance

High performance parallel computing of flows in complex geometries: I. Methods

International Nuclear Information System (INIS)

Gourdain, N; Gicquel, L; Montagnac, M; Vermorel, O; Staffelbach, G; Garcia, M; Boussuge, J-F; Gazaix, M; Poinsot, T

2009-01-01

Efficient numerical tools coupled with high-performance computers, have become a key element of the design process in the fields of energy supply and transportation. However flow phenomena that occur in complex systems such as gas turbines and aircrafts are still not understood mainly because of the models that are needed. In fact, most computational fluid dynamics (CFD) predictions as found today in industry focus on a reduced or simplified version of the real system (such as a periodic sector) and are usually solved with a steady-state assumption. This paper shows how to overcome such barriers and how such a new challenge can be addressed by developing flow solvers running on high-end computing platforms, using thousands of computing cores. Parallel strategies used by modern flow solvers are discussed with particular emphases on mesh-partitioning, load balancing and communication. Two examples are used to illustrate these concepts: a multi-block structured code and an unstructured code. Parallel computing strategies used with both flow solvers are detailed and compared. This comparison indicates that mesh-partitioning and load balancing are more straightforward with unstructured grids than with multi-block structured meshes. However, the mesh-partitioning stage can be challenging for unstructured grids, mainly due to memory limitations of the newly developed massively parallel architectures. Finally, detailed investigations show that the impact of mesh-partitioning on the numerical CFD solutions, due to rounding errors and block splitting, may be of importance and should be accurately addressed before qualifying massively parallel CFD tools for a routine industrial use.

Effects of fast ions and an external inductive electric field on the neoclassical parallel flow, current, and rotation in general toroidal systems

International Nuclear Information System (INIS)

Nakajima, Noriyoshi; Okamoto, Masao.

1992-05-01

Effects of external momentum sources, i.e., fast ions produced by the neutral beam injection and an external inductive electric field, on the neoclassical ion parallel flow, current, and rotation are analytically investigated for a simple plasma in general toroidal systems. It is shown that the contribution of the external sources to the ion parallel flow becomes large as the collision frequency of thermal ions increases because of the momentum conservation of Coulomb collisions and sharply decreasing viscosity coefficients, with collision frequency. As a result, the beam-driven parallel flow of thermal ions becomes comparable to that of electrons in the Pfirsh-Schluter collisionality regime, whereas in the 1/μ or banana regime it is smaller than that of electrons by the order of √(m e /m i ) (m e and m i are electron and ion masses). This beam-driven ion parallel flow can not produce a large beam-driven current because of the cancellation with electron parallel flow, but produces a large toroidal rotation of ions. As both electrons and ions approach the Pfirsh-Schluter collisionality regime the contribution of thermodynamical forces becomes negligibly small and the large toroidal rotation of ions is predominated by the beam-driven component in the non-axisymmetric configuration with large helical ripples. (author)

Non-collider searches for stable massive particles

Energy Technology Data Exchange (ETDEWEB)

Burdin, S. [Department of Physics, University of Liverpool, Liverpool L69 7ZE (United Kingdom); Fairbairn, M. [Department of Physics, King’s College London, London WC2R 2LS (United Kingdom); Mermod, P., E-mail: philippe.mermod@cern.ch [Particle Physics Department, University of Geneva, 1211 Geneva 4 (Switzerland); Milstead, D., E-mail: milstead@physto.se [Department of Physics, Stockholm University, 106 91 Stockholm (Sweden); Pinfold, J. [Physics Department, University of Alberta, Edmonton, Alberta, Canada T6G 0V1 (Canada); Sloan, T. [Department of Physics, Lancaster University, Lancaster LA1 4YB (United Kingdom); Taylor, W. [Department of Physics and Astronomy, York University, Toronto, ON, Canada M3J 1P3 (Canada)

2015-06-26

The theoretical motivation for exotic stable massive particles (SMPs) and the results of SMP searches at non-collider facilities are reviewed. SMPs are defined such that they would be sufficiently long-lived so as to still exist in the cosmos either as Big Bang relics or secondary collision products, and sufficiently massive such that they are typically beyond the reach of any conceivable accelerator-based experiment. The discovery of SMPs would address a number of important questions in modern physics, such as the origin and composition of dark matter and the unification of the fundamental forces. This review outlines the scenarios predicting SMPs and the techniques used at non-collider experiments to look for SMPs in cosmic rays and bound in matter. The limits so far obtained on the fluxes and matter densities of SMPs which possess various detection-relevant properties such as electric and magnetic charge are given.

High-Efficient Parallel CAVLC Encoders on Heterogeneous Multicore Architectures

Directory of Open Access Journals (Sweden)

H. Y. Su

2012-04-01

Full Text Available This article presents two high-efficient parallel realizations of the context-based adaptive variable length coding (CAVLC based on heterogeneous multicore processors. By optimizing the architecture of the CAVLC encoder, three kinds of dependences are eliminated or weaken, including the context-based data dependence, the memory accessing dependence and the control dependence. The CAVLC pipeline is divided into three stages: two scans, coding, and lag packing, and be implemented on two typical heterogeneous multicore architectures. One is a block-based SIMD parallel CAVLC encoder on multicore stream processor STORM. The other is a component-oriented SIMT parallel encoder on massively parallel architecture GPU. Both of them exploited rich data-level parallelism. Experiments results show that compared with the CPU version, more than 70 times of speedup can be obtained for STORM and over 50 times for GPU. The implementation of encoder on STORM can make a real-time processing for 1080p @30fps and GPU-based version can satisfy the requirements for 720p real-time encoding. The throughput of the presented CAVLC encoders is more than 10 times higher than that of published software encoders on DSP and multicore platforms.

Military Curricula for Vocational & Technical Education. Basic Electricity and Electronics Individualized Learning System. CANTRAC A-100-0010. Module Six: Parallel Circuits. Study Booklet.

Science.gov (United States)

Chief of Naval Education and Training Support, Pensacola, FL.

This individualized learning module on parallel circuits is one in a series of modules for a course in basic electricity and electronics. The course is one of a number of military-developed curriculum packages selected for adaptation to vocational instructional and curriculum development in a civilian setting. Four lessons are included in the…

Device for balancing parallel strings

Science.gov (United States)

Mashikian, Matthew S.

1985-01-01

A battery plant is described which features magnetic circuit means in association with each of the battery strings in the battery plant for balancing the electrical current flow through the battery strings by equalizing the voltage across each of the battery strings. Each of the magnetic circuit means generally comprises means for sensing the electrical current flow through one of the battery strings, and a saturable reactor having a main winding connected electrically in series with the battery string, a bias winding connected to a source of alternating current and a control winding connected to a variable source of direct current controlled by the sensing means. Each of the battery strings is formed by a plurality of batteries connected electrically in series, and these battery strings are connected electrically in parallel across common bus conductors.

Effect of the depth base along the vertical on the electrical parameters of a vertical parallel silicon solar cell in open and short circuit

Directory of Open Access Journals (Sweden)

Gokhan Sahin

2018-03-01

Full Text Available This article presented a modeling study of effect of the depth base initiating on vertical parallel silicon solar cell’s photovoltaic conversion efficiency. After the resolution of the continuity equation of excess minority carriers, we calculated the electrical parameters such as the photocurrent density, the photovoltage, series resistance and shunt resistances, diffusion capacitance, electric power, fill factor and the photovoltaic conversion efficiency. We determined the maximum electric power, the operating point of the solar cell and photovoltaic conversion efficiency according to the depth z in the base. We showed that the photocurrent density decreases with the depth z. The photovoltage decreased when the depth base increases. Series and shunt resistances were deduced from electrical model and were influenced and the applied the depth base. The capacity decreased with the depth z of the base. We had studied the influence of the variation of the depth z on the electrical parameters in the base. Keywords: Depth base, Conversion efficiency, Electrical parameters, Open circuit, Short circuit

A new parallel-type hybrid electric-vehicle

International Nuclear Information System (INIS)

David Huang, K.; Tzeng, S.-C.

2004-01-01

This new system promises an internal-combustion engine that always maintains optimal operating conditions. The system comprises two parts: (1) an internal-combustion power-distribution device and (2) an integrated design involving the engine and electronic motor. The internal-combustion power-distribution device provides an engine capable of constantly operating in an optimal fashion, minimizing emissions and maximizing thermal-efficiency. The electric motor can generate extra power. Notably, the integrated torque design comprises three helical gears. This design can release the power of the engine or electric motor separately, or can integrate these two different powers into a hybridized power system

Massive Gravity

OpenAIRE

de Rham, Claudia

2014-01-01

We review recent progress in massive gravity. We start by showing how different theories of massive gravity emerge from a higher-dimensional theory of general relativity, leading to the Dvali–Gabadadze–Porrati model (DGP), cascading gravity, and ghost-free massive gravity. We then explore their theoretical and phenomenological consistency, proving the absence of Boulware–Deser ghosts and reviewing the Vainshtein mechanism and the cosmological solutions in these models. Finally, we present alt...

Solid holography and massive gravity

International Nuclear Information System (INIS)

Alberte, Lasma; Baggioli, Matteo; Khmelnitsky, Andrei; Pujolàs, Oriol

2016-01-01

Momentum dissipation is an important ingredient in condensed matter physics that requires a translation breaking sector. In the bottom-up gauge/gravity duality, this implies that the gravity dual is massive. We start here a systematic analysis of holographic massive gravity (HMG) theories, which admit field theory dual interpretations and which, therefore, might store interesting condensed matter applications. We show that there are many phases of HMG that are fully consistent effective field theories and which have been left overlooked in the literature. The most important distinction between the different HMG phases is that they can be clearly separated into solids and fluids. This can be done both at the level of the unbroken spacetime symmetries as well as concerning the elastic properties of the dual materials. We extract the modulus of rigidity of the solid HMG black brane solutions and show how it relates to the graviton mass term. We also consider the implications of the different HMGs on the electric response. We show that the types of response that can be consistently described within this framework is much wider than what is captured by the narrow class of models mostly considered so far.

Solid holography and massive gravity

Energy Technology Data Exchange (ETDEWEB)

Alberte, Lasma [Abdus Salam International Centre for Theoretical Physics,Strada Costiera 11, 34151, Trieste (Italy); Baggioli, Matteo [Institut de Física d’Altes Energies (IFAE),The Barcelona Institute of Science and Technology (BIST), Campus UAB, 08193 Bellaterra, Barcelona (Spain); Department of Physics, Institute for Condensed Matter Theory, University of Illinois,1110 W. Green Street, Urbana, IL 61801 (United States); Khmelnitsky, Andrei [Abdus Salam International Centre for Theoretical Physics, Strada Costiera 11, 34151, Trieste (Italy); Pujolàs, Oriol [Institut de Física d’Altes Energies (IFAE),The Barcelona Institute of Science and Technology (BIST), Campus UAB, 08193 Bellaterra, Barcelona (Spain)

2016-02-17

Momentum dissipation is an important ingredient in condensed matter physics that requires a translation breaking sector. In the bottom-up gauge/gravity duality, this implies that the gravity dual is massive. We start here a systematic analysis of holographic massive gravity (HMG) theories, which admit field theory dual interpretations and which, therefore, might store interesting condensed matter applications. We show that there are many phases of HMG that are fully consistent effective field theories and which have been left overlooked in the literature. The most important distinction between the different HMG phases is that they can be clearly separated into solids and fluids. This can be done both at the level of the unbroken spacetime symmetries as well as concerning the elastic properties of the dual materials. We extract the modulus of rigidity of the solid HMG black brane solutions and show how it relates to the graviton mass term. We also consider the implications of the different HMGs on the electric response. We show that the types of response that can be consistently described within this framework is much wider than what is captured by the narrow class of models mostly considered so far.

Parallel electric fields detected via conjugate electron echoes during the Echo 7 sounding rocket flight

Science.gov (United States)

Nemzek, R. J.; Winckler, J. R.

1991-01-01

Electron detectors on the Echo 7 active sounding rocket experiment measured 'conjugate echoes' resulting from artificial electron beam injections. Analysis of the drift motion of the electrons after a complete bounce leads to measurements of the magnetospheric convection electric field mapped to ionospheric altitudes. The magnetospheric field was highly variable, changing by tens of mV/m on time scales of as little as hundreds of millisec. While the smallest-scale magnetospheric field irregularities were mapped out by ionospheric conductivity, larger-scale features were enhanced by up to 50 mV/m in the ionosphere. The mismatch between magnetospheric and ionspheric convection fields indicates a violation of the equipotential field line condition. The parallel fields occurred in regions roughly 10 km across and probably supported a total potential drop of 10-100 V.

Neurite, a finite difference large scale parallel program for the simulation of electrical signal propagation in neurites under mechanical loading.

Directory of Open Access Journals (Sweden)

Julián A García-Grajales

Full Text Available With the growing body of research on traumatic brain injury and spinal cord injury, computational neuroscience has recently focused its modeling efforts on neuronal functional deficits following mechanical loading. However, in most of these efforts, cell damage is generally only characterized by purely mechanistic criteria, functions of quantities such as stress, strain or their corresponding rates. The modeling of functional deficits in neurites as a consequence of macroscopic mechanical insults has been rarely explored. In particular, a quantitative mechanically based model of electrophysiological impairment in neuronal cells, Neurite, has only very recently been proposed. In this paper, we present the implementation details of this model: a finite difference parallel program for simulating electrical signal propagation along neurites under mechanical loading. Following the application of a macroscopic strain at a given strain rate produced by a mechanical insult, Neurite is able to simulate the resulting neuronal electrical signal propagation, and thus the corresponding functional deficits. The simulation of the coupled mechanical and electrophysiological behaviors requires computational expensive calculations that increase in complexity as the network of the simulated cells grows. The solvers implemented in Neurite--explicit and implicit--were therefore parallelized using graphics processing units in order to reduce the burden of the simulation costs of large scale scenarios. Cable Theory and Hodgkin-Huxley models were implemented to account for the electrophysiological passive and active regions of a neurite, respectively, whereas a coupled mechanical model accounting for the neurite mechanical behavior within its surrounding medium was adopted as a link between electrophysiology and mechanics. This paper provides the details of the parallel implementation of Neurite, along with three different application examples: a long myelinated axon

User's guide of TOUGH2-EGS-MP: A Massively Parallel Simulator with Coupled Geomechanics for Fluid and Heat Flow in Enhanced Geothermal Systems VERSION 1.0

Energy Technology Data Exchange (ETDEWEB)

Xiong, Yi [Colorado School of Mines, Golden, CO (United States); Fakcharoenphol, Perapon [Colorado School of Mines, Golden, CO (United States); Wang, Shihao [Colorado School of Mines, Golden, CO (United States); Winterfeld, Philip H. [Colorado School of Mines, Golden, CO (United States); Zhang, Keni [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Wu, Yu-Shu [Colorado School of Mines, Golden, CO (United States)

2013-12-01

TOUGH2-EGS-MP is a parallel numerical simulation program coupling geomechanics with fluid and heat flow in fractured and porous media, and is applicable for simulation of enhanced geothermal systems (EGS). TOUGH2-EGS-MP is based on the TOUGH2-MP code, the massively parallel version of TOUGH2. In TOUGH2-EGS-MP, the fully-coupled flow-geomechanics model is developed from linear elastic theory for thermo-poro-elastic systems and is formulated in terms of mean normal stress as well as pore pressure and temperature. Reservoir rock properties such as porosity and permeability depend on rock deformation, and the relationships between these two, obtained from poro-elasticity theories and empirical correlations, are incorporated into the simulation. This report provides the user with detailed information on the TOUGH2-EGS-MP mathematical model and instructions for using it for Thermal-Hydrological-Mechanical (THM) simulations. The mathematical model includes the fluid and heat flow equations, geomechanical equation, and discretization of those equations. In addition, the parallel aspects of the code, such as domain partitioning and communication between processors, are also included. Although TOUGH2-EGS-MP has the capability for simulating fluid and heat flows coupled with geomechanical effects, it is up to the user to select the specific coupling process, such as THM or only TH, in a simulation. There are several example problems illustrating applications of this program. These example problems are described in detail and their input data are presented. Their results demonstrate that this program can be used for field-scale geothermal reservoir simulation in porous and fractured media with fluid and heat flow coupled with geomechanical effects.

Module Six: Parallel Circuits; Basic Electricity and Electronics Individualized Learning System.

Science.gov (United States)

Bureau of Naval Personnel, Washington, DC.

In this module the student will learn the rules that govern the characteristics of parallel circuits; the relationships between voltage, current, resistance and power; and the results of common troubles in parallel circuits. The module is divided into four lessons: rules of voltage and current, rules for resistance and power, variational analysis,…

Efficient linear precoding for massive MIMO systems using truncated polynomial expansion

KAUST Repository

Müller, Axel

2014-06-01

Massive multiple-input multiple-output (MIMO) techniques have been proposed as a solution to satisfy many requirements of next generation cellular systems. One downside of massive MIMO is the increased complexity of computing the precoding, especially since the relatively \\'antenna-efficient\\' regularized zero-forcing (RZF) is preferred to simple maximum ratio transmission. We develop in this paper a new class of precoders for single-cell massive MIMO systems. It is based on truncated polynomial expansion (TPE) and mimics the advantages of RZF, while offering reduced and scalable computational complexity that can be implemented in a convenient parallel fashion. Using random matrix theory we provide a closed-form expression of the signal-to-interference-and-noise ratio under TPE precoding and compare it to previous works on RZF. Furthermore, the sum rate maximizing polynomial coefficients in TPE precoding are calculated. By simulation, we find that to maintain a fixed peruser rate loss as compared to RZF, the polynomial degree does not need to scale with the system, but it should be increased with the quality of the channel knowledge and signal-to-noise ratio. © 2014 IEEE.

Review on Automotive Power Generation System on Plug-in Hybrid Electric Vehicles & Electric Vehicles

Directory of Open Access Journals (Sweden)

Leong Yap Wee

2016-01-01

Full Text Available Regenerative braking is a function to recharge power bank on the Plug-in electric vehicles (PHEV and electric vehicles (EV. The weakness of this system is, it can only perform its function when the vehicle is slowing down or by stepping the brake foot pedal. In other words, the electricity recharging system is inconsistent, non-continuous and geography dependent. To overcome the weakness of the regenerative braking system, it is suggested that to apply another generator which is going to be parallel with the regenerative braking system so that continuous charging can be achieved. Since the ironless electricity generator has a less counter electromotive force (CEMF comparing to an ironcored electricity generator and no cogging torque. Applying the ironless electricity generator parallel to the regenerative braking system is seen one of the options which creates sustainable charging system compared to cored electricity generator.

Effect of the depth base along the vertical on the electrical parameters of a vertical parallel silicon solar cell in open and short circuit

Science.gov (United States)

Sahin, Gokhan; Kerimli, Genber

2018-03-01

This article presented a modeling study of effect of the depth base initiating on vertical parallel silicon solar cell's photovoltaic conversion efficiency. After the resolution of the continuity equation of excess minority carriers, we calculated the electrical parameters such as the photocurrent density, the photovoltage, series resistance and shunt resistances, diffusion capacitance, electric power, fill factor and the photovoltaic conversion efficiency. We determined the maximum electric power, the operating point of the solar cell and photovoltaic conversion efficiency according to the depth z in the base. We showed that the photocurrent density decreases with the depth z. The photovoltage decreased when the depth base increases. Series and shunt resistances were deduced from electrical model and were influenced and the applied the depth base. The capacity decreased with the depth z of the base. We had studied the influence of the variation of the depth z on the electrical parameters in the base.

Towards anatomic scale agent-based modeling with a massively parallel spatially explicit general-purpose model of enteric tissue (SEGMEnT_HPC).

Science.gov (United States)

Cockrell, Robert Chase; Christley, Scott; Chang, Eugene; An, Gary

2015-01-01

Perhaps the greatest challenge currently facing the biomedical research community is the ability to integrate highly detailed cellular and molecular mechanisms to represent clinical disease states as a pathway to engineer effective therapeutics. This is particularly evident in the representation of organ-level pathophysiology in terms of abnormal tissue structure, which, through histology, remains a mainstay in disease diagnosis and staging. As such, being able to generate anatomic scale simulations is a highly desirable goal. While computational limitations have previously constrained the size and scope of multi-scale computational models, advances in the capacity and availability of high-performance computing (HPC) resources have greatly expanded the ability of computational models of biological systems to achieve anatomic, clinically relevant scale. Diseases of the intestinal tract are exemplary examples of pathophysiological processes that manifest at multiple scales of spatial resolution, with structural abnormalities present at the microscopic, macroscopic and organ-levels. In this paper, we describe a novel, massively parallel computational model of the gut, the Spatially Explicitly General-purpose Model of Enteric Tissue_HPC (SEGMEnT_HPC), which extends an existing model of the gut epithelium, SEGMEnT, in order to create cell-for-cell anatomic scale simulations. We present an example implementation of SEGMEnT_HPC that simulates the pathogenesis of ileal pouchitis, and important clinical entity that affects patients following remedial surgery for ulcerative colitis.

Comparative Analysis of Torque and Acceleration of Pre- and Post-Transmission Parallel Hybrid Drivetrains

Directory of Open Access Journals (Sweden)

Zulkifli Saiful A.

2016-01-01

Full Text Available Parallel hybrid electric vehicles (HEV can be classified according to the location of the electric motor with respect to the transmission unit for the internal combustion engine (ICE: they can be pre-transmission or posttransmission parallel hybrid. A split-axle parallel HEV – in which the ICE and electric motor provide propulsion power to different axles – is a sub-type of the post-transmission hybrid, since addition of torque and power from the two power sources occurs after the vehicle’s transmission. The term ‘through-the-road’ (TTR hybrid is also used for the split-parallel HEV, since power coupling between the ICE and electric motor is not through some mechanical device but through the vehicle itself, its wheels and the road on which it moves. The present work presents torquespeed relationship of the split-parallel hybrid and analyses simulation results of torque profiles and acceleration performance of pre-transmission and post-transmission hybrid configurations, using three different sizes of electric motor. Different operating regions of the pre-trans and post-trans motors are observed, leading to different speed and torque profiles. Although ICE average efficiency in the post-trans hybrid is slightly lower than in the pre-trans hybrid, the post-trans hybrid vehicle has better fuel economy and acceleration performance than the pre-trans hybrid vehicle.

Opportunities and challenges for the integration of massively parallel genomic sequencing into clinical practice: lessons from the ClinSeq project.

Science.gov (United States)

Biesecker, Leslie G

2012-04-01

The debate surrounding the return of results from high-throughput genomic interrogation encompasses many important issues including ethics, law, economics, and social policy. As well, the debate is also informed by the molecular, genetic, and clinical foundations of the emerging field of clinical genomics, which is based on this new technology. This article outlines the main biomedical considerations of sequencing technologies and demonstrates some of the early clinical experiences with the technology to enable the debate to stay focused on real-world practicalities. These experiences are based on early data from the ClinSeq project, which is a project to pilot the use of massively parallel sequencing in a clinical research context with a major aim to develop modes of returning results to individual subjects. The study has enrolled >900 subjects and generated exome sequence data on 572 subjects. These data are beginning to be interpreted and returned to the subjects, which provides examples of the potential usefulness and pitfalls of clinical genomics. There are numerous genetic results that can be readily derived from a genome including rare, high-penetrance traits, and carrier states. However, much work needs to be done to develop the tools and resources for genomic interpretation. The main lesson learned is that a genome sequence may be better considered as a health-care resource, rather than a test, one that can be interpreted and used over the lifetime of the patient.

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...

Reconstruction of the 1997/1998 El Nino from TOPEX/POSEIDON and TOGA/TAO Data Using a Massively Parallel Pacific-Ocean Model and Ensemble Kalman Filter

Science.gov (United States)

Keppenne, C. L.; Rienecker, M.; Borovikov, A. Y.

1999-01-01

Two massively parallel data assimilation systems in which the model forecast-error covariances are estimated from the distribution of an ensemble of model integrations are applied to the assimilation of 97-98 TOPEX/POSEIDON altimetry and TOGA/TAO temperature data into a Pacific basin version the NASA Seasonal to Interannual Prediction Project (NSIPP)ls quasi-isopycnal ocean general circulation model. in the first system, ensemble of model runs forced by an ensemble of atmospheric model simulations is used to calculate asymptotic error statistics. The data assimilation then occurs in the reduced phase space spanned by the corresponding leading empirical orthogonal functions. The second system is an ensemble Kalman filter in which new error statistics are computed during each assimilation cycle from the time-dependent ensemble distribution. The data assimilation experiments are conducted on NSIPP's 512-processor CRAY T3E. The two data assimilation systems are validated by withholding part of the data and quantifying the extent to which the withheld information can be inferred from the assimilation of the remaining data. The pros and cons of each system are discussed.

Design, construction, and testing of a hysteresis controlled inverter for paralleling

OpenAIRE

Fillmore, Paul F.

2003-01-01

The U. S. Navy is pursuing an all electric ship that will require enormous amounts of power for applications such as electric propulsion. Reliability and redundancy in the electronics are imperative, since failure of a critical system could leave a ship stranded and vulnerable. A parallel inverter drive topology has been proposed to provide reliability and redundancy through load sharing. The parallel architecture enables some functionality in the event that one of the inverters fails. This t...

D2-D8 system with massive strings and the Lifshitz spacetimes

Energy Technology Data Exchange (ETDEWEB)

Singh, Harvendra [Theory Division, Saha Institute of Nuclear Physics,1/AF, Bidhannagar, Kolkata 700064 (India); Homi Bhabha National Institute,Anushakti Nagar, Mumbai 400094 (India)

2017-04-04

The Romans’ type IIA supergravity allows fundamental strings to have explicit mass term at the tree level. We show that there exists a (F1,D2,D8) brane configuration which gives rise to Lif{sub 4}{sup (2)}×R{sup 1}×S{sup 5} vacua supported by the massive strings. The presence of D8-branes naturally excites massive fundamental strings. A compactification on circle relates these Lifshitz massive type-IIA background with the axion-flux Lif{sub 4}{sup (2)}×S{sup 1}×S{sup 5} vacua in ordinary type-IIB theory. The massive T-duality in eight dimensions further relates them to yet another (Lif)-tilde {sub 4}{sup (2)}×S{sup 1}×S{sup 5} vacua constituted by (F1,D0,D6) system in ordinary type IIA theory. The latter vacua after compactification to four dimensions generate two ‘distinct’ electric charges and a constant magnetic field, all living over 2-dimensional plane. This somewhat reminds us of a similar set up in quantum Hall systems.

Xyce parallel electronic simulator : users' guide. Version 5.1.

Energy Technology Data Exchange (ETDEWEB)

Mei, Ting; Rankin, Eric Lamont; Thornquist, Heidi K.; Santarelli, Keith R.; Fixel, Deborah A.; Coffey, Todd Stirling; Russo, Thomas V.; Schiek, Richard Louis; Keiter, Eric Richard; Pawlowski, Roger Patrick

2009-11-01

This manual describes the use of the Xyce Parallel Electronic Simulator. Xyce has been designed as a SPICE-compatible, high-performance analog circuit simulator, and has been written to support the simulation needs of the Sandia National Laboratories electrical designers. This development has focused on improving capability over the current state-of-the-art in the following areas: (1) Capability to solve extremely large circuit problems by supporting large-scale parallel computing platforms (up to thousands of processors). Note that this includes support for most popular parallel and serial computers. (2) Improved performance for all numerical kernels (e.g., time integrator, nonlinear and linear solvers) through state-of-the-art algorithms and novel techniques. (3) Device models which are specifically tailored to meet Sandia's needs, including some radiation-aware devices (for Sandia users only). (4) Object-oriented code design and implementation using modern coding practices that ensure that the Xyce Parallel Electronic Simulator will be maintainable and extensible far into the future. Xyce is a parallel code in the most general sense of the phrase - a message passing parallel implementation - which allows it to run efficiently on the widest possible number of computing platforms. These include serial, shared-memory and distributed-memory parallel as well as heterogeneous platforms. Careful attention has been paid to the specific nature of circuit-simulation problems to ensure that optimal parallel efficiency is achieved as the number of processors grows. The development of Xyce provides a platform for computational research and development aimed specifically at the needs of the Laboratory. With Xyce, Sandia has an 'in-house' capability with which both new electrical (e.g., device model development) and algorithmic (e.g., faster time-integration methods, parallel solver algorithms) research and development can be performed. As a result, Xyce is a

Xyce Parallel Electronic Simulator : users' guide, version 4.1.

Energy Technology Data Exchange (ETDEWEB)

Mei, Ting; Rankin, Eric Lamont; Thornquist, Heidi K.; Santarelli, Keith R.; Fixel, Deborah A.; Coffey, Todd Stirling; Russo, Thomas V.; Schiek, Richard Louis; Keiter, Eric Richard; Pawlowski, Roger Patrick

2009-02-01

This manual describes the use of the Xyce Parallel Electronic Simulator. Xyce has been designed as a SPICE-compatible, high-performance analog circuit simulator, and has been written to support the simulation needs of the Sandia National Laboratories electrical designers. This development has focused on improving capability over the current state-of-the-art in the following areas: (1) Capability to solve extremely large circuit problems by supporting large-scale parallel computing platforms (up to thousands of processors). Note that this includes support for most popular parallel and serial computers. (2) Improved performance for all numerical kernels (e.g., time integrator, nonlinear and linear solvers) through state-of-the-art algorithms and novel techniques. (3) Device models which are specifically tailored to meet Sandia's needs, including some radiation-aware devices (for Sandia users only). (4) Object-oriented code design and implementation using modern coding practices that ensure that the Xyce Parallel Electronic Simulator will be maintainable and extensible far into the future. Xyce is a parallel code in the most general sense of the phrase - a message passing parallel implementation - which allows it to run efficiently on the widest possible number of computing platforms. These include serial, shared-memory and distributed-memory parallel as well as heterogeneous platforms. Careful attention has been paid to the specific nature of circuit-simulation problems to ensure that optimal parallel efficiency is achieved as the number of processors grows. The development of Xyce provides a platform for computational research and development aimed specifically at the needs of the Laboratory. With Xyce, Sandia has an 'in-house' capability with which both new electrical (e.g., device model development) and algorithmic (e.g., faster time-integration methods, parallel solver algorithms) research and development can be performed. As a result, Xyce is a

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

Science.gov (United States)

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

2011-01-01

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

Non-invasive terahertz field imaging inside parallel plate waveguides

DEFF Research Database (Denmark)

Iwaszczuk, Krzysztof; Andryieuski, Andrei; Lavrinenko, Andrei

2011-01-01

We present a non-invasive broadband air photonic method of imaging of the electric field of THz pulses propagating inside a tapered parallel plate waveguide. The method is based on field-enhanced second harmonic generation of the fundamental laser beam in an external electric field. We apply...

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).

GPU: the biggest key processor for AI and parallel processing

Science.gov (United States)

Baji, Toru

2017-07-01

Two types of processors exist in the market. One is the conventional CPU and the other is Graphic Processor Unit (GPU). Typical CPU is composed of 1 to 8 cores while GPU has thousands of cores. CPU is good for sequential processing, while GPU is good to accelerate software with heavy parallel executions. GPU was initially dedicated for 3D graphics. However from 2006, when GPU started to apply general-purpose cores, it was noticed that this architecture can be used as a general purpose massive-parallel processor. NVIDIA developed a software framework Compute Unified Device Architecture (CUDA) that make it possible to easily program the GPU for these application. With CUDA, GPU started to be used in workstations and supercomputers widely. Recently two key technologies are highlighted in the industry. The Artificial Intelligence (AI) and Autonomous Driving Cars. AI requires a massive parallel operation to train many-layers of neural networks. With CPU alone, it was impossible to finish the training in a practical time. The latest multi-GPU system with P100 makes it possible to finish the training in a few hours. For the autonomous driving cars, TOPS class of performance is required to implement perception, localization, path planning processing and again SoC with integrated GPU will play a key role there. In this paper, the evolution of the GPU which is one of the biggest commercial devices requiring state-of-the-art fabrication technology will be introduced. Also overview of the GPU demanding key application like the ones described above will be introduced.

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.

Parallel community climate model: Description and user`s guide

Energy Technology Data Exchange (ETDEWEB)

Drake, J.B.; Flanery, R.E.; Semeraro, B.D.; Worley, P.H. [and others

1996-07-15

This report gives an overview of a parallel version of the NCAR Community Climate Model, CCM2, implemented for MIMD massively parallel computers using a message-passing programming paradigm. The parallel implementation was developed on an Intel iPSC/860 with 128 processors and on the Intel Delta with 512 processors, and the initial target platform for the production version of the code is the Intel Paragon with 2048 processors. Because the implementation uses a standard, portable message-passing libraries, the code has been easily ported to other multiprocessors supporting a message-passing programming paradigm. The parallelization strategy used is to decompose the problem domain into geographical patches and assign each processor the computation associated with a distinct subset of the patches. With this decomposition, the physics calculations involve only grid points and data local to a processor and are performed in parallel. Using parallel algorithms developed for the semi-Lagrangian transport, the fast Fourier transform and the Legendre transform, both physics and dynamics are computed in parallel with minimal data movement and modest change to the original CCM2 source code. Sequential or parallel history tapes are written and input files (in history tape format) are read sequentially by the parallel code to promote compatibility with production use of the model on other computer systems. A validation exercise has been performed with the parallel code and is detailed along with some performance numbers on the Intel Paragon and the IBM SP2. A discussion of reproducibility of results is included. A user`s guide for the PCCM2 version 2.1 on the various parallel machines completes the report. Procedures for compilation, setup and execution are given. A discussion of code internals is included for those who may wish to modify and use the program in their own research.

New Parallel Algorithms for Landscape Evolution Model

Science.gov (United States)

Jin, Y.; Zhang, H.; Shi, Y.

2017-12-01

Most landscape evolution models (LEM) developed in the last two decades solve the diffusion equation to simulate the transportation of surface sediments. This numerical approach is difficult to parallelize due to the computation of drainage area for each node, which needs huge amount of communication if run in parallel. In order to overcome this difficulty, we developed two parallel algorithms for LEM with a stream net. One algorithm handles the partition of grid with traditional methods and applies an efficient global reduction algorithm to do the computation of drainage areas and transport rates for the stream net; the other algorithm is based on a new partition algorithm, which partitions the nodes in catchments between processes first, and then partitions the cells according to the partition of nodes. Both methods focus on decreasing communication between processes and take the advantage of massive computing techniques, and numerical experiments show that they are both adequate to handle large scale problems with millions of cells. We implemented the two algorithms in our program based on the widely used finite element library deal.II, so that it can be easily coupled with ASPECT.

Parallel time domain solvers for electrically large transient scattering problems

KAUST Repository

Liu, Yang; Yucel, Abdulkadir; Bagcý , Hakan; Michielssen, Eric

2014-01-01

scattering from perfect electrically conducting objects are obtained by enforcing electric field boundary conditions and implicitly time advance electric surface current densities by iteratively solving sparse systems of equations at all time steps. Contrary

High performance statistical computing with parallel R: applications to biology and climate modelling

International Nuclear Information System (INIS)

Samatova, Nagiza F; Branstetter, Marcia; Ganguly, Auroop R; Hettich, Robert; Khan, Shiraj; Kora, Guruprasad; Li, Jiangtian; Ma, Xiaosong; Pan, Chongle; Shoshani, Arie; Yoginath, Srikanth

2006-01-01

Ultrascale computing and high-throughput experimental technologies have enabled the production of scientific data about complex natural phenomena. With this opportunity, comes a new problem - the massive quantities of data so produced. Answers to fundamental questions about the nature of those phenomena remain largely hidden in the produced data. The goal of this work is to provide a scalable high performance statistical data analysis framework to help scientists perform interactive analyses of these raw data to extract knowledge. Towards this goal we have been developing an open source parallel statistical analysis package, called Parallel R, that lets scientists employ a wide range of statistical analysis routines on high performance shared and distributed memory architectures without having to deal with the intricacies of parallelizing these routines

Design and implementation of an integrated architecture for massive parallel data treatment of analogue signals supplied by silicon detectors of very high spatial resolution

International Nuclear Information System (INIS)

Michel, J.

1993-02-01

This doctorate thesis studies an integrated architecture designed to a parallel massive treatment of analogue signals supplied by silicon detectors of very high spatial resolution. The first chapter is an introduction presenting the general outline and the triggering conditions of the spectrometer. Chapter two describes the operational structure of a microvertex detector made of Si micro-plates associated to the measuring chains. Information preconditioning is related to the pre-amplification stage, to the pile-up effects and to the reduction in the time characteristic due to the high counting rates. The chapter three describes the architecture of the analogue delay buffer, makes an analysis of the intrinsic noise and presents the operational testings and input/output control operations. The fourth chapter is devoted to the description of the analogue pulse shape processor and gives also the testings and the corresponding measurements on the circuit. Finally, the chapter five deals with the simplest modeling of the entire conditioning chain. Also, the testings and measuring procedures are here discussed. In conclusion the author presents some prospects for improving the signal-to-noise ratio by summation of the de-convoluted micro-paths. 78 refs., 78 figs., 1 annexe

Accelerating Monte Carlo Molecular Simulations Using Novel Extrapolation Schemes Combined with Fast Database Generation on Massively Parallel Machines

KAUST Repository

Amir, Sahar Z.

2013-05-01

We introduce an efficient thermodynamically consistent technique to extrapolate and interpolate normalized Canonical NVT ensemble averages like pressure and energy for Lennard-Jones (L-J) fluids. Preliminary results show promising applicability in oil and gas modeling, where accurate determination of thermodynamic properties in reservoirs is challenging. The thermodynamic interpolation and thermodynamic extrapolation schemes predict ensemble averages at different thermodynamic conditions from expensively simulated data points. The methods reweight and reconstruct previously generated database values of Markov chains at neighboring temperature and density conditions. To investigate the efficiency of these methods, two databases corresponding to different combinations of normalized density and temperature are generated. One contains 175 Markov chains with 10,000,000 MC cycles each and the other contains 3000 Markov chains with 61,000,000 MC cycles each. For such massive database creation, two algorithms to parallelize the computations have been investigated. The accuracy of the thermodynamic extrapolation scheme is investigated with respect to classical interpolation and extrapolation. Finally, thermodynamic interpolation benefiting from four neighboring Markov chains points is implemented and compared with previous schemes. The thermodynamic interpolation scheme using knowledge from the four neighboring points proves to be more accurate than the thermodynamic extrapolation from the closest point only, while both thermodynamic extrapolation and thermodynamic interpolation are more accurate than the classical interpolation and extrapolation. The investigated extrapolation scheme has great potential in oil and gas reservoir modeling.That is, such a scheme has the potential to speed up the MCMC thermodynamic computation to be comparable with conventional Equation of State approaches in efficiency. In particular, this makes it applicable to large-scale optimization of L

Application of affymetrix array and massively parallel signature sequencing for identification of genes involved in prostate cancer progression

International Nuclear Information System (INIS)

Oudes, Asa J; Roach, Jared C; Walashek, Laura S; Eichner, Lillian J; True, Lawrence D; Vessella, Robert L; Liu, Alvin Y

2005-01-01

Affymetrix GeneChip Array and Massively Parallel Signature Sequencing (MPSS) are two high throughput methodologies used to profile transcriptomes. Each method has certain strengths and weaknesses; however, no comparison has been made between the data derived from Affymetrix arrays and MPSS. In this study, two lineage-related prostate cancer cell lines, LNCaP and C4-2, were used for transcriptome analysis with the aim of identifying genes associated with prostate cancer progression. Affymetrix GeneChip array and MPSS analyses were performed. Data was analyzed with GeneSpring 6.2 and in-house perl scripts. Expression array results were verified with RT-PCR. Comparison of the data revealed that both technologies detected genes the other did not. In LNCaP, 3,180 genes were only detected by Affymetrix and 1,169 genes were only detected by MPSS. Similarly, in C4-2, 4,121 genes were only detected by Affymetrix and 1,014 genes were only detected by MPSS. Analysis of the combined transcriptomes identified 66 genes unique to LNCaP cells and 33 genes unique to C4-2 cells. Expression analysis of these genes in prostate cancer specimens showed CA1 to be highly expressed in bone metastasis but not expressed in primary tumor and EPHA7 to be expressed in normal prostate and primary tumor but not bone metastasis. Our data indicates that transcriptome profiling with a single methodology will not fully assess the expression of all genes in a cell line. A combination of transcription profiling technologies such as DNA array and MPSS provides a more robust means to assess the expression profile of an RNA sample. Finally, genes that were differentially expressed in cell lines were also differentially expressed in primary prostate cancer and its metastases

Massively parallel signature sequencing and bioinformatics analysis identifies up-regulation of TGFBI and SOX4 in human glioblastoma.

Directory of Open Access Journals (Sweden)

Biaoyang Lin

Full Text Available BACKGROUND: A comprehensive network-based understanding of molecular pathways abnormally altered in glioblastoma multiforme (GBM is essential for developing effective therapeutic approaches for this deadly disease. METHODOLOGY/PRINCIPAL FINDINGS: Applying a next generation sequencing technology, massively parallel signature sequencing (MPSS, we identified a total of 4535 genes that are differentially expressed between normal brain and GBM tissue. The expression changes of three up-regulated genes, CHI3L1, CHI3L2, and FOXM1, and two down-regulated genes, neurogranin and L1CAM, were confirmed by quantitative PCR. Pathway analysis revealed that TGF- beta pathway related genes were significantly up-regulated in GBM tumor samples. An integrative pathway analysis of the TGF beta signaling network identified two alternative TGF-beta signaling pathways mediated by SOX4 (sex determining region Y-box 4 and TGFBI (Transforming growth factor beta induced. Quantitative RT-PCR and immunohistochemistry staining demonstrated that SOX4 and TGFBI expression is elevated in GBM tissues compared with normal brain tissues at both the RNA and protein levels. In vitro functional studies confirmed that TGFBI and SOX4 expression is increased by TGF-beta stimulation and decreased by a specific inhibitor of TGF-beta receptor 1 kinase. CONCLUSIONS/SIGNIFICANCE: Our MPSS database for GBM and normal brain tissues provides a useful resource for the scientific community. The identification of non-SMAD mediated TGF-beta signaling pathways acting through SOX4 and TGFBI (GENE ID:7045 in GBM indicates that these alternative pathways should be considered, in addition to the canonical SMAD mediated pathway, in the development of new therapeutic strategies targeting TGF-beta signaling in GBM. Finally, the construction of an extended TGF-beta signaling network with overlaid gene expression changes between GBM and normal brain extends our understanding of the biology of GBM.

A Pervasive Parallel Processing Framework for Data Visualization and Analysis at Extreme Scale

Energy Technology Data Exchange (ETDEWEB)

Moreland, Kenneth [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Geveci, Berk [Kitware, Inc., Clifton Park, NY (United States)

2014-11-01

The evolution of the computing world from teraflop to petaflop has been relatively effortless, with several of the existing programming models scaling effectively to the petascale. The migration to exascale, however, poses considerable challenges. All industry trends infer that the exascale machine will be built using processors containing hundreds to thousands of cores per chip. It can be inferred that efficient concurrency on exascale machines requires a massive amount of concurrent threads, each performing many operations on a localized piece of data. Currently, visualization libraries and applications are based off what is known as the visualization pipeline. In the pipeline model, algorithms are encapsulated as filters with inputs and outputs. These filters are connected by setting the output of one component to the input of another. Parallelism in the visualization pipeline is achieved by replicating the pipeline for each processing thread. This works well for today’s distributed memory parallel computers but cannot be sustained when operating on processors with thousands of cores. Our project investigates a new visualization framework designed to exhibit the pervasive parallelism necessary for extreme scale machines. Our framework achieves this by defining algorithms in terms of worklets, which are localized stateless operations. Worklets are atomic operations that execute when invoked unlike filters, which execute when a pipeline request occurs. The worklet design allows execution on a massive amount of lightweight threads with minimal overhead. Only with such fine-grained parallelism can we hope to fill the billions of threads we expect will be necessary for efficient computation on an exascale machine.

Advanced Electrical Machines and Machine-Based Systems for Electric and Hybrid Vehicles

OpenAIRE

Ming Cheng; Le Sun; Giuseppe Buja; Lihua Song

2015-01-01

The paper presents a number of advanced solutions on electric machines and machine-based systems for the powertrain of electric vehicles (EVs). Two types of systems are considered, namely the drive systems designated to the EV propulsion and the power split devices utilized in the popular series-parallel hybrid electric vehicle architecture. After reviewing the main requirements for the electric drive systems, the paper illustrates advanced electric machine topologies, including a stator perm...

Domain-Specific Acceleration and Auto-Parallelization of Legacy Scientific Code in FORTRAN 77 using Source-to-Source Compilation

OpenAIRE

Vanderbauwhede, Wim; Davidson, Gavin

2017-01-01

Massively parallel accelerators such as GPGPUs, manycores and FPGAs represent a powerful and affordable tool for scientists who look to speed up simulations of complex systems. However, porting code to such devices requires a detailed understanding of heterogeneous programming tools and effective strategies for parallelization. In this paper we present a source to source compilation approach with whole-program analysis to automatically transform single-threaded FORTRAN 77 legacy code into Ope...

Parallelized Seeded Region Growing Using CUDA

Directory of Open Access Journals (Sweden)

Seongjin Park

2014-01-01

Full Text Available This paper presents a novel method for parallelizing the seeded region growing (SRG algorithm using Compute Unified Device Architecture (CUDA technology, with intention to overcome the theoretical weakness of SRG algorithm of its computation time being directly proportional to the size of a segmented region. The segmentation performance of the proposed CUDA-based SRG is compared with SRG implementations on single-core CPUs, quad-core CPUs, and shader language programming, using synthetic datasets and 20 body CT scans. Based on the experimental results, the CUDA-based SRG outperforms the other three implementations, advocating that it can substantially assist the segmentation during massive CT screening tests.

Monte Carlo simulations of quantum systems on massively parallel supercomputers

International Nuclear Information System (INIS)

Ding, H.Q.

1993-01-01

A large class of quantum physics applications uses operator representations that are discrete integers by nature. This class includes magnetic properties of solids, interacting bosons modeling superfluids and Cooper pairs in superconductors, and Hubbard models for strongly correlated electrons systems. This kind of application typically uses integer data representations and the resulting algorithms are dominated entirely by integer operations. The authors implemented an efficient algorithm for one such application on the Intel Touchstone Delta and iPSC/860. The algorithm uses a multispin coding technique which allows significant data compactification and efficient vectorization of Monte Carlo updates. The algorithm regularly switches between two data decompositions, corresponding naturally to different Monte Carlo updating processes and observable measurements such that only nearest-neighbor communications are needed within a given decomposition. On 128 nodes of Intel Delta, this algorithm updates 183 million spins per second (compared to 21 million on CM-2 and 6.2 million on a Cray Y-MP). A systematic performance analysis shows a better than 90% efficiency in the parallel implementation

ParaBTM: A Parallel Processing Framework for Biomedical Text Mining on Supercomputers.

Science.gov (United States)

Xing, Yuting; Wu, Chengkun; Yang, Xi; Wang, Wei; Zhu, En; Yin, Jianping

2018-04-27

A prevailing way of extracting valuable information from biomedical literature is to apply text mining methods on unstructured texts. However, the massive amount of literature that needs to be analyzed poses a big data challenge to the processing efficiency of text mining. In this paper, we address this challenge by introducing parallel processing on a supercomputer. We developed paraBTM, a runnable framework that enables parallel text mining on the Tianhe-2 supercomputer. It employs a low-cost yet effective load balancing strategy to maximize the efficiency of parallel processing. We evaluated the performance of paraBTM on several datasets, utilizing three types of named entity recognition tasks as demonstration. Results show that, in most cases, the processing efficiency can be greatly improved with parallel processing, and the proposed load balancing strategy is simple and effective. In addition, our framework can be readily applied to other tasks of biomedical text mining besides NER.

The big chill puts the electric system under tension

International Nuclear Information System (INIS)

Huet, Sylvestre

2012-01-01

Written at the occasion of a cold wave in France in February 2012 with a new peak in electricity consumption, the article first analyses the specific meteorological conditions associated with this event, and then outlines that the massive use of electric heating makes the French system particularly sensitive to temperatures, but also that the peak is also due to the massive use of electric domestic appliances at about 7 p.m. He describes how this peak is faced in terms of energy sources and outlines that there was no risk for grid security. He comments the availability of nuclear and hydroelectric energy, and of other energies (oil, coal, gas), and the margin levels. He finally states that costs of a cold wave are predictable and could be mitigated by supporting the installation of energy-saving or non-electric heating systems

A two-level parallel direct search implementation for arbitrarily sized objective functions

Energy Technology Data Exchange (ETDEWEB)

Hutchinson, S.A.; Shadid, N.; Moffat, H.K. [Sandia National Labs., Albuquerque, NM (United States)] [and others

1994-12-31

In the past, many optimization schemes for massively parallel computers have attempted to achieve parallel efficiency using one of two methods. In the case of large and expensive objective function calculations, the optimization itself may be run in serial and the objective function calculations parallelized. In contrast, if the objective function calculations are relatively inexpensive and can be performed on a single processor, then the actual optimization routine itself may be parallelized. In this paper, a scheme based upon the Parallel Direct Search (PDS) technique is presented which allows the objective function calculations to be done on an arbitrarily large number (p{sub 2}) of processors. If, p, the number of processors available, is greater than or equal to 2p{sub 2} then the optimization may be parallelized as well. This allows for efficient use of computational resources since the objective function calculations can be performed on the number of processors that allow for peak parallel efficiency and then further speedup may be achieved by parallelizing the optimization. Results are presented for an optimization problem which involves the solution of a PDE using a finite-element algorithm as part of the objective function calculation. The optimum number of processors for the finite-element calculations is less than p/2. Thus, the PDS method is also parallelized. Performance comparisons are given for a nCUBE 2 implementation.

Second International Workshop on Software Engineering and Code Design in Parallel Meteorological and Oceanographic Applications

Science.gov (United States)

OKeefe, Matthew (Editor); Kerr, Christopher L. (Editor)

1998-01-01

This report contains the abstracts and technical papers from the Second International Workshop on Software Engineering and Code Design in Parallel Meteorological and Oceanographic Applications, held June 15-18, 1998, in Scottsdale, Arizona. The purpose of the workshop is to bring together software developers in meteorology and oceanography to discuss software engineering and code design issues for parallel architectures, including Massively Parallel Processors (MPP's), Parallel Vector Processors (PVP's), Symmetric Multi-Processors (SMP's), Distributed Shared Memory (DSM) multi-processors, and clusters. Issues to be discussed include: (1) code architectures for current parallel models, including basic data structures, storage allocation, variable naming conventions, coding rules and styles, i/o and pre/post-processing of data; (2) designing modular code; (3) load balancing and domain decomposition; (4) techniques that exploit parallelism efficiently yet hide the machine-related details from the programmer; (5) tools for making the programmer more productive; and (6) the proliferation of programming models (F--, OpenMP, MPI, and HPF).

On the adequacy of message-passing parallel supercomputers for solving neutron transport problems

International Nuclear Information System (INIS)

Azmy, Y.Y.

1990-01-01

A coarse-grained, static-scheduling parallelization of the standard iterative scheme used for solving the discrete-ordinates approximation of the neutron transport equation is described. The parallel algorithm is based on a decomposition of the angular domain along the discrete ordinates, thus naturally producing a set of completely uncoupled systems of equations in each iteration. Implementation of the parallel code on Intcl's iPSC/2 hypercube, and solutions to test problems are presented as evidence of the high speedup and efficiency of the parallel code. The performance of the parallel code on the iPSC/2 is analyzed, and a model for the CPU time as a function of the problem size (order of angular quadrature) and the number of participating processors is developed and validated against measured CPU times. The performance model is used to speculate on the potential of massively parallel computers for significantly speeding up real-life transport calculations at acceptable efficiencies. We conclude that parallel computers with a few hundred processors are capable of producing large speedups at very high efficiencies in very large three-dimensional problems. 10 refs., 8 figs

Dynamic file-access characteristics of a production parallel scientific workload

Science.gov (United States)

Kotz, David; Nieuwejaar, Nils

1994-01-01

Multiprocessors have permitted astounding increases in computational performance, but many cannot meet the intense I/O requirements of some scientific applications. An important component of any solution to this I/O bottleneck is a parallel file system that can provide high-bandwidth access to tremendous amounts of data in parallel to hundreds or thousands of processors. Most successful systems are based on a solid understanding of the expected workload, but thus far there have been no comprehensive workload characterizations of multiprocessor file systems. This paper presents the results of a three week tracing study in which all file-related activity on a massively parallel computer was recorded. Our instrumentation differs from previous efforts in that it collects information about every I/O request and about the mix of jobs running in a production environment. We also present the results of a trace-driven caching simulation and recommendations for designers of multiprocessor file systems.

Parallel Evolutionary Optimization for Neuromorphic Network Training

Energy Technology Data Exchange (ETDEWEB)

Schuman, Catherine D [ORNL; Disney, Adam [University of Tennessee (UT); Singh, Susheela [North Carolina State University (NCSU), Raleigh; Bruer, Grant [University of Tennessee (UT); Mitchell, John Parker [University of Tennessee (UT); Klibisz, Aleksander [University of Tennessee (UT); Plank, James [University of Tennessee (UT)

2016-01-01

One of the key impediments to the success of current neuromorphic computing architectures is the issue of how best to program them. Evolutionary optimization (EO) is one promising programming technique; in particular, its wide applicability makes it especially attractive for neuromorphic architectures, which can have many different characteristics. In this paper, we explore different facets of EO on a spiking neuromorphic computing model called DANNA. We focus on the performance of EO in the design of our DANNA simulator, and on how to structure EO on both multicore and massively parallel computing systems. We evaluate how our parallel methods impact the performance of EO on Titan, the U.S.'s largest open science supercomputer, and BOB, a Beowulf-style cluster of Raspberry Pi's. We also focus on how to improve the EO by evaluating commonality in higher performing neural networks, and present the result of a study that evaluates the EO performed by Titan.

Implementation of parallel processing in the basf2 framework for Belle II

International Nuclear Information System (INIS)

Itoh, Ryosuke; Lee, Soohyung; Katayama, N; Mineo, S; Moll, A; Kuhr, T; Heck, M

2012-01-01

Recent PC servers are equipped with multi-core CPUs and it is desired to utilize the full processing power of them for the data analysis in large scale HEP experiments. A software framework basf2 is being developed for the use in the Belle II experiment, a new generation B-factory experiment at KEK, and the parallel event processing to utilize the multi-core CPUs is in its design for the use in the massive data production. The details of the implementation of event parallel processing in the basf2 framework are discussed with the report of preliminary performance study in the realistic use on a 32 core PC server.

Electric Mars: A large trans-terminator electric potential drop on closed magnetic field lines above Utopia Planitia

Science.gov (United States)

Collinson, Glyn; Mitchell, David; Xu, Shaosui; Glocer, Alex; Grebowsky, Joseph; Hara, Takuya; Lillis, Robert; Espley, Jared; Mazelle, Christian; Sauvaud, Jean-André; Fedorov, Andrey; Liemohn, Mike; Andersson, Laila; Jakosky, Bruce

2017-02-01

Parallel electric fields and their associated electric potential structures play a crucial role in ionospheric-magnetospheric interactions at any planet. Although there is abundant evidence that parallel electric fields play key roles in Martian ionospheric outflow and auroral electron acceleration, the fields themselves are challenging to directly measure due to their relatively weak nature. Using measurements by the Solar Wind Electron Analyzer instrument aboard the NASA Mars Atmosphere and Volatile EvolutioN (MAVEN) Mars Scout, we present the discovery and measurement of a substantial (ΦMars=7.7 ± 0.6 V) parallel electric potential drop on closed magnetic field lines spanning the terminator from day to night above the great impact basin of Utopia Planitia, a region largely free of crustal magnetic fields. A survey of the previous 26 orbits passing over a range of longitudes revealed similar signatures on seven orbits, with a mean potential drop (ΦMars) of 10.9 ± 0.8 V, suggestive that although trans-terminator electric fields of comparable strength are not ubiquitous, they may be common, at least at these northerly latitudes.

Electric Mars: A Large Trans-Terminator Electric Potential Drop on Closed Magnetic Field Lines Above Utopia Planitia

Science.gov (United States)

Collinson, Glyn; Mitchell, David; Xu, Shaosui; Glocer, Alex; Grebowsky, Joseph; Hara, Takuya; Lillis, Robert; Espley, Jared; Mazelle, Christian; Sauvaud, Jean-Andre

2017-01-01

Abstract Parallel electric fields and their associated electric potential structures play a crucial role inionospheric-magnetospheric interactions at any planet. Although there is abundant evidence that parallel electric fields play key roles in Martian ionospheric outflow and auroral electron acceleration, the fields themselves are challenging to directly measure due to their relatively weak nature. Using measurements by the Solar Wind Electron Analyzer instrument aboard the NASA Mars Atmosphere and Volatile EvolutioN(MAVEN) Mars Scout, we present the discovery and measurement of a substantial (Phi) Mars 7.7 +/-0.6 V) parallel electric potential drop on closed magnetic field lines spanning the terminator from day to night above the great impact basin of Utopia Planitia, a region largely free of crustal magnetic fields. A survey of the previous 26 orbits passing over a range of longitudes revealed similar signatures on seven orbits, with a mean potential drop (Phi) Mars of 10.9 +/- 0.8 V, suggestive that although trans-terminator electric fields of comparable strength are not ubiquitous, they may be common, at least at these northerly latitudes.

3D multiphysics modeling of superconducting cavities with a massively parallel simulation suite

Directory of Open Access Journals (Sweden)

Oleksiy Kononenko

2017-10-01

Full Text Available Radiofrequency cavities based on superconducting technology are widely used in particle accelerators for various applications. The cavities usually have high quality factors and hence narrow bandwidths, so the field stability is sensitive to detuning from the Lorentz force and external loads, including vibrations and helium pressure variations. If not properly controlled, the detuning can result in a serious performance degradation of a superconducting accelerator, so an understanding of the underlying detuning mechanisms can be very helpful. Recent advances in the simulation suite ace3p have enabled realistic multiphysics characterization of such complex accelerator systems on supercomputers. In this paper, we present the new capabilities in ace3p for large-scale 3D multiphysics modeling of superconducting cavities, in particular, a parallel eigensolver for determining mechanical resonances, a parallel harmonic response solver to calculate the response of a cavity to external vibrations, and a numerical procedure to decompose mechanical loads, such as from the Lorentz force or piezoactuators, into the corresponding mechanical modes. These capabilities have been used to do an extensive rf-mechanical analysis of dressed TESLA-type superconducting cavities. The simulation results and their implications for the operational stability of the Linac Coherent Light Source-II are discussed.

A statistical study of high-altitude electric fields measured on the Viking satellite

International Nuclear Information System (INIS)

Lindqvist, P.A.; Marklund, G.T.

1990-01-01

Characteristics of high-altitude data from the Viking electric field instrument are presented in a statistical study based on 109 Viking orbits. The study is focused in particular on the signatures of and relationships between various parameters measured by the electric field instrument, such as the parallel and transverse (to B) components of the electric field instrument, such as electric field variability. A major goal of the Viking mission was to investigate the occurrence and properties of parallel electric fields and their role in the auroral acceleration process. The results in this paper on the altitude distribution of the electric field variability confirm earlier findings on the distribution of small-scale electric fields and indicate the presence of parallel fields up to about 11,000 km altitude. The directly measured parallel electric field is also investigated in some detail. It is in general directed upward with an average value of 1 mV/m, but depends on, for example, altitude and plasma density. Possible sources of error in the measurement of the parallel field are also considered and accounted for

Touch imprint cytology with massively parallel sequencing (TIC-seq): a simple and rapid method to snapshot genetic alterations in tumors.

Science.gov (United States)

Amemiya, Kenji; Hirotsu, Yosuke; Goto, Taichiro; Nakagomi, Hiroshi; Mochizuki, Hitoshi; Oyama, Toshio; Omata, Masao

2016-12-01

Identifying genetic alterations in tumors is critical for molecular targeting of therapy. In the clinical setting, formalin-fixed paraffin-embedded (FFPE) tissue is usually employed for genetic analysis. However, DNA extracted from FFPE tissue is often not suitable for analysis because of its low levels and poor quality. Additionally, FFPE sample preparation is time-consuming. To provide early treatment for cancer patients, a more rapid and robust method is required for precision medicine. We present a simple method for genetic analysis, called touch imprint cytology combined with massively paralleled sequencing (touch imprint cytology [TIC]-seq), to detect somatic mutations in tumors. We prepared FFPE tissues and TIC specimens from tumors in nine lung cancer patients and one patient with breast cancer. We found that the quality and quantity of TIC DNA was higher than that of FFPE DNA, which requires microdissection to enrich DNA from target tissues. Targeted sequencing using a next-generation sequencer obtained sufficient sequence data using TIC DNA. Most (92%) somatic mutations in lung primary tumors were found to be consistent between TIC and FFPE DNA. We also applied TIC DNA to primary and metastatic tumor tissues to analyze tumor heterogeneity in a breast cancer patient, and showed that common and distinct mutations among primary and metastatic sites could be classified into two distinct histological subtypes. TIC-seq is an alternative and feasible method to analyze genomic alterations in tumors by simply touching the cut surface of specimens to slides. © 2016 The Authors. Cancer Medicine published by John Wiley & Sons Ltd.

Creation of vector bosons by an electric field in curved spacetime

International Nuclear Information System (INIS)

Kangal, E. Ersin; Yanar, Hilmi; Havare, Ali; Sogut, Kenan

2014-01-01

We investigate the creation rate of massive spin-1 bosons in the de Sitter universe by a time-dependent electric field via the Duffin–Kemmer–Petiau (DKP) equation. Complete solutions are given by the Whittaker functions and particle creation rate is computed by using the Bogoliubov transformation technique. We analyze the influence of the electric field on the particle creation rate for the strong and vanishing electric fields. We show that the electric field amplifies the creation rate of charged, massive spin-1 particles. This effect is analyzed by considering similar calculations performed for scalar and spin-1/2 particles. -- Highlights: •Duffin–Kemmer–Petiau equation is solved exactly in the presence of an electrical field. •Solutions were made in (1+1)-dimensional curved spacetime. •Particle creation rate for the de Sitter model is calculated. •Pure gravitational or pure electrical field effect on the creation rate is analyzed

Military Curricula for Vocational & Technical Education. Basic Electricity and Electronics Individualized Learning System. CANTRAC A-100-0010. Module Fourteen: Parallel AC Resistive-Reactive Circuits. Study Booklet.

Science.gov (United States)

Chief of Naval Education and Training Support, Pensacola, FL.

This individualized learning module on parallel alternating current resistive-reaction circuits is one in a series of modules for a course in basic electricity and electronics. The course is one of a number of military-developed curriculum packages selected for adaptation to vocational instructional and curriculum development in a civilian…

Load-balancing techniques for a parallel electromagnetic particle-in-cell code

Energy Technology Data Exchange (ETDEWEB)

PLIMPTON,STEVEN J.; SEIDEL,DAVID B.; PASIK,MICHAEL F.; COATS,REBECCA S.

2000-01-01

QUICKSILVER is a 3-d electromagnetic particle-in-cell simulation code developed and used at Sandia to model relativistic charged particle transport. It models the time-response of electromagnetic fields and low-density-plasmas in a self-consistent manner: the fields push the plasma particles and the plasma current modifies the fields. Through an LDRD project a new parallel version of QUICKSILVER was created to enable large-scale plasma simulations to be run on massively-parallel distributed-memory supercomputers with thousands of processors, such as the Intel Tflops and DEC CPlant machines at Sandia. The new parallel code implements nearly all the features of the original serial QUICKSILVER and can be run on any platform which supports the message-passing interface (MPI) standard as well as on single-processor workstations. This report describes basic strategies useful for parallelizing and load-balancing particle-in-cell codes, outlines the parallel algorithms used in this implementation, and provides a summary of the modifications made to QUICKSILVER. It also highlights a series of benchmark simulations which have been run with the new code that illustrate its performance and parallel efficiency. These calculations have up to a billion grid cells and particles and were run on thousands of processors. This report also serves as a user manual for people wishing to run parallel QUICKSILVER.

Load-balancing techniques for a parallel electromagnetic particle-in-cell code

International Nuclear Information System (INIS)

Plimpton, Steven J.; Seidel, David B.; Pasik, Michael F.; Coats, Rebecca S.

2000-01-01

QUICKSILVER is a 3-d electromagnetic particle-in-cell simulation code developed and used at Sandia to model relativistic charged particle transport. It models the time-response of electromagnetic fields and low-density-plasmas in a self-consistent manner: the fields push the plasma particles and the plasma current modifies the fields. Through an LDRD project a new parallel version of QUICKSILVER was created to enable large-scale plasma simulations to be run on massively-parallel distributed-memory supercomputers with thousands of processors, such as the Intel Tflops and DEC CPlant machines at Sandia. The new parallel code implements nearly all the features of the original serial QUICKSILVER and can be run on any platform which supports the message-passing interface (MPI) standard as well as on single-processor workstations. This report describes basic strategies useful for parallelizing and load-balancing particle-in-cell codes, outlines the parallel algorithms used in this implementation, and provides a summary of the modifications made to QUICKSILVER. It also highlights a series of benchmark simulations which have been run with the new code that illustrate its performance and parallel efficiency. These calculations have up to a billion grid cells and particles and were run on thousands of processors. This report also serves as a user manual for people wishing to run parallel QUICKSILVER

The massive transformation in Ti-Al alloys: mechanistic observations

International Nuclear Information System (INIS)

Zhang, X.D.; Godfrey, S.; Weaver, M.; Strangwood, M.; Kaufman, M.J.; Loretto, M.H.

1996-01-01

The massive α→γ m transformation, as observed using analytical transmission electron microscopy, in Ti-49Al, Ti-48Al-2Nb-2Mn, Ti-55Al-25Ta and Ti-50Al-20Ta alloys is described. Conventional solution heating and quenching experiments have been combined with the more rapid quenching possible using electron beam melting in order to provide further insight into the early stages of the transformation of these alloys. It is shown that the γ develops first at grain boundaries as lamellae in one of the grains and that these lamellae intersect and spread into the adjacent grain in a massive manner. Consequently, there is no orientation relationship between the massive gamma (γ m ) and the grain being consumed whereas there is the expected relation between the γ m and the first grain which is inherited from the lamellae. It is further shown that the γ m grows as an f.c.c. phase after initially growing with the L1 0 structure. Furthermore, it is shown that the massive f.c.c. phase then orders to the L1 0 structure producing APDB-like defects which are actually thin 90 degree domains separating adjacent domains that have the same orientation yet are out of phase. The advancing γ m interface tends to facet parallel either to one of its four {111} planes or to the basal plane in the grain being consumed by impinging on existing γ lamellae. Thin microtwins and α 2 platelets then form in the γ m presumably due, respectively, to transformation stresses and supersaturation of the γ m with titanium for alloys containing ∼48% Al; indeed, there is a local depletion in aluminium across the α 2 platelets as determined using fine probe microanalysis

Parallel heater system for subsurface formations

Science.gov (United States)

Harris, Christopher Kelvin [Houston, TX; Karanikas, John Michael [Houston, TX; Nguyen, Scott Vinh [Houston, TX

2011-10-25

A heating system for a subsurface formation is disclosed. The system includes a plurality of substantially horizontally oriented or inclined heater sections located in a hydrocarbon containing layer in the formation. At least a portion of two of the heater sections are substantially parallel to each other. The ends of at least two of the heater sections in the layer are electrically coupled to a substantially horizontal, or inclined, electrical conductor oriented substantially perpendicular to the ends of the at least two heater sections.

Radiation-magnetohydrodynamics of fusion plasmas on parallel supercomputers

International Nuclear Information System (INIS)

Yasar, O.; Moses, G.A.; Tautges, T.J.

1993-01-01

A parallel computational model to simulate fusion plasmas in the radiation-magnetohydrodynamics (R-MHD) framework is presented. Plasmas are often treated in a fluid dynamics context (magnetohydrodynamics, MHD), but when the flow field is coupled with the radiation field it falls into a more complex category, radiation magnetohydrodynamics (R-MHD), where the interaction between the flow field and the radiation field is nonlinear. The solution for the radiation field usually dominates the R-MHD computation. To solve for the radiation field, one usually chooses the S N discrete ordinates method (a deterministic method) rather than the Monte Carlo method if the geometry is not complex. The discrete ordinates method on a massively parallel processor (Intel iPSC/860) is implemented. The speedup is 14 for a run on 16 processors and the performance is 3.7 times better than a single CRAY YMP processor implementation. (orig./DG)

A LiFePO4 battery pack capacity estimation approach considering in-parallel cell safety in electric vehicles

International Nuclear Information System (INIS)

Wang, Limei; Cheng, Yong; Zhao, Xiuliang

2015-01-01

Highlights: • Find the influence of in-parallel battery cell variations on battery pack capacity. • Redefine the battery module capacity with considering ANY battery cell safety. • Discuss the safety end-of-charge voltage for an aged in-parallel battery module. • Build an algorithm for battery pack capacity estimation with the charge curve. • Bench tests are used to verify the validity of the proposed algorithm. - Abstract: In electric vehicles (EVs), several battery cells are connected in parallel to establish a battery module. The safety of the battery module is influenced by inconsistent battery cell performance which causes uneven currents flowing through internal in-parallel battery cells. A battery cell model is developed based on the Matlab–Simscape platform and validated by tests. The battery cell model is used to construct simulation models for analyzing the effect of battery cell inconsistency on the performance of an in-parallel battery module. Simulation results indicate that the state-of-charge (SOC) of a battery module cannot characterize the SOC of ALL the internal battery cells in the battery module. When the battery management system (BMS) controls the end-of-charge (EOC) time according to the SOC of a battery module, some internal battery cells are over-charged. To guarantee the safety of ALL battery cells through the whole battery life, a safety EOC voltage of the battery module should be set according to the number of battery cells in the battery module and the applied charge current. Simulations reveal that the SOC of the “normal battery module” is related to its charge voltage when aged battery module is charged to the EOC voltage. Then, a function describing their relationship is established. Both the capacity and the charge voltage shift are estimated by comparing the measured voltage-to-capacity curve with the standard one provided by the manufactory. A battery pack capacity estimation method is proposed according to the SOC

Greybody factors of massive charged fermionic fields in a charged two-dimensional dilatonic black hole

Energy Technology Data Exchange (ETDEWEB)

Becar, Ramon [Universidad Catolica de Temuco, Departamento de Ciencias Matematicas y Fisicas, Temuco (Chile); Gonzalez, P.A. [Universidad Diego Portales, Facultad de Ingenieria, Santiago (Chile); Saavedra, Joel [Pontificia Universidad Catolica de Valparaiso, Instituto de Fisica, Valparaiso (Chile); Vasquez, Yerko [Universidad de La Serena, Departamento de Fisica, Facultad de Ciencias, La Serena (Chile)

2015-02-01

We study massive charged fermionic perturbations in the background of a charged two-dimensional dilatonic black hole, and we solve the Dirac equation analytically. Then we compute the reflection and transmission coefficients and the absorption cross section for massive charged fermionic fields, and we show that the absorption cross section vanishes at the low- and high-frequency limits. However, there is a range of frequencies where the absorption cross section is not null. Furthermore, we study the effect of the mass and electric charge of the fermionic field over the absorption cross section. (orig.)

Massive Submucosal Ganglia in Colonic Inertia.

Science.gov (United States)

Naemi, Kaveh; Stamos, Michael J; Wu, Mark Li-Cheng

2018-02-01

- Colonic inertia is a debilitating form of primary chronic constipation with unknown etiology and diagnostic criteria, often requiring pancolectomy. We have occasionally observed massively enlarged submucosal ganglia containing at least 20 perikarya, in addition to previously described giant ganglia with greater than 8 perikarya, in cases of colonic inertia. These massively enlarged ganglia have yet to be formally recognized. - To determine whether such "massive submucosal ganglia," defined as ganglia harboring at least 20 perikarya, characterize colonic inertia. - We retrospectively reviewed specimens from colectomies of patients with colonic inertia and compared the prevalence of massive submucosal ganglia occurring in this setting to the prevalence of massive submucosal ganglia occurring in a set of control specimens from patients lacking chronic constipation. - Seven of 8 specimens affected by colonic inertia harbored 1 to 4 massive ganglia, for a total of 11 massive ganglia. One specimen lacked massive ganglia but had limited sampling and nearly massive ganglia. Massive ganglia occupied both superficial and deep submucosal plexus. The patient with 4 massive ganglia also had 1 mitotically active giant ganglion. Only 1 massive ganglion occupied the entire set of 10 specimens from patients lacking chronic constipation. - We performed the first, albeit distinctly small, study of massive submucosal ganglia and showed that massive ganglia may be linked to colonic inertia. Further, larger studies are necessary to determine whether massive ganglia are pathogenetic or secondary phenomena, and whether massive ganglia or mitotically active ganglia distinguish colonic inertia from other types of chronic constipation.

Energy Efficiency Comparison between Hydraulic Hybrid and Hybrid Electric Vehicles

Directory of Open Access Journals (Sweden)

Jia-Shiun Chen

2015-05-01

Full Text Available Conventional vehicles tend to consume considerable amounts of fuel, which generates exhaust gases and environmental pollution during intermittent driving cycles. Therefore, prospective vehicle designs favor improved exhaust emissions and energy consumption without compromising vehicle performance. Although pure electric vehicles feature high performance and low pollution characteristics, their limitations are their short driving range and high battery costs. Hybrid electric vehicles (HEVs are comparatively environmentally friendly and energy efficient, but cost substantially more compared with conventional vehicles. Hydraulic hybrid vehicles (HHVs are mainly operated using engines, or using alternate combinations of engine and hydraulic power sources while vehicles accelerate. When the hydraulic system accumulator is depleted, the conventional engine reengages; concurrently, brake-regenerated power is recycled and reused by employing hydraulic motor–pump modules in circulation patterns to conserve fuel and recycle brake energy. This study adopted MATLAB Simulink to construct complete HHV and HEV models for backward simulations. New European Driving Cycles were used to determine the changes in fuel economy. The output of power components and the state-of-charge of energy could be retrieved. Varying power component models, energy storage component models, and series or parallel configurations were combined into seven different vehicle configurations: the conventional manual transmission vehicle, series hybrid electric vehicle, series hydraulic hybrid vehicle, parallel hybrid electric vehicle, parallel hydraulic hybrid vehicle, purely electric vehicle, and hydraulic-electric hybrid vehicle. The simulation results show that fuel consumption was 21.80% lower in the series hydraulic hybrid vehicle compared to the series hybrid electric vehicle; additionally, fuel consumption was 3.80% lower in the parallel hybrid electric vehicle compared to the

GROMACS 4.5: A high-throughput and highly parallel open source molecular simulation toolkit

Energy Technology Data Exchange (ETDEWEB)

Pronk, Sander [Science for Life Lab., Stockholm (Sweden); KTH Royal Institute of Technology, Stockholm (Sweden); Pall, Szilard [Science for Life Lab., Stockholm (Sweden); KTH Royal Institute of Technology, Stockholm (Sweden); Schulz, Roland [Univ. of Tennessee, Knoxville, TN (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Larsson, Per [Univ. of Virginia, Charlottesville, VA (United States); Bjelkmar, Par [Science for Life Lab., Stockholm (Sweden); Stockholm Univ., Stockholm (Sweden); Apostolov, Rossen [Science for Life Lab., Stockholm (Sweden); KTH Royal Institute of Technology, Stockholm (Sweden); Shirts, Michael R. [Univ. of Virginia, Charlottesville, VA (United States); Smith, Jeremy C. [Univ. of Tennessee, Knoxville, TN (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Kasson, Peter M. [Univ. of Virginia, Charlottesville, VA (United States); van der Spoel, David [Science for Life Lab., Stockholm (Sweden); Uppsala Univ., Uppsala (Sweden); Hess, Berk [Science for Life Lab., Stockholm (Sweden); KTH Royal Institute of Technology, Stockholm (Sweden); Lindahl, Erik [Science for Life Lab., Stockholm (Sweden); KTH Royal Institute of Technology, Stockholm (Sweden); Stockholm Univ., Stockholm (Sweden)

2013-02-13

In this study, molecular simulation has historically been a low-throughput technique, but faster computers and increasing amounts of genomic and structural data are changing this by enabling large-scale automated simulation of, for instance, many conformers or mutants of biomolecules with or without a range of ligands. At the same time, advances in performance and scaling now make it possible to model complex biomolecular interaction and function in a manner directly testable by experiment. These applications share a need for fast and efficient software that can be deployed on massive scale in clusters, web servers, distributed computing or cloud resources. As a result, we present a range of new simulation algorithms and features developed during the past 4 years, leading up to the GROMACS 4.5 software package. The software now automatically handles wide classes of biomolecules, such as proteins, nucleic acids and lipids, and comes with all commonly used force fields for these molecules built-in. GROMACS supports several implicit solvent models, as well as new free-energy algorithms, and the software now uses multithreading for efficient parallelization even on low-end systems, including windows-based workstations. Together with hand-tuned assembly kernels and state-of-the-art parallelization, this provides extremely high performance and cost efficiency for high-throughput as well as massively parallel simulations.

A search for stable massive particles carrying electric charges in the range of 2e to 6e in proton-proton collisions at $\\sqrt{s}$ = 7 TeV recorded with the ATLAS detector at the LHC

CERN Document Server

Zimmermann, Simone

This dissertation presents a search for long-lived, multi-charged particles using the ATLAS detector at the LHC. Motivation for this search arose from an unexploited search regime at ATLAS of stable massive particles with electric charges of |q| = 2e to |q| = 5e. Additional motivation can be found in several beyond the Standard Model physics theories. Proton-proton collisions recorded during the 2011 LHC running at $\\sqrt{s}$ = 7 TeV, corresponding to an integrated luminosity of 4.4 $fb^{-1}$, are examined in a signature-based analysis. The search seeks out charged particle tracks exhibiting anomalously high ionization consistent with stable massive particles with electric charges in the range from |q| = 2e to |q| = 6e. For this search, new variables of specific energy loss per path length dE/dx are used in the candidate selection. One of these variables, the TRT dE/dx, is developed in the course of this thesis and is described in detail. No excess is observed with respect to the prediction of Standard Model...

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.

Rubus: A compiler for seamless and extensible parallelism

Science.gov (United States)

Adnan, Muhammad; Aslam, Faisal; Sarwar, Syed Mansoor

2017-01-01

Nowadays, a typical processor may have multiple processing cores on a single chip. Furthermore, a special purpose processing unit called Graphic Processing Unit (GPU), originally designed for 2D/3D games, is now available for general purpose use in computers and mobile devices. However, the traditional programming languages which were designed to work with machines having single core CPUs, cannot utilize the parallelism available on multi-core processors efficiently. Therefore, to exploit the extraordinary processing power of multi-core processors, researchers are working on new tools and techniques to facilitate parallel programming. To this end, languages like CUDA and OpenCL have been introduced, which can be used to write code with parallelism. The main shortcoming of these languages is that programmer needs to specify all the complex details manually in order to parallelize the code across multiple cores. Therefore, the code written in these languages is difficult to understand, debug and maintain. Furthermore, to parallelize legacy code can require rewriting a significant portion of code in CUDA or OpenCL, which can consume significant time and resources. Thus, the amount of parallelism achieved is proportional to the skills of the programmer and the time spent in code optimizations. This paper proposes a new open source compiler, Rubus, to achieve seamless parallelism. The Rubus compiler relieves the programmer from manually specifying the low-level details. It analyses and transforms a sequential program into a parallel program automatically, without any user intervention. This achieves massive speedup and better utilization of the underlying hardware without a programmer’s expertise in parallel programming. For five different benchmarks, on average a speedup of 34.54 times has been achieved by Rubus as compared to Java on a basic GPU having only 96 cores. Whereas, for a matrix multiplication benchmark the average execution speedup of 84 times has been

Rubus: A compiler for seamless and extensible parallelism.

Directory of Open Access Journals (Sweden)

Muhammad Adnan

Full Text Available Nowadays, a typical processor may have multiple processing cores on a single chip. Furthermore, a special purpose processing unit called Graphic Processing Unit (GPU, originally designed for 2D/3D games, is now available for general purpose use in computers and mobile devices. However, the traditional programming languages which were designed to work with machines having single core CPUs, cannot utilize the parallelism available on multi-core processors efficiently. Therefore, to exploit the extraordinary processing power of multi-core processors, researchers are working on new tools and techniques to facilitate parallel programming. To this end, languages like CUDA and OpenCL have been introduced, which can be used to write code with parallelism. The main shortcoming of these languages is that programmer needs to specify all the complex details manually in order to parallelize the code across multiple cores. Therefore, the code written in these languages is difficult to understand, debug and maintain. Furthermore, to parallelize legacy code can require rewriting a significant portion of code in CUDA or OpenCL, which can consume significant time and resources. Thus, the amount of parallelism achieved is proportional to the skills of the programmer and the time spent in code optimizations. This paper proposes a new open source compiler, Rubus, to achieve seamless parallelism. The Rubus compiler relieves the programmer from manually specifying the low-level details. It analyses and transforms a sequential program into a parallel program automatically, without any user intervention. This achieves massive speedup and better utilization of the underlying hardware without a programmer's expertise in parallel programming. For five different benchmarks, on average a speedup of 34.54 times has been achieved by Rubus as compared to Java on a basic GPU having only 96 cores. Whereas, for a matrix multiplication benchmark the average execution speedup of 84

New massive gravity

NARCIS (Netherlands)

Bergshoeff, Eric A.; Hohm, Olaf; Townsend, Paul K.

2012-01-01

We present a brief review of New Massive Gravity, which is a unitary theory of massive gravitons in three dimensions obtained by considering a particular combination of the Einstein-Hilbert and curvature squared terms.

STABLE ISOTOPE GEOCHEMISTRY OF MASSIVE ICE

Directory of Open Access Journals (Sweden)

Yurij K. Vasil’chuk

2016-01-01

Full Text Available The paper summarises stable-isotope research on massive ice in the Russian and North American Arctic, and includes the latest understanding of massive-ice formation. A new classification of massive-ice complexes is proposed, encompassing the range and variabilityof massive ice. It distinguishes two new categories of massive-ice complexes: homogeneousmassive-ice complexes have a similar structure, properties and genesis throughout, whereasheterogeneous massive-ice complexes vary spatially (in their structure and properties andgenetically within a locality and consist of two or more homogeneous massive-ice bodies.Analysis of pollen and spores in massive ice from Subarctic regions and from ice and snow cover of Arctic ice caps assists with interpretation of the origin of massive ice. Radiocarbon ages of massive ice and host sediments are considered together with isotope values of heavy oxygen and deuterium from massive ice plotted at a uniform scale in order to assist interpretation and correlation of the ice.

Parallel nanostructuring of GeSbTe film with particle mask

Energy Technology Data Exchange (ETDEWEB)

Wang, Z.B.; Hong, M.H.; Wang, Q.F.; Chong, T.C. [Data Storage Institute, DSI Building, 5 Engineering Drive 1, 117608, Singapore (Singapore); Department of Electrical and Computer Engineering, National University of Singapore, 119260, Singapore (Singapore); Luk' yanchuk, B.S.; Huang, S.M.; Shi, L.P. [Data Storage Institute, DSI Building, 5 Engineering Drive 1, 117608, Singapore (Singapore)

2004-09-01

Parallel nanostructuring of a GeSbTe film may significantly improve the recording performance in data storage. In this paper, a method that permits direct and massively parallel nanopatterning of the substrate surface by laser irradiation is investigated. Polystyrene spherical particles were deposited on the surface in a monolayer array by self-assembly. The array was then irradiated with a 248-nm KrF laser. A sub-micron nanodent array can be obtained after single-pulse irradiation. These nanodents change their shapes at different laser energies. The optical near-field distribution around the particles was calculated according to the exact solution of the light-scattering problem. The influence of the presence of the substrate on the optical near field was also studied. The mechanisms for the generation of the nanodent structures are discussed. (orig.)

Genome-wide massively parallel sequencing of formaldehyde fixed-paraffin embedded (FFPE tumor tissues for copy-number- and mutation-analysis.

Directory of Open Access Journals (Sweden)

Michal R Schweiger

Full Text Available BACKGROUND: Cancer re-sequencing programs rely on DNA isolated from fresh snap frozen tissues, the preparation of which is combined with additional preservation efforts. Tissue samples at pathology departments are routinely stored as formalin-fixed and paraffin-embedded (FFPE samples and their use would open up access to a variety of clinical trials. However, FFPE preparation is incompatible with many down-stream molecular biology techniques such as PCR based amplification methods and gene expression studies. METHODOLOGY/PRINCIPAL FINDINGS: Here we investigated the sample quality requirements of FFPE tissues for massively parallel short-read sequencing approaches. We evaluated key variables of pre-fixation, fixation related and post-fixation processes that occur in routine medical service (e.g. degree of autolysis, duration of fixation and of storage. We also investigated the influence of tissue storage time on sequencing quality by using material that was up to 18 years old. Finally, we analyzed normal and tumor breast tissues using the Sequencing by Synthesis technique (Illumina Genome Analyzer, Solexa to simultaneously localize genome-wide copy number alterations and to detect genomic variations such as substitutions and point-deletions and/or insertions in FFPE tissue samples. CONCLUSIONS/SIGNIFICANCE: The application of second generation sequencing techniques on small amounts of FFPE material opens up the possibility to analyze tissue samples which have been collected during routine clinical work as well as in the context of clinical trials. This is in particular important since FFPE samples are amply available from surgical tumor resections and histopathological diagnosis, and comprise tissue from precursor lesions, primary tumors, lymphogenic and/or hematogenic metastases. Large-scale studies using this tissue material will result in a better prediction of the prognosis of cancer patients and the early identification of patients which

Efficient high-precision matrix algebra on parallel architectures for nonlinear combinatorial optimization

KAUST Repository

Gunnels, John; Lee, Jon; Margulies, Susan

2010-01-01

We provide a first demonstration of the idea that matrix-based algorithms for nonlinear combinatorial optimization problems can be efficiently implemented. Such algorithms were mainly conceived by theoretical computer scientists for proving efficiency. We are able to demonstrate the practicality of our approach by developing an implementation on a massively parallel architecture, and exploiting scalable and efficient parallel implementations of algorithms for ultra high-precision linear algebra. Additionally, we have delineated and implemented the necessary algorithmic and coding changes required in order to address problems several orders of magnitude larger, dealing with the limits of scalability from memory footprint, computational efficiency, reliability, and interconnect perspectives. © Springer and Mathematical Programming Society 2010.

Efficient high-precision matrix algebra on parallel architectures for nonlinear combinatorial optimization

KAUST Repository

Gunnels, John

2010-06-01

We provide a first demonstration of the idea that matrix-based algorithms for nonlinear combinatorial optimization problems can be efficiently implemented. Such algorithms were mainly conceived by theoretical computer scientists for proving efficiency. We are able to demonstrate the practicality of our approach by developing an implementation on a massively parallel architecture, and exploiting scalable and efficient parallel implementations of algorithms for ultra high-precision linear algebra. Additionally, we have delineated and implemented the necessary algorithmic and coding changes required in order to address problems several orders of magnitude larger, dealing with the limits of scalability from memory footprint, computational efficiency, reliability, and interconnect perspectives. © Springer and Mathematical Programming Society 2010.

The Parallel System for Integrating Impact Models and Sectors (pSIMS)

Science.gov (United States)

Elliott, Joshua; Kelly, David; Chryssanthacopoulos, James; Glotter, Michael; Jhunjhnuwala, Kanika; Best, Neil; Wilde, Michael; Foster, Ian

2014-01-01

We present a framework for massively parallel climate impact simulations: the parallel System for Integrating Impact Models and Sectors (pSIMS). This framework comprises a) tools for ingesting and converting large amounts of data to a versatile datatype based on a common geospatial grid; b) tools for translating this datatype into custom formats for site-based models; c) a scalable parallel framework for performing large ensemble simulations, using any one of a number of different impacts models, on clusters, supercomputers, distributed grids, or clouds; d) tools and data standards for reformatting outputs to common datatypes for analysis and visualization; and e) methodologies for aggregating these datatypes to arbitrary spatial scales such as administrative and environmental demarcations. By automating many time-consuming and error-prone aspects of large-scale climate impacts studies, pSIMS accelerates computational research, encourages model intercomparison, and enhances reproducibility of simulation results. We present the pSIMS design and use example assessments to demonstrate its multi-model, multi-scale, and multi-sector versatility.

Massive graviton geons

Science.gov (United States)

Aoki, Katsuki; Maeda, Kei-ichi; Misonoh, Yosuke; Okawa, Hirotada

2018-02-01

We find vacuum solutions such that massive gravitons are confined in a local spacetime region by their gravitational energy in asymptotically flat spacetimes in the context of the bigravity theory. We call such self-gravitating objects massive graviton geons. The basic equations can be reduced to the Schrödinger-Poisson equations with the tensor "wave function" in the Newtonian limit. We obtain a nonspherically symmetric solution with j =2 , ℓ=0 as well as a spherically symmetric solution with j =0 , ℓ=2 in this system where j is the total angular momentum quantum number and ℓ is the orbital angular momentum quantum number, respectively. The energy eigenvalue of the Schrödinger equation in the nonspherical solution is smaller than that in the spherical solution. We then study the perturbative stability of the spherical solution and find that there is an unstable mode in the quadrupole mode perturbations which may be interpreted as the transition mode to the nonspherical solution. The results suggest that the nonspherically symmetric solution is the ground state of the massive graviton geon. The massive graviton geons may decay in time due to emissions of gravitational waves but this timescale can be quite long when the massive gravitons are nonrelativistic and then the geons can be long-lived. We also argue possible prospects of the massive graviton geons: applications to the ultralight dark matter scenario, nonlinear (in)stability of the Minkowski spacetime, and a quantum transition of the spacetime.

Molecular dynamics beyonds the limits: Massive scaling on 72 racks of a BlueGene/P and supercooled glass dynamics of a 1 billion particles system

KAUST Repository

Allsopp, Nicholas; Ruocco, Giancarlo; Fratalocchi, Andrea

2012-01-01

We report scaling results on the world's largest supercomputer of our recently developed Billions-Body Molecular Dynamics (BBMD) package, which was especially designed for massively parallel simulations of the short-range atomic dynamics

A MapReduce-Based Parallel Frequent Pattern Growth Algorithm for Spatiotemporal Association Analysis of Mobile Trajectory Big Data

Directory of Open Access Journals (Sweden)

Dawen Xia

2018-01-01

Full Text Available Frequent pattern mining is an effective approach for spatiotemporal association analysis of mobile trajectory big data in data-driven intelligent transportation systems. While existing parallel algorithms have been successfully applied to frequent pattern mining of large-scale trajectory data, two major challenges are how to overcome the inherent defects of Hadoop to cope with taxi trajectory big data including massive small files and how to discover the implicitly spatiotemporal frequent patterns with MapReduce. To conquer these challenges, this paper presents a MapReduce-based Parallel Frequent Pattern growth (MR-PFP algorithm to analyze the spatiotemporal characteristics of taxi operating using large-scale taxi trajectories with massive small file processing strategies on a Hadoop platform. More specifically, we first implement three methods, that is, Hadoop Archives (HAR, CombineFileInputFormat (CFIF, and Sequence Files (SF, to overcome the existing defects of Hadoop and then propose two strategies based on their performance evaluations. Next, we incorporate SF into Frequent Pattern growth (FP-growth algorithm and then implement the optimized FP-growth algorithm on a MapReduce framework. Finally, we analyze the characteristics of taxi operating in both spatial and temporal dimensions by MR-PFP in parallel. The results demonstrate that MR-PFP is superior to existing Parallel FP-growth (PFP algorithm in efficiency and scalability.

A new class of massively parallel direction splitting for the incompressible Navier–Stokes equations

KAUST Repository

Guermond, J.L.

2011-06-01

We introduce in this paper a new direction splitting algorithm for solving the incompressible Navier-Stokes equations. The main originality of the method consists of using the operator (I-∂xx)(I-∂yy)(I-∂zz) for approximating the pressure correction instead of the Poisson operator as done in all the contemporary projection methods. The complexity of the proposed algorithm is significantly lower than that of projection methods, and it is shown the have the same stability properties as the Poisson-based pressure-correction techniques, either in standard or rotational form. The first-order (in time) version of the method is proved to have the same convergence properties as the classical first-order projection techniques. Numerical tests reveal that the second-order version of the method has the same convergence rate as its second-order projection counterpart as well. The method is suitable for parallel implementation and preliminary tests show excellent parallel performance on a distributed memory cluster of up to 1024 processors. The method has been validated on the three-dimensional lid-driven cavity flow using grids composed of up to 2×109 points. © 2011 Elsevier B.V.

Field-parallel Acceleration: Comment on the Paper “Electric Currents on the Flare Ribbons: Observations and Standard Model” by Janvier et al. (2014, ApJ, 788, 60)

Energy Technology Data Exchange (ETDEWEB)

Haerendel, G. [Max Planck Institute for Extraterrestrial Physics, Garching (Germany)

2017-10-01

It is proposed that the coincidence of higher brightness and upward electric current observed by Janvier et al. during a flare indicates electron acceleration by field-parallel potential drops sustained by extremely strong field-aligned currents of order 10{sup 4} A m{sup −2}. A few consequences are discussed here.

Stable massive particles at colliders

Energy Technology Data Exchange (ETDEWEB)

Fairbairn, M.; /Stockholm U.; Kraan, A.C.; /Pennsylvania U.; Milstead, D.A.; /Stockholm U.; Sjostrand, T.; /Lund U.; Skands, P.; /Fermilab; Sloan, T.; /Lancaster U.

2006-11-01

We review the theoretical motivations and experimental status of searches for stable massive particles (SMPs) which could be sufficiently long-lived as to be directly detected at collider experiments. The discovery of such particles would address a number of important questions in modern physics including the origin and composition of dark matter in the universe and the unification of the fundamental forces. This review describes the techniques used in SMP-searches at collider experiments and the limits so far obtained on the production of SMPs which possess various colour, electric and magnetic charge quantum numbers. We also describe theoretical scenarios which predict SMPs, the phenomenology needed to model their production at colliders and interactions with matter. In addition, the interplay between collider searches and open questions in cosmology such as dark matter composition are addressed.

Electrical characterization of γ-Al2O3 thin film parallel plate capacitive sensor for trace moisture detection

Science.gov (United States)

Kumar, Lokesh; Kumar, Shailesh; Khan, S. A.; Islam, Tariqul

2012-10-01

A moisture sensor was fabricated based on porous thin film of γ-Al2O3 formed between the parallel gold electrodes. The sensor works on capacitive technique. The sensing film was fabricated by dipcoating of aluminium hydroxide sol solution obtained from the sol-gel method. The porous structure of the film of γ-Al2O3 phase was obtained by sintering the film at 450 °C for 1 h. The electrical parameters of the sensor have been determined by Agilent 4294A impedance analyzer. The sensor so obtained is found to be sensitive in moisture range 100-600 ppmV. The response time of the sensor in ppmV range moisture is very low ~ 24 s and recovery time is ~ 37 s.

SIERRA Mechanics, an emerging massively parallel HPC capability, for use in coupled THMC analyses of HLW repositories in clay/shale

International Nuclear Information System (INIS)

Bean, J.E.; Sanchez, M.; Arguello, J.G.

2012-01-01

Document available in extended abstract form only. Because, until recently, U.S. efforts had been focused on the volcanic tuff site at Yucca Mountain, radioactive waste disposal in U.S. clay/shale formations has not been considered for many years. However, advances in multi-physics computational modeling and research into clay mineralogy continue to improve the scientific basis for assessing nuclear waste repository performance in such formations. Disposal of high-level radioactive waste (HLW) in suitable clay/shale formations is attractive because the material is essentially impermeable and self-sealing, conditions are chemically reducing, and sorption tends to prevent radionuclide transport. Vertically and laterally extensive shale and clay formations exist in multiple locations in the contiguous 48 states. This paper describes an emerging massively parallel (MP) high performance computing (HPC) capability - SIERRA Mechanics - that is applicable to the simulation of coupled-physics processes occurring within a potential clay/shale repository for disposal of HLW within the U.S. The SIERRA Mechanics code development project has been underway at Sandia National Laboratories for approximately the past decade under the auspices of the U.S. Department of Energy's Advanced Scientific Computing (ASC) program. SIERRA Mechanics was designed and developed from its inception to run on the latest and most sophisticated massively parallel computing hardware, with the capability to span the hardware range from single workstations to systems with thousands of processors. The foundation of SIERRA Mechanics is the SIERRA tool-kit, which provides finite element application-code services such as: (1) mesh and field data management, both parallel and distributed; (2) transfer operators for mapping field variables from one mechanics application to another; (3) a solution controller for code coupling; and (4) included third party libraries (e.g., solver libraries, communications

Reduced energy consumption by massive thermoelectric waste heat recovery in light duty trucks

Science.gov (United States)

Magnetto, D.; Vidiella, G.

2012-06-01

The main objective of the EC funded HEATRECAR project is to reduce the energy consumption and curb CO2 emissions of vehicles by massively harvesting electrical energy from the exhaust system and re-use this energy to supply electrical components within the vehicle or to feed the power train of hybrid electrical vehicles. HEATRECAR is targeting light duty trucks and focuses on the development and the optimization of a Thermo Electric Generator (TEG) including heat exchanger, thermoelectric modules and DC/DC converter. The main objective of the project is to design, optimize and produce a prototype system to be tested on a 2.3l diesel truck. The base case is a Thermo Electric Generator (TEG) producing 1 KWel at 130 km/h. We present the system design and estimated output power from benchmark Bi2Te3 modules. We discuss key drivers for the optimization of the thermal-to-electric efficiency, such as materials, thermo-mechanical aspects and integration.

Exploration Of Deep Learning Algorithms Using Openacc Parallel Programming Model

KAUST Repository

Hamam, Alwaleed A.

2017-03-13

Deep learning is based on a set of algorithms that attempt to model high level abstractions in data. Specifically, RBM is a deep learning algorithm that used in the project to increase it\\'s time performance using some efficient parallel implementation by OpenACC tool with best possible optimizations on RBM to harness the massively parallel power of NVIDIA GPUs. GPUs development in the last few years has contributed to growing the concept of deep learning. OpenACC is a directive based ap-proach for computing where directives provide compiler hints to accelerate code. The traditional Restricted Boltzmann Ma-chine is a stochastic neural network that essentially perform a binary version of factor analysis. RBM is a useful neural net-work basis for larger modern deep learning model, such as Deep Belief Network. RBM parameters are estimated using an efficient training method that called Contrastive Divergence. Parallel implementation of RBM is available using different models such as OpenMP, and CUDA. But this project has been the first attempt to apply OpenACC model on RBM.

Exploration Of Deep Learning Algorithms Using Openacc Parallel Programming Model

KAUST Repository

Hamam, Alwaleed A.; Khan, Ayaz H.

2017-01-01

Deep learning is based on a set of algorithms that attempt to model high level abstractions in data. Specifically, RBM is a deep learning algorithm that used in the project to increase it's time performance using some efficient parallel implementation by OpenACC tool with best possible optimizations on RBM to harness the massively parallel power of NVIDIA GPUs. GPUs development in the last few years has contributed to growing the concept of deep learning. OpenACC is a directive based ap-proach for computing where directives provide compiler hints to accelerate code. The traditional Restricted Boltzmann Ma-chine is a stochastic neural network that essentially perform a binary version of factor analysis. RBM is a useful neural net-work basis for larger modern deep learning model, such as Deep Belief Network. RBM parameters are estimated using an efficient training method that called Contrastive Divergence. Parallel implementation of RBM is available using different models such as OpenMP, and CUDA. But this project has been the first attempt to apply OpenACC model on RBM.