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.

Massively Parallel QCD

International Nuclear Information System (INIS)

Soltz, R; Vranas, P; Blumrich, M; Chen, D; Gara, A; Giampap, M; Heidelberger, P; Salapura, V; Sexton, J; Bhanot, G

2007-01-01

The theory of the strong nuclear force, Quantum Chromodynamics (QCD), can be numerically simulated from first principles on massively-parallel supercomputers using the method of Lattice Gauge Theory. We describe the special programming requirements of lattice QCD (LQCD) as well as the optimal supercomputer hardware architectures that it suggests. We demonstrate these methods on the BlueGene massively-parallel supercomputer and argue that LQCD and the BlueGene architecture are a natural match. This can be traced to the simple fact that LQCD is a regular lattice discretization of space into lattice sites while the BlueGene supercomputer is a discretization of space into compute nodes, and that both are constrained by requirements of locality. This simple relation is both technologically important and theoretically intriguing. The main result of this paper is the speedup of LQCD using up to 131,072 CPUs on the largest BlueGene/L supercomputer. The speedup is perfect with sustained performance of about 20% of peak. This corresponds to a maximum of 70.5 sustained TFlop/s. At these speeds LQCD and BlueGene are poised to produce the next generation of strong interaction physics theoretical results

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.

Programming massively parallel processors a hands-on approach

CERN Document Server

Kirk, David B

2010-01-01

Programming Massively Parallel Processors discusses basic concepts about parallel programming and GPU architecture. ""Massively parallel"" refers to the use of a large number of processors to perform a set of computations in a coordinated parallel way. The book details various techniques for constructing parallel programs. It also discusses the development process, performance level, floating-point format, parallel patterns, and dynamic parallelism. The book serves as a teaching guide where parallel programming is the main topic of the course. It builds on the basics of C programming for CUDA, a parallel programming environment that is supported on NVI- DIA GPUs. Composed of 12 chapters, the book begins with basic information about the GPU as a parallel computer source. It also explains the main concepts of CUDA, data parallelism, and the importance of memory access efficiency using CUDA. The target audience of the book is graduate and undergraduate students from all science and engineering disciplines who ...

Neural Parallel Engine: A toolbox for massively parallel neural signal processing.

Science.gov (United States)

Tam, Wing-Kin; Yang, Zhi

2018-05-01

Large-scale neural recordings provide detailed information on neuronal activities and can help elicit the underlying neural mechanisms of the brain. However, the computational burden is also formidable when we try to process the huge data stream generated by such recordings. In this study, we report the development of Neural Parallel Engine (NPE), a toolbox for massively parallel neural signal processing on graphical processing units (GPUs). It offers a selection of the most commonly used routines in neural signal processing such as spike detection and spike sorting, including advanced algorithms such as exponential-component-power-component (EC-PC) spike detection and binary pursuit spike sorting. We also propose a new method for detecting peaks in parallel through a parallel compact operation. Our toolbox is able to offer a 5× to 110× speedup compared with its CPU counterparts depending on the algorithms. A user-friendly MATLAB interface is provided to allow easy integration of the toolbox into existing workflows. Previous efforts on GPU neural signal processing only focus on a few rudimentary algorithms, are not well-optimized and often do not provide a user-friendly programming interface to fit into existing workflows. There is a strong need for a comprehensive toolbox for massively parallel neural signal processing. A new toolbox for massively parallel neural signal processing has been created. It can offer significant speedup in processing signals from large-scale recordings up to thousands of channels. Copyright © 2018 Elsevier B.V. All rights reserved.

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 spin-4 analog of 3D massive gravity

NARCIS (Netherlands)

Bergshoeff, Eric A.; Kovacevic, Marija; Rosseel, Jan; Townsend, Paul K.; Yin, Yihao

2011-01-01

A sixth-order, but ghost-free, gauge-invariant action is found for a fourth-rank symmetric tensor potential in a three-dimensional (3D) Minkowski spacetime. It propagates two massive modes of spin 4 that are interchanged by parity and is thus a spin-4 analog of linearized 'new massive gravity'. Also

Exact Solutions in 3D New Massive Gravity

Science.gov (United States)

Ahmedov, Haji; Aliev, Alikram N.

2011-01-01

We show that the field equations of new massive gravity (NMG) consist of a massive (tensorial) Klein-Gordon-type equation with a curvature-squared source term and a constraint equation. We also show that, for algebraic type D and N spacetimes, the field equations of topologically massive gravity (TMG) can be thought of as the “square root” of the massive Klein-Gordon-type equation. Using this fact, we establish a simple framework for mapping all types D and N solutions of TMG into NMG. Finally, we present new examples of types D and N solutions to NMG.

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

RAMA: A file system for massively parallel computers

Science.gov (United States)

Miller, Ethan L.; Katz, Randy H.

1993-01-01

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

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

Complexity growth in minimal massive 3D gravity

Science.gov (United States)

Qaemmaqami, Mohammad M.

2018-01-01

We study the complexity growth by using "complexity =action " (CA) proposal in the minimal massive 3D gravity (MMG) model which is proposed for resolving the bulk-boundary clash problem of topologically massive gravity (TMG). We observe that the rate of the complexity growth for Banados-Teitelboim-Zanelli (BTZ) black hole saturates the proposed bound by physical mass of the BTZ black hole in the MMG model, when the angular momentum parameter and the inner horizon of black hole goes to zero.

Parallel 3-D method of characteristics in MPACT

International Nuclear Information System (INIS)

Kochunas, B.; Dovvnar, T. J.; Liu, Z.

2013-01-01

A new parallel 3-D MOC kernel has been developed and implemented in MPACT which makes use of the modular ray tracing technique to reduce computational requirements and to facilitate parallel decomposition. The parallel model makes use of both distributed and shared memory parallelism which are implemented with the MPI and OpenMP standards, respectively. The kernel is capable of parallel decomposition of problems in space, angle, and by characteristic rays up to 0(104) processors. Initial verification of the parallel 3-D MOC kernel was performed using the Takeda 3-D transport benchmark problems. The eigenvalues computed by MPACT are within the statistical uncertainty of the benchmark reference and agree well with the averages of other participants. The MPACT k eff differs from the benchmark results for rodded and un-rodded cases by 11 and -40 pcm, respectively. The calculations were performed for various numbers of processors and parallel decompositions up to 15625 processors; all producing the same result at convergence. The parallel efficiency of the worst case was 60%, while very good efficiency (>95%) was observed for cases using 500 processors. The overall run time for the 500 processor case was 231 seconds and 19 seconds for the case with 15625 processors. Ongoing work is focused on developing theoretical performance models and the implementation of acceleration techniques to minimize the number of iterations to converge. (authors)

3D, parallel fluid-structure interaction code

CSIR Research Space (South Africa)

Oxtoby, Oliver F

2011-01-01

Full Text Available The authors describe the development of a 3D parallel Fluid–Structure–Interaction (FSI) solver and its application to benchmark problems. Fluid and solid domains are discretised using and edge-based finite-volume scheme for efficient parallel...

Frontiers of massively parallel scientific computation

International Nuclear Information System (INIS)

Fischer, J.R.

1987-07-01

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

Massively parallel quantum computer simulator

NARCIS (Netherlands)

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

2007-01-01

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

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

The 2nd Symposium on the Frontiers of Massively Parallel Computations

Science.gov (United States)

Mills, Ronnie (Editor)

1988-01-01

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

Massively parallel multicanonical simulations

Science.gov (United States)

Gross, Jonathan; Zierenberg, Johannes; Weigel, Martin; Janke, Wolfhard

2018-03-01

Generalized-ensemble Monte Carlo simulations such as the multicanonical method and similar techniques are among the most efficient approaches for simulations of systems undergoing discontinuous phase transitions or with rugged free-energy landscapes. As Markov chain methods, they are inherently serial computationally. It was demonstrated recently, however, that a combination of independent simulations that communicate weight updates at variable intervals allows for the efficient utilization of parallel computational resources for multicanonical simulations. Implementing this approach for the many-thread architecture provided by current generations of graphics processing units (GPUs), we show how it can be efficiently employed with of the order of 104 parallel walkers and beyond, thus constituting a versatile tool for Monte Carlo simulations in the era of massively parallel computing. We provide the fully documented source code for the approach applied to the paradigmatic example of the two-dimensional Ising model as starting point and reference for practitioners in the field.

Impact analysis on a massively parallel computer

International Nuclear Information System (INIS)

Zacharia, T.; Aramayo, G.A.

1994-01-01

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

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....

Massively parallel evolutionary computation on GPGPUs

CERN Document Server

Tsutsui, Shigeyoshi

2013-01-01

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

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 electrical conductivity imaging of the subsurface: Applications to hydrocarbon exploration

Science.gov (United States)

Newman, Gregory A.; Commer, Michael

2009-07-01

Three-dimensional (3D) geophysical imaging is now receiving considerable attention for electrical conductivity mapping of potential offshore oil and gas reservoirs. The imaging technology employs controlled source electromagnetic (CSEM) and magnetotelluric (MT) fields and treats geological media exhibiting transverse anisotropy. Moreover when combined with established seismic methods, direct imaging of reservoir fluids is possible. Because of the size of the 3D conductivity imaging problem, strategies are required exploiting computational parallelism and optimal meshing. The algorithm thus developed has been shown to scale to tens of thousands of processors. In one imaging experiment, 32,768 tasks/processors on the IBM Watson Research Blue Gene/L supercomputer were successfully utilized. Over a 24 hour period we were able to image a large scale field data set that previously required over four months of processing time on distributed clusters based on Intel or AMD processors utilizing 1024 tasks on an InfiniBand fabric. Electrical conductivity imaging using massively parallel computational resources produces results that cannot be obtained otherwise and are consistent with timeframes required for practical exploration problems.

Massively parallel electrical conductivity imaging of the subsurface: Applications to hydrocarbon exploration

International Nuclear Information System (INIS)

Newman, Gregory A; Commer, Michael

2009-01-01

Three-dimensional (3D) geophysical imaging is now receiving considerable attention for electrical conductivity mapping of potential offshore oil and gas reservoirs. The imaging technology employs controlled source electromagnetic (CSEM) and magnetotelluric (MT) fields and treats geological media exhibiting transverse anisotropy. Moreover when combined with established seismic methods, direct imaging of reservoir fluids is possible. Because of the size of the 3D conductivity imaging problem, strategies are required exploiting computational parallelism and optimal meshing. The algorithm thus developed has been shown to scale to tens of thousands of processors. In one imaging experiment, 32,768 tasks/processors on the IBM Watson Research Blue Gene/L supercomputer were successfully utilized. Over a 24 hour period we were able to image a large scale field data set that previously required over four months of processing time on distributed clusters based on Intel or AMD processors utilizing 1024 tasks on an InfiniBand fabric. Electrical conductivity imaging using massively parallel computational resources produces results that cannot be obtained otherwise and are consistent with timeframes required for practical exploration problems.

Massively parallel sequencing of forensic STRs

DEFF Research Database (Denmark)

Parson, Walther; Ballard, David; Budowle, Bruce

2016-01-01

The DNA Commission of the International Society for Forensic Genetics (ISFG) is reviewing factors that need to be considered ahead of the adoption by the forensic community of short tandem repeat (STR) genotyping by massively parallel sequencing (MPS) technologies. MPS produces sequence data that...

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.

CALTRANS: A parallel, deterministic, 3D neutronics code

Energy Technology Data Exchange (ETDEWEB)

Carson, L.; Ferguson, J.; Rogers, J.

1994-04-01

Our efforts to parallelize the deterministic solution of the neutron transport equation has culminated in a new neutronics code CALTRANS, which has full 3D capability. In this article, we describe the layout and algorithms of CALTRANS and present performance measurements of the code on a variety of platforms. Explicit implementation of the parallel algorithms of CALTRANS using both the function calls of the Parallel Virtual Machine software package (PVM 3.2) and the Meiko CS-2 tagged message passing library (based on the Intel NX/2 interface) are provided in appendices.

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

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.

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

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

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 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.

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

Parallel Implementation of the Multi-Dimensional Spectral Code SPECT3D on large 3D grids.

Science.gov (United States)

Golovkin, Igor E.; Macfarlane, Joseph J.; Woodruff, Pamela R.; Pereyra, Nicolas A.

2006-10-01

The multi-dimensional collisional-radiative, spectral analysis code SPECT3D can be used to study radiation from complex plasmas. SPECT3D can generate instantaneous and time-gated images and spectra, space-resolved and streaked spectra, which makes it a valuable tool for post-processing hydrodynamics calculations and direct comparison between simulations and experimental data. On large three dimensional grids, transporting radiation along lines of sight (LOS) requires substantial memory and CPU resources. Currently, the parallel option in SPECT3D is based on parallelization over photon frequencies and allows for a nearly linear speed-up for a variety of problems. In addition, we are introducing a new parallel mechanism that will greatly reduce memory requirements. In the new implementation, spatial domain decomposition will be utilized allowing transport along a LOS to be performed only on the mesh cells the LOS crosses. The ability to operate on a fraction of the grid is crucial for post-processing the results of large-scale three-dimensional hydrodynamics simulations. We will present a parallel implementation of the code and provide a scalability study performed on a Linux cluster.

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.

Massive-Star Magnetospheres: Now in 3-D!

Science.gov (United States)

Townsend, Richard

Magnetic fields are unexpected in massive stars, due to the absence of a dynamo convection zone beneath their surface layers. Nevertheless, kilogauss-strength, ordered fields were detected in a small subset of these stars over three decades ago, and the intervening years have witnessed the steady expansion of this subset. A distinctive feature of magnetic massive stars is that they harbor magnetospheres --- circumstellar environments where the magnetic field interacts strongly with the star's radiation-driven wind, confining it and channelling it into energetic shocks. A wide range of observational signatures are associated with these magnetospheres, in diagnostics ranging from X-rays all the way through to radio emission. Moreover, these magnetospheres can play an important role in massive-star evolution, by amplifying angular momentum loss in the wind. Recent progress in understanding massive-star magnetospheres has largely been driven by magnetohydrodynamical (MHD) simulations. However, these have been restricted to two- dimensional axisymmetric configurations, with three-dimensional configurations possible only in certain special cases. These restrictions are limiting further progress; we therefore propose to develop completely general three-dimensional models for the magnetospheres of massive stars, on the one hand to understand their observational properties and exploit them as plasma-physics laboratories, and on the other to gain a comprehensive understanding of how they influence the evolution of their host star. For weak- and intermediate-field stars, the models will be based on 3-D MHD simulations using a modified version of the ZEUS-MP code. For strong-field stars, we will extend our existing Rigid Field Hydrodynamics (RFHD) code to handle completely arbitrary field topologies. To explore a putative 'photoionization-moderated mass loss' mechanism for massive-star magnetospheres, we will also further develop a photoionization code we have recently

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

PIXIE3D: An efficient, fully implicit, parallel, 3D extended MHD code for fusion plasma modeling

International Nuclear Information System (INIS)

Chacon, L.

2007-01-01

PIXIE3D is a modern, parallel, state-of-the-art extended MHD code that employs fully implicit methods for efficiency and accuracy. It features a general geometry formulation, and is therefore suitable for the study of many magnetic fusion configurations of interest. PIXIE3D advances the state of the art in extended MHD modeling in two fundamental ways. Firstly, it employs a novel conservative finite volume scheme which is remarkably robust and stable, and demands very small physical and/or numerical dissipation. This is a fundamental requirement when one wants to study fusion plasmas with realistic conductivities. Secondly, PIXIE3D features fully-implicit time stepping, employing Newton-Krylov methods for inverting the associated nonlinear systems. These methods have been shown to be scalable and efficient when preconditioned properly. Novel preconditioned ideas (so-called physics based), which were prototypes in the context of reduced MHD, have been adapted for 3D primitive-variable resistive MHD in PIXIE3D, and are currently being extended to Hall MHD. PIXIE3D is fully parallel, employing PETSc for parallelism. PIXIE3D has been thoroughly benchmarked against linear theory and against other available extended MHD codes on nonlinear test problems (such as the GEM reconnection challenge). We are currently in the process of extending such comparisons to fusion-relevant problems in realistic geometries. In this talk, we will describe both the spatial discretization approach and the preconditioning strategy employed for extended MHD in PIXIE3D. We will report on recent benchmarking studies between PIXIE3D and other 3D extended MHD codes, and will demonstrate its usefulness in a variety of fusion-relevant configurations such as Tokamaks and Reversed Field Pinches. (Author)

Kundt solutions of minimal massive 3D gravity

Science.gov (United States)

Deger, Nihat Sadik; Sarıoǧlu, Ã.-zgür

2015-11-01

We construct Kundt solutions of minimal massive gravity theory and show that, similar to topologically massive gravity (TMG), most of them are constant scalar invariant (CSI) spacetimes that correspond to deformations of round and warped (A)dS. We also find an explicit non-CSI Kundt solution at the merger point. Finally, we give their algebraic classification with respect to the traceless Ricci tensor (Segre classification) and show that their Segre types match with the types of their counterparts in TMG.

The DANTE Boltzmann transport solver: An unstructured mesh, 3-D, spherical harmonics algorithm compatible with parallel computer architectures

International Nuclear Information System (INIS)

McGhee, J.M.; Roberts, R.M.; Morel, J.E.

1997-01-01

A spherical harmonics research code (DANTE) has been developed which is compatible with parallel computer architectures. DANTE provides 3-D, multi-material, deterministic, transport capabilities using an arbitrary finite element mesh. The linearized Boltzmann transport equation is solved in a second order self-adjoint form utilizing a Galerkin finite element spatial differencing scheme. The core solver utilizes a preconditioned conjugate gradient algorithm. Other distinguishing features of the code include options for discrete-ordinates and simplified spherical harmonics angular differencing, an exact Marshak boundary treatment for arbitrarily oriented boundary faces, in-line matrix construction techniques to minimize memory consumption, and an effective diffusion based preconditioner for scattering dominated problems. Algorithm efficiency is demonstrated for a massively parallel SIMD architecture (CM-5), and compatibility with MPP multiprocessor platforms or workstation clusters is anticipated

Minimal massive 3D gravity

International Nuclear Information System (INIS)

Bergshoeff, Eric; Merbis, Wout; Hohm, Olaf; Routh, Alasdair J; Townsend, Paul K

2014-01-01

We present an alternative to topologically massive gravity (TMG) with the same ‘minimal’ bulk properties; i.e. a single local degree of freedom that is realized as a massive graviton in linearization about an anti-de Sitter (AdS) vacuum. However, in contrast to TMG, the new ‘minimal massive gravity’ has both a positive energy graviton and positive central charges for the asymptotic AdS-boundary conformal algebra. (paper)

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.

Performance Analysis of 3D Massive MIMO Cellular Systems with Collaborative Base Station

Directory of Open Access Journals (Sweden)

Xingwang Li

2014-01-01

Full Text Available Massive MIMO have drawn considerable attention as they enable significant capacity and coverage improvement in wireless cellular network. However, pilot contamination is a great challenge in massive MIMO systems. Under this circumstance, cooperation and three-dimensional (3D MIMO are emerging technologies to eliminate the pilot contamination and to enhance the performance relative to the traditional interference-limited implementations. Motivated by this, we investigate the achievable sum rate performance of MIMO systems in the uplink employing cooperative base station (BS and 3D MIMO systems. In our model, we consider the effects of both large-scale and small-scale fading, as well as the spatial correlation and indoor-to-outdoor high-rise propagation environment. In particular, we investigate the cooperative communication model based on 3D MIMO and propose a closed-form lower bound on the sum rate. Utilizing this bound, we pursue a “large-system” analysis and provide the asymptotic expression when the number of antennas at the BS grows large, and when the numbers of antennas at transceiver grow large with a fixed ratio. We demonstrate that the lower bound is very tight and becomes exact in the massive MIMO system limits. Finally, under the sum rate maximization condition, we derive the optimal number of UTs to be served.

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.

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

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

A parallel implementation of 3-d CT image reconstruction on a hypercube multiprocessor

International Nuclear Information System (INIS)

Chen, C.M.; Lee, S.Y.; Cho, Z.H.

1990-01-01

In this paper, the authors describe how image reconstruction in computerized tomography (CT) can be parallelized on a message-passing multiprocessor. In particular, the results obtained from parallel implementation of 3-D CT image reconstruction for parallel beam geometries on the Intel hypercube, iPSC/2, are presented. A two stage pipelining approach is employed for filtering (convolution) and backprojection. The conventional sequential convolution algorithm is modified such that the symmetry of the filter kernel is fully utilized for parallelization. In the backprojection stage, the 3-D incremental algorithm, the authors' recently developed backprojection scheme which is shown to be faster than conventional algorithm, is parallelized

3D Massive MIMO Systems: Channel Modeling and Performance Analysis

KAUST Repository

Nadeem, Qurrat-Ul-Ain

2015-03-01

Multiple-input-multiple-output (MIMO) systems of current LTE releases are capable of adaptation in the azimuth only. More recently, the trend is to enhance the system performance by exploiting the channel\\'s degrees of freedom in the elevation through the dynamic adaptation of the vertical antenna beam pattern. This necessitates the derivation and characterization of three-dimensional (3D) channels. Over the years, channel models have evolved to address the challenges of wireless communication technologies. In parallel to theoretical studies on channel modeling, many standardized channel models like COST-based models, 3GPP SCM, WINNER, ITU have emerged that act as references for industries and telecommunication companies to assess system-level and link-level performances of advanced signal processing techniques over real-like channels. Given the existing channels are only two dimensional (2D) in nature; a large effort in channel modeling is needed to study the impact of the channel component in the elevation direction. The first part of this work sheds light on the current 3GPP activity around 3D channel modeling and beamforming, an aspect that to our knowledge has not been extensively covered by a research publication. The standardized MIMO channel model is presented, that incorporates both the propagation effects of the environment and the radio effects of the antennas. In order to facilitate future studies on the use of 3D beamforming, the main features of the proposed 3D channel model are discussed. A brief overview of the future 3GPP 3D channel model being outlined for the next generation of wireless networks is also provided. In the subsequent part of this work, we present an information-theoretic channel model for MIMO systems that supports the elevation dimension. The model is based on the principle of maximum entropy, which enables us to determine the distribution of the channel matrix consistent with the prior information on the angles of departure and

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...

Practical 3-D Beam Pattern Based Channel Modeling for Multi-Polarized Massive MIMO Systems.

Science.gov (United States)

Aghaeinezhadfirouzja, Saeid; Liu, Hui; Balador, Ali

2018-04-12

In this paper, a practical non-stationary three-dimensional (3-D) channel models for massive multiple-input multiple-output (MIMO) systems, considering beam patterns for different antenna elements, is proposed. The beam patterns using dipole antenna elements with different phase excitation toward the different direction of travels (DoTs) contributes various correlation weights for rays related towards/from the cluster, thus providing different elevation angle of arrivals (EAoAs) and elevation angle of departures (EAoDs) for each antenna element. These include the movements of the user that makes our channel to be a non-stationary model of clusters at the receiver (RX) on both the time and array axes. In addition, their impacts on 3-D massive MIMO channels are investigated via statistical properties including received spatial correlation. Additionally, the impact of elevation/azimuth angles of arrival on received spatial correlation is discussed. Furthermore, experimental validation of the proposed 3-D channel models on azimuth and elevation angles of the polarized antenna are specifically evaluated and compared through simulations. The proposed 3-D generic models are verified using relevant measurement data.

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.

High Performance Programming Using Explicit Shared Memory Model on the Cray T3D

Science.gov (United States)

Saini, Subhash; Simon, Horst D.; Lasinski, T. A. (Technical Monitor)

1994-01-01

The Cray T3D is the first-phase system in Cray Research Inc.'s (CRI) three-phase massively parallel processing program. In this report we describe the architecture of the T3D, as well as the CRAFT (Cray Research Adaptive Fortran) programming model, and contrast it with PVM, which is also supported on the T3D We present some performance data based on the NAS Parallel Benchmarks to illustrate both architectural and software features of the T3D.

Parallel Processor for 3D Recovery from Optical Flow

Directory of Open Access Journals (Sweden)

Jose Hugo Barron-Zambrano

2009-01-01

Full Text Available 3D recovery from motion has received a major effort in computer vision systems in the recent years. The main problem lies in the number of operations and memory accesses to be performed by the majority of the existing techniques when translated to hardware or software implementations. This paper proposes a parallel processor for 3D recovery from optical flow. Its main feature is the maximum reuse of data and the low number of clock cycles to calculate the optical flow, along with the precision with which 3D recovery is achieved. The results of the proposed architecture as well as those from processor synthesis are presented.

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 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...

A parallel algorithm for 3D dislocation dynamics

International Nuclear Information System (INIS)

Wang Zhiqiang; Ghoniem, Nasr; Swaminarayan, Sriram; LeSar, Richard

2006-01-01

Dislocation dynamics (DD), a discrete dynamic simulation method in which dislocations are the fundamental entities, is a powerful tool for investigation of plasticity, deformation and fracture of materials at the micron length scale. However, severe computational difficulties arising from complex, long-range interactions between these curvilinear line defects limit the application of DD in the study of large-scale plastic deformation. We present here the development of a parallel algorithm for accelerated computer simulations of DD. By representing dislocations as a 3D set of dislocation particles, we show here that the problem of an interacting ensemble of dislocations can be converted to a problem of a particle ensemble, interacting with a long-range force field. A grid using binary space partitioning is constructed to keep track of node connectivity across domains. We demonstrate the computational efficiency of the parallel micro-plasticity code and discuss how O(N) methods map naturally onto the parallel data structure. Finally, we present results from applications of the parallel code to deformation in single crystal fcc metals

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.

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.

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 3D gyrokinetic particle-in-cell simulation of fusion plasma microturbulence on parallel computers

Science.gov (United States)

Williams, T. J.

1992-12-01

One of the grand challenge problems now supported by HPCC is the Numerical Tokamak Project. A goal of this project is the study of low-frequency micro-instabilities in tokamak plasmas, which are believed to cause energy loss via turbulent thermal transport across the magnetic field lines. An important tool in this study is gyrokinetic particle-in-cell (PIC) simulation. Gyrokinetic, as opposed to fully-kinetic, methods are particularly well suited to the task because they are optimized to study the frequency and wavelength domain of the microinstabilities. Furthermore, many researchers now employ low-noise delta(f) methods to greatly reduce statistical noise by modelling only the perturbation of the gyrokinetic distribution function from a fixed background, not the entire distribution function. In spite of the increased efficiency of these improved algorithms over conventional PIC algorithms, gyrokinetic PIC simulations of tokamak micro-turbulence are still highly demanding of computer power--even fully-vectorized codes on vector supercomputers. For this reason, we have worked for several years to redevelop these codes on massively parallel computers. We have developed 3D gyrokinetic PIC simulation codes for SIMD and MIMD parallel processors, using control-parallel, data-parallel, and domain-decomposition message-passing (DDMP) programming paradigms. This poster summarizes our earlier work on codes for the Connection Machine and BBN TC2000 and our development of a generic DDMP code for distributed-memory parallel machines. We discuss the memory-access issues which are of key importance in writing parallel PIC codes, with special emphasis on issues peculiar to gyrokinetic PIC. We outline the domain decompositions in our new DDMP code and discuss the interplay of different domain decompositions suited for the particle-pushing and field-solution components of the PIC algorithm.

Parallel Optimization of 3D Cardiac Electrophysiological Model Using GPU

Directory of Open Access Journals (Sweden)

Yong Xia

2015-01-01

Full Text Available Large-scale 3D virtual heart model simulations are highly demanding in computational resources. This imposes a big challenge to the traditional computation resources based on CPU environment, which already cannot meet the requirement of the whole computation demands or are not easily available due to expensive costs. GPU as a parallel computing environment therefore provides an alternative to solve the large-scale computational problems of whole heart modeling. In this study, using a 3D sheep atrial model as a test bed, we developed a GPU-based simulation algorithm to simulate the conduction of electrical excitation waves in the 3D atria. In the GPU algorithm, a multicellular tissue model was split into two components: one is the single cell model (ordinary differential equation and the other is the diffusion term of the monodomain model (partial differential equation. Such a decoupling enabled realization of the GPU parallel algorithm. Furthermore, several optimization strategies were proposed based on the features of the virtual heart model, which enabled a 200-fold speedup as compared to a CPU implementation. In conclusion, an optimized GPU algorithm has been developed that provides an economic and powerful platform for 3D whole heart simulations.

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.

Reactor Dosimetry Applications Using RAPTOR-M3G:. a New Parallel 3-D Radiation Transport Code

Science.gov (United States)

Longoni, Gianluca; Anderson, Stanwood L.

2009-08-01

The numerical solution of the Linearized Boltzmann Equation (LBE) via the Discrete Ordinates method (SN) requires extensive computational resources for large 3-D neutron and gamma transport applications due to the concurrent discretization of the angular, spatial, and energy domains. This paper will discuss the development RAPTOR-M3G (RApid Parallel Transport Of Radiation - Multiple 3D Geometries), a new 3-D parallel radiation transport code, and its application to the calculation of ex-vessel neutron dosimetry responses in the cavity of a commercial 2-loop Pressurized Water Reactor (PWR). RAPTOR-M3G is based domain decomposition algorithms, where the spatial and angular domains are allocated and processed on multi-processor computer architectures. As compared to traditional single-processor applications, this approach reduces the computational load as well as the memory requirement per processor, yielding an efficient solution methodology for large 3-D problems. Measured neutron dosimetry responses in the reactor cavity air gap will be compared to the RAPTOR-M3G predictions. This paper is organized as follows: Section 1 discusses the RAPTOR-M3G methodology; Section 2 describes the 2-loop PWR model and the numerical results obtained. Section 3 addresses the parallel performance of the code, and Section 4 concludes this paper with final remarks and future work.

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

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

International Nuclear Information System (INIS)

Laurent, C.; Chassery, J.M.; Peyrin, F.; Girerd, C.

1996-01-01

This paper deals with the parallel implementations of reconstruction methods in 3D tomography. 3D tomography requires voluminous data and long computation times. Parallel computing, on MIMD computers, seems to be a good approach to manage this problem. In this study, we present the different steps of the parallelization on an abstract parallel computer. Depending on the method, we use two main approaches to parallelize the algorithms: the local approach and the global approach. Experimental results on MIMD computers are presented. Two 3D images reconstructed from realistic data are showed

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.

A parallel algorithm for 3D particle tracking and Lagrangian trajectory reconstruction

International Nuclear Information System (INIS)

Barker, Douglas; Zhang, Yuanhui; Lifflander, Jonathan; Arya, Anshu

2012-01-01

Particle-tracking methods are widely used in fluid mechanics and multi-target tracking research because of their unique ability to reconstruct long trajectories with high spatial and temporal resolution. Researchers have recently demonstrated 3D tracking of several objects in real time, but as the number of objects is increased, real-time tracking becomes impossible due to data transfer and processing bottlenecks. This problem may be solved by using parallel processing. In this paper, a parallel-processing framework has been developed based on frame decomposition and is programmed using the asynchronous object-oriented Charm++ paradigm. This framework can be a key step in achieving a scalable Lagrangian measurement system for particle-tracking velocimetry and may lead to real-time measurement capabilities. The parallel tracking algorithm was evaluated with three data sets including the particle image velocimetry standard 3D images data set #352, a uniform data set for optimal parallel performance and a computational-fluid-dynamics-generated non-uniform data set to test trajectory reconstruction accuracy, consistency with the sequential version and scalability to more than 500 processors. The algorithm showed strong scaling up to 512 processors and no inherent limits of scalability were seen. Ultimately, up to a 200-fold speedup is observed compared to the serial algorithm when 256 processors were used. The parallel algorithm is adaptable and could be easily modified to use any sequential tracking algorithm, which inputs frames of 3D particle location data and outputs particle trajectories

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

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.

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.

Shared memory parallelism for 3D cartesian discrete ordinates solver

International Nuclear Information System (INIS)

Moustafa, S.; Dutka-Malen, I.; Plagne, L.; Poncot, A.; Ramet, P.

2013-01-01

This paper describes the design and the performance of DOMINO, a 3D Cartesian SN solver that implements two nested levels of parallelism (multi-core + SIMD - Single Instruction on Multiple Data) on shared memory computation nodes. DOMINO is written in C++, a multi-paradigm programming language that enables the use of powerful and generic parallel programming tools such as Intel TBB and Eigen. These two libraries allow us to combine multi-thread parallelism with vector operations in an efficient and yet portable way. As a result, DOMINO can exploit the full power of modern multi-core processors and is able to tackle very large simulations, that usually require large HPC clusters, using a single computing node. For example, DOMINO solves a 3D full core PWR eigenvalue problem involving 26 energy groups, 288 angular directions (S16), 46*10 6 spatial cells and 1*10 12 DoFs within 11 hours on a single 32-core SMP node. This represents a sustained performance of 235 GFlops and 40.74% of the SMP node peak performance for the DOMINO sweep implementation. The very high Flops/Watt ratio of DOMINO makes it a very interesting building block for a future many-nodes nuclear simulation tool. (authors)

Development of parallel 3D discrete ordinates transport program on JASMIN framework

International Nuclear Information System (INIS)

Cheng, T.; Wei, J.; Shen, H.; Zhong, B.; Deng, L.

2015-01-01

A parallel 3D discrete ordinates radiation transport code JSNT-S is developed, aiming at simulating real-world radiation shielding and reactor physics applications in a reasonable time. Through the patch-based domain partition algorithm, the memory requirement is shared among processors and a space-angle parallel sweeping algorithm is developed based on data-driven algorithm. Acceleration methods such as partial current rebalance are implemented. The correctness is proved through the VENUS-3 and other benchmark models. In the radiation shielding calculation of the Qinshan-II reactor pressure vessel model with 24.3 billion DoF, only 88 seconds is required and the overall parallel efficiency of 44% is achieved on 1536 CPU cores. (author)

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

Simulating streamer discharges in 3D with the parallel adaptive Afivo framework

NARCIS (Netherlands)

H.J. Teunissen (Jannis); U. M. Ebert (Ute)

2017-01-01

htmlabstractWe present an open-source plasma fluid code for 2D, cylindrical and 3D simulations of streamer discharges, based on the Afivo framework that features adaptive mesh refinement, geometric multigrid methods for Poisson's equation, and OpenMP parallelism. We describe the numerical

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.

3-D electromagnetic plasma particle simulations on the Intel Delta parallel computer

International Nuclear Information System (INIS)

Wang, J.; Liewer, P.C.

1994-01-01

A three-dimensional electromagnetic PIC code has been developed on the 512 node Intel Touchstone Delta MIMD parallel computer. This code is based on the General Concurrent PIC algorithm which uses a domain decomposition to divide the computation among the processors. The 3D simulation domain can be partitioned into 1-, 2-, or 3-dimensional sub-domains. Particles must be exchanged between processors as they move among the subdomains. The Intel Delta allows one to use this code for very-large-scale simulations (i.e. over 10 8 particles and 10 6 grid cells). The parallel efficiency of this code is measured, and the overall code performance on the Delta is compared with that on Cray supercomputers. It is shown that their code runs with a high parallel efficiency of ≥ 95% for large size problems. The particle push time achieved is 115 nsecs/particle/time step for 162 million particles on 512 nodes. Comparing with the performance on a single processor Cray C90, this represents a factor of 58 speedup. The code uses a finite-difference leap frog method for field solve which is significantly more efficient than fast fourier transforms on parallel computers. The performance of this code on the 128 node Cray T3D will also be discussed

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

An efficient parallel algorithm: Poststack and prestack Kirchhoff 3D depth migration using flexi-depth iterations

Science.gov (United States)

Rastogi, Richa; Srivastava, Abhishek; Khonde, Kiran; Sirasala, Kirannmayi M.; Londhe, Ashutosh; Chavhan, Hitesh

2015-07-01

This paper presents an efficient parallel 3D Kirchhoff depth migration algorithm suitable for current class of multicore architecture. The fundamental Kirchhoff depth migration algorithm exhibits inherent parallelism however, when it comes to 3D data migration, as the data size increases the resource requirement of the algorithm also increases. This challenges its practical implementation even on current generation high performance computing systems. Therefore a smart parallelization approach is essential to handle 3D data for migration. The most compute intensive part of Kirchhoff depth migration algorithm is the calculation of traveltime tables due to its resource requirements such as memory/storage and I/O. In the current research work, we target this area and develop a competent parallel algorithm for post and prestack 3D Kirchhoff depth migration, using hybrid MPI+OpenMP programming techniques. We introduce a concept of flexi-depth iterations while depth migrating data in parallel imaging space, using optimized traveltime table computations. This concept provides flexibility to the algorithm by migrating data in a number of depth iterations, which depends upon the available node memory and the size of data to be migrated during runtime. Furthermore, it minimizes the requirements of storage, I/O and inter-node communication, thus making it advantageous over the conventional parallelization approaches. The developed parallel algorithm is demonstrated and analysed on Yuva II, a PARAM series of supercomputers. Optimization, performance and scalability experiment results along with the migration outcome show the effectiveness of the parallel algorithm.

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.

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

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...

Quantitative analysis of pulmonary perfusion using time-resolved parallel 3D MRI - initial results

International Nuclear Information System (INIS)

Fink, C.; Buhmann, R.; Plathow, C.; Puderbach, M.; Kauczor, H.U.; Risse, F.; Ley, S.; Meyer, F.J.

2004-01-01

Purpose: to assess the use of time-resolved parallel 3D MRI for a quantitative analysis of pulmonary perfusion in patients with cardiopulmonary disease. Materials and methods: eight patients with pulmonary embolism or pulmonary hypertension were examined with a time-resolved 3D gradient echo pulse sequence with parallel imaging techniques (FLASH 3D, TE/TR: 0.8/1.9 ms; flip angle: 40 ; GRAPPA). A quantitative perfusion analysis based on indicator dilution theory was performed using a dedicated software. Results: patients with pulmonary embolism or chronic thromboembolic pulmonary hypertension revealed characteristic wedge-shaped perfusion defects at perfusion MRI. They were characterized by a decreased pulmonary blood flow (PBF) and pulmonary blood volume (PBV) and increased mean transit time (MTT). Patients with primary pulmonary hypertension or eisenmenger syndrome showed a more homogeneous perfusion pattern. The mean MTT of all patients was 3.3 - 4.7 s. The mean PBF and PBV showed a broader interindividual variation (PBF: 104-322 ml/100 ml/min; PBV: 8 - 21 ml/100 ml). Conclusion: time-resolved parallel 3D MRI allows at least a semi-quantitative assessment of lung perfusion. Future studies will have to assess the clinical value of this quantitative information for the diagnosis and management of cardiopulmonary disease. (orig.) [de

Master actions for massive spin-3 particles in D = 2 + 1

Energy Technology Data Exchange (ETDEWEB)

Leite Mendonca, Elias; Dalmazi, Denis [UNESP, Campus de Guaratingueta, DFQ, Guaratingueta, SP (Brazil)

2016-04-15

We present here a relationship between massive self-dual models for spin-3 particles in D = 2 + 1 via the master action procedure. Starting with a first-order model (in the derivatives) S{sub SD(1)} we have constructed a master action which interpolates between a sequence of four self-dual models S{sub SD(i)} where i = 1, 2, 3, 4. By analyzing the particle content of the mixing terms, we give additional arguments that explain why it is apparently impossible to jump from the fourth-order model to a higher-order model. We have also analyzed similarities and differences between the fourth-order K-term in the spin-2 case and the analogous fourth-order term in the spin-3 context. (orig.)

3D Massive MIMO Systems: Modeling and Performance Analysis

KAUST Repository

Nadeem, Qurrat-Ul-Ain

2015-07-30

Multiple-input-multiple-output (MIMO) systems of current LTE releases are capable of adaptation in the azimuth only. Recently, the trend is to enhance system performance by exploiting the channel’s degrees of freedom in the elevation, which necessitates the characterization of 3D channels. We present an information-theoretic channel model for MIMO systems that supports the elevation dimension. The model is based on the principle of maximum entropy, which enables us to determine the distribution of the channel matrix consistent with the prior information on the angles. Based on this model, we provide analytical expression for the cumulative density function (CDF) of the mutual information (MI) for systems with a single receive and finite number of transmit antennas in the general signalto- interference-plus-noise-ratio (SINR) regime. The result is extended to systems with finite receive antennas in the low SINR regime. A Gaussian approximation to the asymptotic behavior of MI distribution is derived for the large number of transmit antennas and paths regime. We corroborate our analysis with simulations that study the performance gains realizable through meticulous selection of the transmit antenna downtilt angles, confirming the potential of elevation beamforming to enhance system performance. The results are directly applicable to the analysis of 5G 3D-Massive MIMO-systems.

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

A novel two-level dynamic parallel data scheme for large 3-D SN calculations

International Nuclear Information System (INIS)

Sjoden, G.E.; Shedlock, D.; Haghighat, A.; Yi, C.

2005-01-01

We introduce a new dynamic parallel memory optimization scheme for executing large scale 3-D discrete ordinates (Sn) simulations on distributed memory parallel computers. In order for parallel transport codes to be truly scalable, they must use parallel data storage, where only the variables that are locally computed are locally stored. Even with parallel data storage for the angular variables, cumulative storage requirements for large discrete ordinates calculations can be prohibitive. To address this problem, Memory Tuning has been implemented into the PENTRAN 3-D parallel discrete ordinates code as an optimized, two-level ('large' array, 'small' array) parallel data storage scheme. Memory Tuning can be described as the process of parallel data memory optimization. Memory Tuning dynamically minimizes the amount of required parallel data in allocated memory on each processor using a statistical sampling algorithm. This algorithm is based on the integral average and standard deviation of the number of fine meshes contained in each coarse mesh in the global problem. Because PENTRAN only stores the locally computed problem phase space, optimal two-level memory assignments can be unique on each node, depending upon the parallel decomposition used (hybrid combinations of angular, energy, or spatial). As demonstrated in the two large discrete ordinates models presented (a storage cask and an OECD MOX Benchmark), Memory Tuning can save a substantial amount of memory per parallel processor, allowing one to accomplish very large scale Sn computations. (authors)

Late gadolinium enhancement cardiac imaging on a 3T scanner with parallel RF transmission technique: prospective comparison of 3D-PSIR and 3D-IR

International Nuclear Information System (INIS)

Schultz, Anthony; Caspar, Thibault; Schaeffer, Mickael; Labani, Aissam; Jeung, Mi-Young; El Ghannudi, Soraya; Roy, Catherine; Ohana, Mickael

2016-01-01

To qualitatively and quantitatively compare different late gadolinium enhancement (LGE) sequences acquired at 3T with a parallel RF transmission technique. One hundred and sixty participants prospectively enrolled underwent a 3T cardiac MRI with 3 different LGE sequences: 3D Phase-Sensitive Inversion-Recovery (3D-PSIR) acquired 5 minutes after injection, 3D Inversion-Recovery (3D-IR) at 9 minutes and 3D-PSIR at 13 minutes. All LGE-positive patients were qualitatively evaluated both independently and blindly by two radiologists using a 4-level scale, and quantitatively assessed with measurement of contrast-to-noise ratio and LGE maximal surface. Statistical analyses were calculated under a Bayesian paradigm using MCMC methods. Fifty patients (70 % men, 56yo ± 19) exhibited LGE (62 % were post-ischemic, 30 % related to cardiomyopathy and 8 % post-myocarditis). Early and late 3D-PSIR were superior to 3D-IR sequences (global quality, estimated coefficient IR > early-PSIR: -2.37 CI = [-3.46; -1.38], prob(coef > 0) = 0 % and late-PSIR > IR: 3.12 CI = [0.62; 4.41], prob(coef > 0) = 100 %), LGE surface estimated coefficient IR > early-PSIR: -0.09 CI = [-1.11; -0.74], prob(coef > 0) = 0 % and late-PSIR > IR: 0.96 CI = [0.77; 1.15], prob(coef > 0) = 100 %. Probabilities for late PSIR being superior to early PSIR concerning global quality and CNR were over 90 %, regardless of the aetiological subgroup. In 3T cardiac MRI acquired with parallel RF transmission technique, 3D-PSIR is qualitatively and quantitatively superior to 3D-IR. (orig.)

Diversity and Multiplexing Technologies by 3D Beams in Polarized Massive MIMO Systems

Directory of Open Access Journals (Sweden)

Xin Su

2016-01-01

Full Text Available Massive multiple input, multiple output (M-MIMO technologies have been proposed to scale up data rates reaching gigabits per second in the forthcoming 5G mobile communications systems. However, one of crucial constraints is a dimension in space to implement the M-MIMO. To cope with the space constraint and to utilize more flexibility in 3D beamforming (3D-BF, we propose antenna polarization in M-MIMO systems. In this paper, we design a polarized M-MIMO (PM-MIMO system associated with 3D-BF applications, where the system architectures for diversity and multiplexing technologies achieved by polarized 3D beams are provided. Different from the conventional 3D-BF achieved by planar M-MIMO technology to control the downtilted beam in a vertical domain, the proposed PM-MIMO realizes 3D-BF via the linear combination of polarized beams. In addition, an effective array selection scheme is proposed to optimize the beam-width and to enhance system performance by the exploration of diversity and multiplexing gains; and a blind channel estimation (BCE approach is also proposed to avoid pilot contamination in PM-MIMO. Based on the Long Term Evolution-Advanced (LTE-A specification, the simulation results finally confirm the validity of our proposals.

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.)

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

High performance 3D neutron transport on peta scale and hybrid architectures within APOLLO3 code

International Nuclear Information System (INIS)

Jamelot, E.; Dubois, J.; Lautard, J-J.; Calvin, C.; Baudron, A-M.

2011-01-01

APOLLO3 code is a common project of CEA, AREVA and EDF for the development of a new generation system for core physics analysis. We present here the parallelization of two deterministic transport solvers of APOLLO3: MINOS, a simplified 3D transport solver on structured Cartesian and hexagonal grids, and MINARET, a transport solver based on triangular meshes on 2D and prismatic ones in 3D. We used two different techniques to accelerate MINOS: a domain decomposition method, combined with an accelerated algorithm using GPU. The domain decomposition is based on the Schwarz iterative algorithm, with Robin boundary conditions to exchange information. The Robin parameters influence the convergence and we detail how we optimized the choice of these parameters. MINARET parallelization is based on angular directions calculation using explicit message passing. Fine grain parallelization is also available for each angular direction using shared memory multithreaded acceleration. Many performance results are presented on massively parallel architectures using more than 103 cores and on hybrid architectures using some tens of GPUs. This work contributes to the HPC development in reactor physics at the CEA Nuclear Energy Division. (author)

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....

Fast implementations of 3D PET reconstruction using vector and parallel programming techniques

International Nuclear Information System (INIS)

Guerrero, T.M.; Cherry, S.R.; Dahlbom, M.; Ricci, A.R.; Hoffman, E.J.

1993-01-01

Computationally intensive techniques that offer potential clinical use have arisen in nuclear medicine. Examples include iterative reconstruction, 3D PET data acquisition and reconstruction, and 3D image volume manipulation including image registration. One obstacle in achieving clinical acceptance of these techniques is the computational time required. This study focuses on methods to reduce the computation time for 3D PET reconstruction through the use of fast computer hardware, vector and parallel programming techniques, and algorithm optimization. The strengths and weaknesses of i860 microprocessor based workstation accelerator boards are investigated in implementations of 3D PET reconstruction

Spin-3 topologically massive gravity

Energy Technology Data Exchange (ETDEWEB)

Chen Bin, E-mail: bchen01@pku.edu.cn [Department of Physics, and State Key Laboratory of Nuclear Physics and Technology, Peking University, Beijing 100871 (China); Center for High Energy Physics, Peking University, Beijing 100871 (China); Long Jiang, E-mail: longjiang0301@gmail.com [Department of Physics, and State Key Laboratory of Nuclear Physics and Technology, Peking University, Beijing 100871 (China); Wu Junbao, E-mail: wujb@ihep.ac.cn [Institute of High Energy Physics, and Theoretical Physics Center for Science Facilities, Chinese Academy of Sciences, Beijing 100049 (China)

2011-11-24

In this Letter, we study the spin-3 topologically massive gravity (TMG), paying special attention to its properties at the chiral point. We propose an action describing the higher spin fields coupled to TMG. We discuss the traceless spin-3 fluctuations around the AdS{sub 3} vacuum and find that there is an extra local massive mode, besides the left-moving and right-moving boundary massless modes. At the chiral point, such extra mode becomes massless and degenerates with the left-moving mode. We show that at the chiral point the only degrees of freedom in the theory are the boundary right-moving graviton and spin-3 field. We conjecture that spin-3 chiral gravity with generalized Brown-Henneaux boundary condition is holographically dual to 2D chiral CFT with classical W{sub 3} algebra and central charge c{sub R}=3l/G.

On the mutual information of 3D massive MIMO systems: An asymptotic approach

KAUST Repository

Nadeem, Qurrat-Ul-Ain

2015-10-01

Motivated by the recent interest in 3D beamforming to enhance system performance, we present an information-theoretic channel model for multiple-input multiple-output (MIMO) systems, that can support the elevation dimension. The principle of maximum entropy is used to determine the distribution of the channel matrix consistent with the prior angular information. We provide an explicit expression for the cumulative density function (CDF) of the mutual information in the large number of transmit antennas and paths regime. The derived Gaussian approximation is quite accurate even for realistic system dimensions. The simulation results study the achievable performance through the meticulous selection of the transmit antenna downtilt angles. The results are directly applicable to the analysis of 5G 3D massive MIMO systems. © 2015 IEEE.

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

Parallel 3D Mortar Element Method for Adaptive Nonconforming Meshes

Science.gov (United States)

Feng, Huiyu; Mavriplis, Catherine; VanderWijngaart, Rob; Biswas, Rupak

2004-01-01

High order methods are frequently used in computational simulation for their high accuracy. An efficient way to avoid unnecessary computation in smooth regions of the solution is to use adaptive meshes which employ fine grids only in areas where they are needed. Nonconforming spectral elements allow the grid to be flexibly adjusted to satisfy the computational accuracy requirements. The method is suitable for computational simulations of unsteady problems with very disparate length scales or unsteady moving features, such as heat transfer, fluid dynamics or flame combustion. In this work, we select the Mark Element Method (MEM) to handle the non-conforming interfaces between elements. A new technique is introduced to efficiently implement MEM in 3-D nonconforming meshes. By introducing an "intermediate mortar", the proposed method decomposes the projection between 3-D elements and mortars into two steps. In each step, projection matrices derived in 2-D are used. The two-step method avoids explicitly forming/deriving large projection matrices for 3-D meshes, and also helps to simplify the implementation. This new technique can be used for both h- and p-type adaptation. This method is applied to an unsteady 3-D moving heat source problem. With our new MEM implementation, mesh adaptation is able to efficiently refine the grid near the heat source and coarsen the grid once the heat source passes. The savings in computational work resulting from the dynamic mesh adaptation is demonstrated by the reduction of the the number of elements used and CPU time spent. MEM and mesh adaptation, respectively, bring irregularity and dynamics to the computer memory access pattern. Hence, they provide a good way to gauge the performance of computer systems when running scientific applications whose memory access patterns are irregular and unpredictable. We select a 3-D moving heat source problem as the Unstructured Adaptive (UA) grid benchmark, a new component of the NAS Parallel

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.

Reconstruction for Time-Domain In Vivo EPR 3D Multigradient Oximetric Imaging—A Parallel Processing Perspective

Directory of Open Access Journals (Sweden)

Christopher D. Dharmaraj

2009-01-01

Full Text Available Three-dimensional Oximetric Electron Paramagnetic Resonance Imaging using the Single Point Imaging modality generates unpaired spin density and oxygen images that can readily distinguish between normal and tumor tissues in small animals. It is also possible with fast imaging to track the changes in tissue oxygenation in response to the oxygen content in the breathing air. However, this involves dealing with gigabytes of data for each 3D oximetric imaging experiment involving digital band pass filtering and background noise subtraction, followed by 3D Fourier reconstruction. This process is rather slow in a conventional uniprocessor system. This paper presents a parallelization framework using OpenMP runtime support and parallel MATLAB to execute such computationally intensive programs. The Intel compiler is used to develop a parallel C++ code based on OpenMP. The code is executed on four Dual-Core AMD Opteron shared memory processors, to reduce the computational burden of the filtration task significantly. The results show that the parallel code for filtration has achieved a speed up factor of 46.66 as against the equivalent serial MATLAB code. In addition, a parallel MATLAB code has been developed to perform 3D Fourier reconstruction. Speedup factors of 4.57 and 4.25 have been achieved during the reconstruction process and oximetry computation, for a data set with 23×23×23 gradient steps. The execution time has been computed for both the serial and parallel implementations using different dimensions of the data and presented for comparison. The reported system has been designed to be easily accessible even from low-cost personal computers through local internet (NIHnet. The experimental results demonstrate that the parallel computing provides a source of high computational power to obtain biophysical parameters from 3D EPR oximetric imaging, almost in real-time.

Reconstruction for time-domain in vivo EPR 3D multigradient oximetric imaging--a parallel processing perspective.

Science.gov (United States)

Dharmaraj, Christopher D; Thadikonda, Kishan; Fletcher, Anthony R; Doan, Phuc N; Devasahayam, Nallathamby; Matsumoto, Shingo; Johnson, Calvin A; Cook, John A; Mitchell, James B; Subramanian, Sankaran; Krishna, Murali C

2009-01-01

Three-dimensional Oximetric Electron Paramagnetic Resonance Imaging using the Single Point Imaging modality generates unpaired spin density and oxygen images that can readily distinguish between normal and tumor tissues in small animals. It is also possible with fast imaging to track the changes in tissue oxygenation in response to the oxygen content in the breathing air. However, this involves dealing with gigabytes of data for each 3D oximetric imaging experiment involving digital band pass filtering and background noise subtraction, followed by 3D Fourier reconstruction. This process is rather slow in a conventional uniprocessor system. This paper presents a parallelization framework using OpenMP runtime support and parallel MATLAB to execute such computationally intensive programs. The Intel compiler is used to develop a parallel C++ code based on OpenMP. The code is executed on four Dual-Core AMD Opteron shared memory processors, to reduce the computational burden of the filtration task significantly. The results show that the parallel code for filtration has achieved a speed up factor of 46.66 as against the equivalent serial MATLAB code. In addition, a parallel MATLAB code has been developed to perform 3D Fourier reconstruction. Speedup factors of 4.57 and 4.25 have been achieved during the reconstruction process and oximetry computation, for a data set with 23 x 23 x 23 gradient steps. The execution time has been computed for both the serial and parallel implementations using different dimensions of the data and presented for comparison. The reported system has been designed to be easily accessible even from low-cost personal computers through local internet (NIHnet). The experimental results demonstrate that the parallel computing provides a source of high computational power to obtain biophysical parameters from 3D EPR oximetric imaging, almost in real-time.

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

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.

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.)

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.

3D-radiative transfer in terrestrial atmosphere: An efficient parallel numerical procedure

Science.gov (United States)

Bass, L. P.; Germogenova, T. A.; Nikolaeva, O. V.; Kokhanovsky, A. A.; Kuznetsov, V. S.

2003-04-01

Light propagation and scattering in terrestrial atmosphere is usually studied in the framework of the 1D radiative transfer theory [1]. However, in reality particles (e.g., ice crystals, solid and liquid aerosols, cloud droplets) are randomly distributed in 3D space. In particular, their concentrations vary both in vertical and horizontal directions. Therefore, 3D effects influence modern cloud and aerosol retrieval procedures, which are currently based on the 1D radiative transfer theory. It should be pointed out that the standard radiative transfer equation allows to study these more complex situations as well [2]. In recent year the parallel version of the 2D and 3D RADUGA code has been developed. This version is successfully used in gammas and neutrons transport problems [3]. Applications of this code to radiative transfer in atmosphere problems are contained in [4]. Possibilities of code RADUGA are presented in [5]. The RADUGA code system is an universal solver of radiative transfer problems for complicated models, including 2D and 3D aerosol and cloud fields with arbitrary scattering anisotropy, light absorption, inhomogeneous underlying surface and topography. Both delta type and distributed light sources can be accounted for in the framework of the algorithm developed. The accurate numerical procedure is based on the new discrete ordinate SWDD scheme [6]. The algorithm is specifically designed for parallel supercomputers. The version RADUGA 5.1(P) can run on MBC1000M [7] (768 processors with 10 Gb of hard disc memory for each processor). The peak productivity is equal 1 Tfl. Corresponding scalar version RADUGA 5.1 is working on PC. As a first example of application of the algorithm developed, we have studied the shadowing effects of clouds on neighboring cloudless atmosphere, depending on the cloud optical thickness, surface albedo, and illumination conditions. This is of importance for modern satellite aerosol retrieval algorithms development. [1] Sobolev

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.

A parallel 3D particle-in-cell code with dynamic load balancing

International Nuclear Information System (INIS)

Wolfheimer, Felix; Gjonaj, Erion; Weiland, Thomas

2006-01-01

A parallel 3D electrostatic Particle-In-Cell (PIC) code including an algorithm for modelling Space Charge Limited (SCL) emission [E. Gjonaj, T. Weiland, 3D-modeling of space-charge-limited electron emission. A charge conserving algorithm, Proceedings of the 11th Biennial IEEE Conference on Electromagnetic Field Computation, 2004] is presented. A domain decomposition technique based on orthogonal recursive bisection is used to parallelize the computation on a distributed memory environment of clustered workstations. For problems with a highly nonuniform and time dependent distribution of particles, e.g., bunch dynamics, a dynamic load balancing between the processes is needed to preserve the parallel performance. The algorithm for the detection of a load imbalance and the redistribution of the tasks among the processes is based on a weight function criterion, where the weight of a cell measures the computational load associated with it. The algorithm is studied with two examples. In the first example, multiple electron bunches as occurring in the S-DALINAC [A. Richter, Operational experience at the S-DALINAC, Proceedings of the Fifth European Particle Accelerator Conference, 1996] accelerator are simulated in the absence of space charge fields. In the second example, the SCL emission and electron trajectories in an electron gun are simulated

A parallel 3D particle-in-cell code with dynamic load balancing

Energy Technology Data Exchange (ETDEWEB)

Wolfheimer, Felix [Technische Universitaet Darmstadt, Institut fuer Theorie Elektromagnetischer Felder, Schlossgartenstr.8, 64283 Darmstadt (Germany)]. E-mail: wolfheimer@temf.de; Gjonaj, Erion [Technische Universitaet Darmstadt, Institut fuer Theorie Elektromagnetischer Felder, Schlossgartenstr.8, 64283 Darmstadt (Germany); Weiland, Thomas [Technische Universitaet Darmstadt, Institut fuer Theorie Elektromagnetischer Felder, Schlossgartenstr.8, 64283 Darmstadt (Germany)

2006-03-01

A parallel 3D electrostatic Particle-In-Cell (PIC) code including an algorithm for modelling Space Charge Limited (SCL) emission [E. Gjonaj, T. Weiland, 3D-modeling of space-charge-limited electron emission. A charge conserving algorithm, Proceedings of the 11th Biennial IEEE Conference on Electromagnetic Field Computation, 2004] is presented. A domain decomposition technique based on orthogonal recursive bisection is used to parallelize the computation on a distributed memory environment of clustered workstations. For problems with a highly nonuniform and time dependent distribution of particles, e.g., bunch dynamics, a dynamic load balancing between the processes is needed to preserve the parallel performance. The algorithm for the detection of a load imbalance and the redistribution of the tasks among the processes is based on a weight function criterion, where the weight of a cell measures the computational load associated with it. The algorithm is studied with two examples. In the first example, multiple electron bunches as occurring in the S-DALINAC [A. Richter, Operational experience at the S-DALINAC, Proceedings of the Fifth European Particle Accelerator Conference, 1996] accelerator are simulated in the absence of space charge fields. In the second example, the SCL emission and electron trajectories in an electron gun are simulated.

3D Hyperpolarized C-13 EPI with Calibrationless Parallel Imaging

DEFF Research Database (Denmark)

Gordon, Jeremy W.; Hansen, Rie Beck; Shin, Peter J.

2018-01-01

With the translation of metabolic MRI with hyperpolarized 13C agents into the clinic, imaging approaches will require large volumetric FOVs to support clinical applications. Parallel imaging techniques will be crucial to increasing volumetric scan coverage while minimizing RF requirements and tem...... strategies to accelerate and undersample hyperpolarized 13C data using 3D blipped EPI acquisitions and multichannel receive coils, and demonstrated its application in a human study of [1-13C]pyruvate metabolism....

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

A dynamical theory for linearized massive superspin 3/2

International Nuclear Information System (INIS)

Gates, James S. Jr.; Koutrolikos, Konstantinos

2014-01-01

We present a new theory of free massive superspin Y=3/2 irreducible representation of the 4D, N=1 Super-Poincaré group, which has linearized non-minimal supergravity (superhelicity Y=3/2) as it’s massless limit. The new results will illuminate the underlying structure of auxiliary superfields required for the description of higher massive superspin systems

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.

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...

FIRST RESULTS FROM THE 3D-HST SURVEY: THE STRIKING DIVERSITY OF MASSIVE GALAXIES AT z > 1

International Nuclear Information System (INIS)

Van Dokkum, Pieter G.; Nelson, Erica; Skelton, Rosalind E.; Bezanson, Rachel; Lundgren, Britt; Brammer, Gabriel; Fumagalli, Mattia; Franx, Marijn; Patel, Shannon; Labbé, Ivo; Rix, Hans-Walter; Schmidt, Kasper B.; Da Cunha, Elisabete; Kriek, Mariska; Bian Fuyan; Fan Xiaohui; Erb, Dawn K.; Förster Schreiber, Natascha; Illingworth, Garth D.; Magee, Dan

2011-01-01

We present first results from the 3D-HST program, a near-IR spectroscopic survey performed with the Wide Field Camera 3 (WFC3) on the HST. We have used 3D-HST spectra to measure redshifts and Hα equivalent widths (EW Hα ) for a complete, stellar mass-limited sample of 34 galaxies at 1 star > 10 11 M ☉ in the COSMOS, GOODS, and AEGIS fields. We find that a substantial fraction of massive galaxies at this epoch are forming stars at a high rate: the fraction of galaxies with EW Hα >10 Å is 59%, compared to 10% among Sloan Digital Sky Survey galaxies of similar masses at z = 0.1. Galaxies with weak Hα emission show absorption lines typical of 2-4 Gyr old stellar populations. The structural parameters of the galaxies, derived from the associated WFC3 F140W imaging data, correlate with the presence of Hα; quiescent galaxies are compact with high Sérsic index and high inferred velocity dispersion, whereas star-forming galaxies are typically large two-armed spiral galaxies, with low Sérsic index. Some of these star-forming galaxies might be progenitors of the most massive S0 and Sa galaxies. Our results challenge the idea that galaxies at fixed mass form a homogeneous population with small scatter in their properties. Instead, we find that massive galaxies form a highly diverse population at z > 1, in marked contrast to the local universe.

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)

3D hydrodynamic simulations of carbon burning in massive stars

Science.gov (United States)

Cristini, A.; Meakin, C.; Hirschi, R.; Arnett, D.; Georgy, C.; Viallet, M.; Walkington, I.

2017-10-01

We present the first detailed 3D hydrodynamic implicit large eddy simulations of turbulent convection of carbon burning in massive stars. Simulations begin with radial profiles mapped from a carbon-burning shell within a 15 M⊙ 1D stellar evolution model. We consider models with 1283, 2563, 5123, and 10243 zones. The turbulent flow properties of these carbon-burning simulations are very similar to the oxygen-burning case. We performed a mean field analysis of the kinetic energy budgets within the Reynolds-averaged Navier-Stokes framework. For the upper convective boundary region, we find that the numerical dissipation is insensitive to resolution for linear mesh resolutions above 512 grid points. For the stiffer, more stratified lower boundary, our highest resolution model still shows signs of decreasing sub-grid dissipation suggesting it is not yet numerically converged. We find that the widths of the upper and lower boundaries are roughly 30 per cent and 10 per cent of the local pressure scaleheights, respectively. The shape of the boundaries is significantly different from those used in stellar evolution models. As in past oxygen-shell-burning simulations, we observe entrainment at both boundaries in our carbon-shell-burning simulations. In the large Péclet number regime found in the advanced phases, the entrainment rate is roughly inversely proportional to the bulk Richardson number, RiB (∝RiB-α, 0.5 ≲ α ≲ 1.0). We thus suggest the use of RiB as a means to take into account the results of 3D hydrodynamics simulations in new 1D prescriptions of convective boundary mixing.

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)

Parallelization of 2-D lattice Boltzmann codes

International Nuclear Information System (INIS)

Suzuki, Soichiro; Kaburaki, Hideo; Yokokawa, Mitsuo.

1996-03-01

Lattice Boltzmann (LB) codes to simulate two dimensional fluid flow are developed on vector parallel computer Fujitsu VPP500 and scalar parallel computer Intel Paragon XP/S. While a 2-D domain decomposition method is used for the scalar parallel LB code, a 1-D domain decomposition method is used for the vector parallel LB code to be vectorized along with the axis perpendicular to the direction of the decomposition. High parallel efficiency of 95.1% by the vector parallel calculation on 16 processors with 1152x1152 grid and 88.6% by the scalar parallel calculation on 100 processors with 800x800 grid are obtained. The performance models are developed to analyze the performance of the LB codes. It is shown by our performance models that the execution speed of the vector parallel code is about one hundred times faster than that of the scalar parallel code with the same number of processors up to 100 processors. We also analyze the scalability in keeping the available memory size of one processor element at maximum. Our performance model predicts that the execution time of the vector parallel code increases about 3% on 500 processors. Although the 1-D domain decomposition method has in general a drawback in the interprocessor communication, the vector parallel LB code is still suitable for the large scale and/or high resolution simulations. (author)

Parallelization of 2-D lattice Boltzmann codes

Energy Technology Data Exchange (ETDEWEB)

Suzuki, Soichiro; Kaburaki, Hideo; Yokokawa, Mitsuo

1996-03-01

Lattice Boltzmann (LB) codes to simulate two dimensional fluid flow are developed on vector parallel computer Fujitsu VPP500 and scalar parallel computer Intel Paragon XP/S. While a 2-D domain decomposition method is used for the scalar parallel LB code, a 1-D domain decomposition method is used for the vector parallel LB code to be vectorized along with the axis perpendicular to the direction of the decomposition. High parallel efficiency of 95.1% by the vector parallel calculation on 16 processors with 1152x1152 grid and 88.6% by the scalar parallel calculation on 100 processors with 800x800 grid are obtained. The performance models are developed to analyze the performance of the LB codes. It is shown by our performance models that the execution speed of the vector parallel code is about one hundred times faster than that of the scalar parallel code with the same number of processors up to 100 processors. We also analyze the scalability in keeping the available memory size of one processor element at maximum. Our performance model predicts that the execution time of the vector parallel code increases about 3% on 500 processors. Although the 1-D domain decomposition method has in general a drawback in the interprocessor communication, the vector parallel LB code is still suitable for the large scale and/or high resolution simulations. (author).

Development of a 3D parallel mechanism robot arm with three vertical-axial pneumatic actuators combined with a stereo vision system.

Science.gov (United States)

Chiang, Mao-Hsiung; Lin, Hao-Ting

2011-01-01

This study aimed to develop a novel 3D parallel mechanism robot driven by three vertical-axial pneumatic actuators with a stereo vision system for path tracking control. The mechanical system and the control system are the primary novel parts for developing a 3D parallel mechanism robot. In the mechanical system, a 3D parallel mechanism robot contains three serial chains, a fixed base, a movable platform and a pneumatic servo system. The parallel mechanism are designed and analyzed first for realizing a 3D motion in the X-Y-Z coordinate system of the robot's end-effector. The inverse kinematics and the forward kinematics of the parallel mechanism robot are investigated by using the Denavit-Hartenberg notation (D-H notation) coordinate system. The pneumatic actuators in the three vertical motion axes are modeled. In the control system, the Fourier series-based adaptive sliding-mode controller with H(∞) tracking performance is used to design the path tracking controllers of the three vertical servo pneumatic actuators for realizing 3D path tracking control of the end-effector. Three optical linear scales are used to measure the position of the three pneumatic actuators. The 3D position of the end-effector is then calculated from the measuring position of the three pneumatic actuators by means of the kinematics. However, the calculated 3D position of the end-effector cannot consider the manufacturing and assembly tolerance of the joints and the parallel mechanism so that errors between the actual position and the calculated 3D position of the end-effector exist. In order to improve this situation, sensor collaboration is developed in this paper. A stereo vision system is used to collaborate with the three position sensors of the pneumatic actuators. The stereo vision system combining two CCD serves to measure the actual 3D position of the end-effector and calibrate the error between the actual and the calculated 3D position of the end-effector. Furthermore, to

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.

Butterfly effect in 3D gravity

Science.gov (United States)

Qaemmaqami, Mohammad M.

2017-11-01

We study the butterfly effect by considering shock wave solutions near the horizon of the anti-de Sitter black hole in some three-dimensional gravity models including 3D Einstein gravity, minimal massive 3D gravity, new massive gravity, generalized massive gravity, Born-Infeld 3D gravity, and new bigravity. We calculate the butterfly velocities of these models and also we consider the critical points and different limits in some of these models. By studying the butterfly effect in the generalized massive gravity, we observe a correspondence between the butterfly velocities and right-left moving degrees of freedom or the central charges of the dual 2D conformal field theories.

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.

A parallel implementation of 3D Zernike moment analysis

Science.gov (United States)

Berjón, Daniel; Arnaldo, Sergio; Morán, Francisco

2011-01-01

Zernike polynomials are a well known set of functions that find many applications in image or pattern characterization because they allow to construct shape descriptors that are invariant against translations, rotations or scale changes. The concepts behind them can be extended to higher dimension spaces, making them also fit to describe volumetric data. They have been less used than their properties might suggest due to their high computational cost. We present a parallel implementation of 3D Zernike moments analysis, written in C with CUDA extensions, which makes it practical to employ Zernike descriptors in interactive applications, yielding a performance of several frames per second in voxel datasets about 2003 in size. In our contribution, we describe the challenges of implementing 3D Zernike analysis in a general-purpose GPU. These include how to deal with numerical inaccuracies, due to the high precision demands of the algorithm, or how to deal with the high volume of input data so that it does not become a bottleneck for the system.

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.

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.

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.

Parallel Computer System for 3D Visualization Stereo on GPU

Science.gov (United States)

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

2018-03-01

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

GPU-based, parallel-line, omni-directional integration of measured acceleration field to obtain the 3D pressure distribution

Science.gov (United States)

Wang, Jin; Zhang, Cao; Katz, Joseph

2016-11-01

A PIV based method to reconstruct the volumetric pressure field by direct integration of the 3D material acceleration directions has been developed. Extending the 2D virtual-boundary omni-directional method (Omni2D, Liu & Katz, 2013), the new 3D parallel-line omni-directional method (Omni3D) integrates the material acceleration along parallel lines aligned in multiple directions. Their angles are set by a spherical virtual grid. The integration is parallelized on a Tesla K40c GPU, which reduced the computing time from three hours to one minute for a single realization. To validate its performance, this method is utilized to calculate the 3D pressure fields in isotropic turbulence and channel flow using the JHU DNS Databases (http://turbulence.pha.jhu.edu). Both integration of the DNS acceleration as well as acceleration from synthetic 3D particles are tested. Results are compared to other method, e.g. solution to the Pressure Poisson Equation (e.g. PPE, Ghaemi et al., 2012) with Bernoulli based Dirichlet boundary conditions, and the Omni2D method. The error in Omni3D prediction is uniformly low, and its sensitivity to acceleration errors is local. It agrees with the PPE/Bernoulli prediction away from the Dirichlet boundary. The Omni3D method is also applied to experimental data obtained using tomographic PIV, and results are correlated with deformation of a compliant wall. ONR.

Incorporation of parallel electrospun fibers for improved topographical guidance in 3D nerve guides

International Nuclear Information System (INIS)

Jeffries, Eric M; Wang Yadong

2013-01-01

Three dimensional (3D) conduits facilitate nerve regeneration. Parallel microfibers have been shown to guide axon extension and Schwann cell migration on flat sheets via topographical cues. However, incorporation of aligned microfibers into 3D conduits to accelerate nerve regeneration has proven challenging. We report an electrospinning technique to incorporate parallel microfibers into 3D constructs at high surface areas while retaining an open architecture. The nerve guide consists of many microchannels lined with a thin layer of longitudinally-aligned microfibers. This design aims to maximize benefits of topographical cues without inhibiting cellular infiltration. We support this hypothesis by demonstrating efficient cell infiltration in vitro. Additionally, this new technique reduces wall thickness compared to our previous design, providing a greater total area for tissue growth. This approach results in an architecture that very closely mimics the structure of decellularized nerve but with larger microchannel diameters to encourage cell infiltration. We believe that reproducing the native architecture is the first step toward matching autograph efficacy. Furthermore, this design can be combined with other biochemical cues to promote nerve regeneration. (paper)

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...

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).

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.

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.

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

Science.gov (United States)

Luke, Edward Allen

1993-01-01

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

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

Advanced quadratures and periodic boundary conditions in parallel 3D Sn transport

International Nuclear Information System (INIS)

Manalo, K.; Yi, C.; Huang, M.; Sjoden, G.

2013-01-01

Significant updates in numerical quadratures have warranted investigation with 3D Sn discrete ordinates transport. We show new applications of quadrature departing from level symmetric ( 2 o) and Pn-Tn (>S 2 o). investigating 3 recently developed quadratures: Even-Odd (EO), Linear-Discontinuous Finite Element - Surface Area (LDFE-SA), and the non-symmetric Icosahedral Quadrature (IC). We discuss implementation changes to 3D Sn codes (applied to Hybrid MOC-Sn TITAN and 3D parallel PENTRAN) that can be performed to accommodate Icosahedral Quadrature, as this quadrature is not 90-degree rotation invariant. In particular, as demonstrated using PENTRAN, the properties of Icosahedral Quadrature are suitable for trivial application using periodic BCs versus that of reflective BCs. In addition to implementing periodic BCs for 3D Sn PENTRAN, we implemented a technique termed 'angular re-sweep' which properly conditions periodic BCs for outer eigenvalue iterative loop convergence. As demonstrated by two simple transport problems (3-group fixed source and 3-group reflected/periodic eigenvalue pin cell), we remark that all of the quadratures we investigated are generally superior to level symmetric quadrature, with Icosahedral Quadrature performing the most efficiently for problems tested. (authors)

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.

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.

Gauge invariant Lagrangian formulation of massive higher spin fields in (A)dS3 space

International Nuclear Information System (INIS)

Buchbinder, I.L.; Snegirev, T.V.; Zinoviev, Yu.M.

2012-01-01

We develop the frame-like formulation of massive bosonic higher spin fields in the case of three-dimensional (A)dS space with the arbitrary cosmological constant. The formulation is based on gauge invariant description by involving the Stueckelberg auxiliary fields. The explicit form of the Lagrangians and the gauge transformation laws are found. The theory can be written in terms of gauge invariant objects similar to the massless theories, thus allowing us to hope to use the same methods for investigation of interactions. In the massive spin 3 field example we are able to rewrite the Lagrangian using the new the so-called separated variables, so that the study of Lagrangian formulation reduces to finding the Lagrangian containing only half of the fields. The same construction takes places for arbitrary integer spin field as well. Further working in terms of separated variables, we build Lagrangian for arbitrary integer spin and write it in terms of gauge invariant objects. Also, we demonstrate how to restore the full set of variables, thus receiving Lagrangian for the massive fields of arbitrary spin in the terms of initial fields.

GPU-accelerated 3-D model-based tracking

International Nuclear Information System (INIS)

Brown, J Anthony; Capson, David W

2010-01-01

Model-based approaches to tracking the pose of a 3-D object in video are effective but computationally demanding. While statistical estimation techniques, such as the particle filter, are often employed to minimize the search space, real-time performance remains unachievable on current generation CPUs. Recent advances in graphics processing units (GPUs) have brought massively parallel computational power to the desktop environment and powerful developer tools, such as NVIDIA Compute Unified Device Architecture (CUDA), have provided programmers with a mechanism to exploit it. NVIDIA GPUs' single-instruction multiple-thread (SIMT) programming model is well-suited to many computer vision tasks, particularly model-based tracking, which requires several hundred 3-D model poses to be dynamically configured, rendered, and evaluated against each frame in the video sequence. Using 6 degree-of-freedom (DOF) rigid hand tracking as an example application, this work harnesses consumer-grade GPUs to achieve real-time, 3-D model-based, markerless object tracking in monocular video.

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.

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.

An efficient implementation of 3D high-resolution imaging for large-scale seismic data with GPU/CPU heterogeneous parallel computing

Science.gov (United States)

Xu, Jincheng; Liu, Wei; Wang, Jin; Liu, Linong; Zhang, Jianfeng

2018-02-01

De-absorption pre-stack time migration (QPSTM) compensates for the absorption and dispersion of seismic waves by introducing an effective Q parameter, thereby making it an effective tool for 3D, high-resolution imaging of seismic data. Although the optimal aperture obtained via stationary-phase migration reduces the computational cost of 3D QPSTM and yields 3D stationary-phase QPSTM, the associated computational efficiency is still the main problem in the processing of 3D, high-resolution images for real large-scale seismic data. In the current paper, we proposed a division method for large-scale, 3D seismic data to optimize the performance of stationary-phase QPSTM on clusters of graphics processing units (GPU). Then, we designed an imaging point parallel strategy to achieve an optimal parallel computing performance. Afterward, we adopted an asynchronous double buffering scheme for multi-stream to perform the GPU/CPU parallel computing. Moreover, several key optimization strategies of computation and storage based on the compute unified device architecture (CUDA) were adopted to accelerate the 3D stationary-phase QPSTM algorithm. Compared with the initial GPU code, the implementation of the key optimization steps, including thread optimization, shared memory optimization, register optimization and special function units (SFU), greatly improved the efficiency. A numerical example employing real large-scale, 3D seismic data showed that our scheme is nearly 80 times faster than the CPU-QPSTM algorithm. Our GPU/CPU heterogeneous parallel computing framework significant reduces the computational cost and facilitates 3D high-resolution imaging for large-scale seismic data.

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.

3D base: a geometrical data base system for the analysis and visualisation of 3D-shapes obtained from parallel serial sections including three different geometrical representations

NARCIS (Netherlands)

Verbeek, F. J.; de Groot, M. M.; Huijsmans, D. P.; Lamers, W. H.; Young, I. T.

1993-01-01

In this paper we discuss a geometrical data base that includes three different geometrical representations of one and the same reconstructed 3D shape: the contour-pile, the voxel enumeration, and the triangulation of a surface. The data base is tailored for 3D shapes obtained from plan-parallel

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.

Externally calibrated parallel imaging for 3D multispectral imaging near metallic implants using broadband ultrashort echo time imaging.

Science.gov (United States)

Wiens, Curtis N; Artz, Nathan S; Jang, Hyungseok; McMillan, Alan B; Reeder, Scott B

2017-06-01

To develop an externally calibrated parallel imaging technique for three-dimensional multispectral imaging (3D-MSI) in the presence of metallic implants. A fast, ultrashort echo time (UTE) calibration acquisition is proposed to enable externally calibrated parallel imaging techniques near metallic implants. The proposed calibration acquisition uses a broadband radiofrequency (RF) pulse to excite the off-resonance induced by the metallic implant, fully phase-encoded imaging to prevent in-plane distortions, and UTE to capture rapidly decaying signal. The performance of the externally calibrated parallel imaging reconstructions was assessed using phantoms and in vivo examples. Phantom and in vivo comparisons to self-calibrated parallel imaging acquisitions show that significant reductions in acquisition times can be achieved using externally calibrated parallel imaging with comparable image quality. Acquisition time reductions are particularly large for fully phase-encoded methods such as spectrally resolved fully phase-encoded three-dimensional (3D) fast spin-echo (SR-FPE), in which scan time reductions of up to 8 min were obtained. A fully phase-encoded acquisition with broadband excitation and UTE enabled externally calibrated parallel imaging for 3D-MSI, eliminating the need for repeated calibration regions at each frequency offset. Significant reductions in acquisition time can be achieved, particularly for fully phase-encoded methods like SR-FPE. Magn Reson Med 77:2303-2309, 2017. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.

Implementation of a Monte Carlo simulation environment for fully 3D PET on a high-performance parallel platform

CERN Document Server

Zaidi, H; Morel, Christian

1998-01-01

This paper describes the implementation of the Eidolon Monte Carlo program designed to simulate fully three-dimensional (3D) cylindrical positron tomographs on a MIMD parallel architecture. The original code was written in Objective-C and developed under the NeXTSTEP development environment. Different steps involved in porting the software on a parallel architecture based on PowerPC 604 processors running under AIX 4.1 are presented. Basic aspects and strategies of running Monte Carlo calculations on parallel computers are described. A linear decrease of the computing time was achieved with the number of computing nodes. The improved time performances resulting from parallelisation of the Monte Carlo calculations makes it an attractive tool for modelling photon transport in 3D positron tomography. The parallelisation paradigm used in this work is independent from the chosen parallel architecture

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...

EUV blank defect and particle inspection with high throughput immersion AFM with 1nm 3D resolution

NARCIS (Netherlands)

Es, M.H. van; Sadeghian Marnani, H.

2016-01-01

Inspection of EUV mask substrates and blanks is demanding. We envision this is a good target application for massively parallel Atomic Force Microscopy (AFM). We envision to do a full surface characterization of EUV masks with AFM enabling 1nm true 3D resolution over the entire surface. The limiting

LB3D : A parallel implementation of the Lattice-Boltzmann method for simulation of interacting amphiphilic fluids

NARCIS (Netherlands)

Schmieschek, S.; Shamardin, L.; Frijters, S.; Krüger, T.; Schiller, U.D.; Harting, J.; Coveney, P.V.

2017-01-01

We introduce the lattice-Boltzmann code LB3D, version 7.1. Building on a parallel program and supporting tools which have enabled research utilising high performance computing resources for nearly two decades, LB3D version 7 provides a subset of the research code functionality as an open source

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

Simulating Growth Kinetics in a Data-Parallel 3D Lattice Photobioreactor

Directory of Open Access Journals (Sweden)

A. V. Husselmann

2013-01-01

Full Text Available Though there have been many attempts to address growth kinetics in algal photobioreactors, surprisingly little have attempted an agent-based modelling (ABM approach. ABM has been heralded as a method of practical scientific inquiry into systems of a complex nature and has been applied liberally in a range of disciplines including ecology, physics, social science, and microbiology with special emphasis on pathogenic bacterial growth. We bring together agent-based simulation with the Photosynthetic Factory (PSF model, as well as certain key bioreactor characteristics in a visual 3D, parallel computing fashion. Despite being at small scale, the simulation gives excellent visual cues on the dynamics of such a reactor, and we further investigate the model in a variety of ways. Our parallel implementation on graphical processing units of the simulation provides key advantages, which we also briefly discuss. We also provide some performance data, along with particular effort in visualisation, using volumetric and isosurface rendering.

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.

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.

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.

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

On 3D Minimal Massive Gravity

CERN Document Server

Alishahiha, Mohsen; Naseh, Ali; Shirzad, Ahmad

2014-12-03

We study linearized equations of motion of the newly proposed three dimensional gravity, known as minimal massive gravity, using its metric formulation. We observe that the resultant linearized equations are exactly the same as that of TMG by making use of a redefinition of the parameters of the model. In particular the model admits logarithmic modes at the critical points. We also study several vacuum solutions of the model, specially at a certain limit where the contribution of Chern-Simons term vanishes.

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...

Plasma and milk concentrations of vitamin D3 and 25-hydroxy vitamin D3 following intravenous injection of vitamin D3 or 25-hydroxy vitamin D3.

OpenAIRE

Hidiroglou, M; Knipfel, J E

1984-01-01

Plasma levels of vitamin D3 or 25-hydroxyvitamin D3 in ewes after administration of a single massive intravenous dose of vitamin D3 (2 X 10(6) IU) or 25-hydroxy vitamin D3 (5 mg) were determined at zero, one, two, three, five, ten and 20 days postinjection. In six ewes injected with vitamin D3 conversion of vitamin D3 to 25-hydroxy vitamin D3 resulted in a six-fold increase in the plasma 25-hydroxy vitamin D3 level within one day. Elevated levels were maintained until day 10 but by day 20 a s...

Dual descriptions of massive spin-2 particles in D=3+1

International Nuclear Information System (INIS)

Dalmazi, Denis

2013-01-01

Full text: Since the sixties (last century) one speculates on the effects of a possible (tiny) mass for the graviton. One expects a decrease in the gravitational interaction at large distances which comes handy regarding the experimental data of the last 15 years on the accelerated expansion of the universe. There has been a growing interest in massive quantum gravity in the last years. Almost all recent works are built up on the top of a free (quadratic) action for a massive spin-2 particle known as massive Fierz-Pauli (FP) theory which has first appeared in 1939. In this theory the basic field is a symmetric rank-2 tensor. It is a common belief in the massive gravity community that the massive FP theory is the unique self-consistent (ghost free, Poincare covariant, correct number of degrees of freedom) description of massive spin-2 particles in terms of a rank-2 tensor. We have shown recently that there are other possibilities if we start with a general (non-symmetric) rank-2 tensor. Here we show how our previous work is related with the well known massive FP theory via the introduction of spectators fields of rank-0 (scalar) and rank-1 (vector). We comment on the introduction of interacting vertices and how they affect the free duality with the massive FP theory (author)

A theoretical concept for a thermal-hydraulic 3D parallel channel core model

International Nuclear Information System (INIS)

Hoeld, A.

2004-01-01

A detailed description of the theoretical concept of the 3D thermal-hydraulic single- and two-phase flow phenomena is presented. The theoretical concept is based on important development lines such as separate treatment of the mass and energy from the momentum balance eqs. The other line is the establishment of a procedure for the calculation of the mass flow distributions into different parallel channels based on the fact that the sum of pressure decrease terms over a closed loop must stay, despite of un-symmetric perturbations, zero. The concept is realized in the experimental code HERO-X3D, concentrating in a first step on an artificial BWR or PWR core which may consist of a central channel, four quadrants, and a bypass channel. (authors)

A parallel code named NEPTUNE for 3D fully electromagnetic and pic simulations

International Nuclear Information System (INIS)

Dong Ye; Yang Wenyuan; Chen Jun; Zhao Qiang; Xia Fang; Ma Yan; Xiao Li; Sun Huifang; Chen Hong; Zhou Haijing; Mao Zeyao; Dong Zhiwei

2010-01-01

A parallel code named NEPTUNE for 3D fully electromagnetic and particle-in-cell (PIC) simulations is introduced, which could run on the Linux system with hundreds to thousand CPUs. NEPTUNE is suitable to simulate entire 3D HPM devices; many HPM devices are simulated and designed by using it. In NEPTUNE code, the electromagnetic fields are updated by using the finite-difference in time domain (FDTD) method of solving Maxwell equations and the particles are moved by using Buneman-Boris advance method of solving relativistic Newton-Lorentz equation. Electromagnetic fields and particles are coupled by using liner weighing interpolation PIC method, and the electric filed components are corrected by using Boris method of solve Poisson equation in order to ensure charge-conservation. NEPTUNE code could construct many complicated geometric structures, such as arbitrary axial-symmetric structures, plane transforming structures, slow-wave-structures, coupling holes, foils, and so on. The boundary conditions used in NEPTUNE code are introduced in brief, including perfectly electric conductor boundary, external wave boundary, and particle boundary. Finally, some typical HPM devices are simulated and test by using NEPTUNE code, including MILO, RBWO, VCO, and RKA. The simulation results are with correct and credible physical images, and the parallel efficiencies are also given. (authors)

Recent progress in modelling 3D lithospheric deformation

Science.gov (United States)

Kaus, B. J. P.; Popov, A.; May, D. A.

2012-04-01

Modelling 3D lithospheric deformation remains a challenging task, predominantly because the variations in rock types, as well as nonlinearities due to for example plastic deformation result in sharp and very large jumps in effective viscosity contrast. As a result, there are only a limited number of 3D codes available, most of which are using direct solvers which are computationally and memory-wise very demanding. As a result, the resolutions for typical model runs are quite modest, despite the use of hundreds of processors (and using much larger computers is unlikely to bring much improvement in this situation). For this reason we recently developed a new 3D deformation code,called LaMEM: Lithosphere and Mantle Evolution Model. LaMEM is written on top of PETSc, and as a result it runs on massive parallel machines and we have a large number of iterative solvers available (including geometric and algebraic multigrid methods). As it remains unclear which solver combinations work best under which conditions, we have implemented most currently suggested methods (such as schur complement reduction or Fully coupled iterations). In addition, we can use either a finite element discretization (with Q1P0, stabilized Q1Q1 or Q2P-1 elements) or a staggered finite difference discretization for the same input geometry, which is based on a marker and cell technique). This gives us he flexibility to test various solver methodologies on the same model setup, in terms of accuracy, speed, memory usage etc. Here, we will report on some features of LaMEM, on recent code additions, as well as on some lessons we learned which are important for modelling 3D lithospheric deformation. Specifically we will discuss: 1) How we combine a particle-and-cell method to make it work with both a finite difference and a (lagrangian, eulerian or ALE) finite element formulation, with only minor code modifications code 2) How finite difference and finite element discretizations compare in terms of

Development of a Stereo Vision Measurement System for a 3D Three-Axial Pneumatic Parallel Mechanism Robot Arm

Directory of Open Access Journals (Sweden)

Chien-Lun Hou

2011-02-01

Full Text Available In this paper, a stereo vision 3D position measurement system for a three-axial pneumatic parallel mechanism robot arm is presented. The stereo vision 3D position measurement system aims to measure the 3D trajectories of the end-effector of the robot arm. To track the end-effector of the robot arm, the circle detection algorithm is used to detect the desired target and the SAD algorithm is used to track the moving target and to search the corresponding target location along the conjugate epipolar line in the stereo pair. After camera calibration, both intrinsic and extrinsic parameters of the stereo rig can be obtained, so images can be rectified according to the camera parameters. Thus, through the epipolar rectification, the stereo matching process is reduced to a horizontal search along the conjugate epipolar line. Finally, 3D trajectories of the end-effector are computed by stereo triangulation. The experimental results show that the stereo vision 3D position measurement system proposed in this paper can successfully track and measure the fifth-order polynomial trajectory and sinusoidal trajectory of the end-effector of the three- axial pneumatic parallel mechanism robot arm.

MICADO: Parallel implementation of a 2D-1D iterative algorithm for the 3D neutron transport problem in prismatic geometries

International Nuclear Information System (INIS)

Fevotte, F.; Lathuiliere, B.

2013-01-01

The large increase in computing power over the past few years now makes it possible to consider developing 3D full-core heterogeneous deterministic neutron transport solvers for reference calculations. Among all approaches presented in the literature, the method first introduced in [1] seems very promising. It consists in iterating over resolutions of 2D and ID MOC problems by taking advantage of prismatic geometries without introducing approximations of a low order operator such as diffusion. However, before developing a solver with all industrial options at EDF, several points needed to be clarified. In this work, we first prove the convergence of this iterative process, under some assumptions. We then present our high-performance, parallel implementation of this algorithm in the MICADO solver. Benchmarking the solver against the Takeda case shows that the 2D-1D coupling algorithm does not seem to affect the spatial convergence order of the MOC solver. As for performance issues, our study shows that even though the data distribution is suited to the 2D solver part, the efficiency of the ID part is sufficient to ensure a good parallel efficiency of the global algorithm. After this study, the main remaining difficulty implementation-wise is about the memory requirement of a vector used for initialization. An efficient acceleration operator will also need to be developed. (authors)

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.

High Performance Programming Using Explicit Shared Memory Model on Cray T3D1

Science.gov (United States)

Simon, Horst D.; Saini, Subhash; Grassi, Charles

1994-01-01

The Cray T3D system is the first-phase system in Cray Research, Inc.'s (CRI) three-phase massively parallel processing (MPP) program. This system features a heterogeneous architecture that closely couples DEC's Alpha microprocessors and CRI's parallel-vector technology, i.e., the Cray Y-MP and Cray C90. An overview of the Cray T3D hardware and available programming models is presented. Under Cray Research adaptive Fortran (CRAFT) model four programming methods (data parallel, work sharing, message-passing using PVM, and explicit shared memory model) are available to the users. However, at this time data parallel and work sharing programming models are not available to the user community. The differences between standard PVM and CRI's PVM are highlighted with performance measurements such as latencies and communication bandwidths. We have found that the performance of neither standard PVM nor CRI s PVM exploits the hardware capabilities of the T3D. The reasons for the bad performance of PVM as a native message-passing library are presented. This is illustrated by the performance of NAS Parallel Benchmarks (NPB) programmed in explicit shared memory model on Cray T3D. In general, the performance of standard PVM is about 4 to 5 times less than obtained by using explicit shared memory model. This degradation in performance is also seen on CM-5 where the performance of applications using native message-passing library CMMD on CM-5 is also about 4 to 5 times less than using data parallel methods. The issues involved (such as barriers, synchronization, invalidating data cache, aligning data cache etc.) while programming in explicit shared memory model are discussed. Comparative performance of NPB using explicit shared memory programming model on the Cray T3D and other highly parallel systems such as the TMC CM-5, Intel Paragon, Cray C90, IBM-SP1, etc. is presented.

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.

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 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

Parallel Jacobian-free Newton Krylov solution of the discrete ordinates method with flux limiters for 3D radiative transfer

International Nuclear Information System (INIS)

Godoy, William F.; Liu Xu

2012-01-01

The present study introduces a parallel Jacobian-free Newton Krylov (JFNK) general minimal residual (GMRES) solution for the discretized radiative transfer equation (RTE) in 3D, absorbing, emitting and scattering media. For the angular and spatial discretization of the RTE, the discrete ordinates method (DOM) and the finite volume method (FVM) including flux limiters are employed, respectively. Instead of forming and storing a large Jacobian matrix, JFNK methods allow for large memory savings as the required Jacobian-vector products are rather approximated by semiexact and numerical formulations, for which convergence and computational times are presented. Parallelization of the GMRES solution is introduced in a combined memory-shared/memory-distributed formulation that takes advantage of the fact that only large vector arrays remain in the JFNK process. Results are presented for 3D test cases including a simple homogeneous, isotropic medium and a more complex non-homogeneous, non-isothermal, absorbing–emitting and anisotropic scattering medium with collimated intensities. Additionally, convergence and stability of Gram–Schmidt and Householder orthogonalizations for the Arnoldi process in the parallel GMRES algorithms are discussed and analyzed. Overall, the introduction of JFNK methods results in a parallel, yet scalable to the tested 2048 processors, and memory affordable solution to 3D radiative transfer problems without compromising the accuracy and convergence of a Newton-like solution.

Fully 3D GPU PET reconstruction

Energy Technology Data Exchange (ETDEWEB)

Herraiz, J.L., E-mail: joaquin@nuclear.fis.ucm.es [Grupo de Fisica Nuclear, Departmento Fisica Atomica, Molecular y Nuclear, Universidad Complutense de Madrid (Spain); Espana, S. [Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA (United States); Cal-Gonzalez, J. [Grupo de Fisica Nuclear, Departmento Fisica Atomica, Molecular y Nuclear, Universidad Complutense de Madrid (Spain); Vaquero, J.J. [Departmento de Bioingenieria e Ingenieria Espacial, Universidad Carlos III, Madrid (Spain); Desco, M. [Departmento de Bioingenieria e Ingenieria Espacial, Universidad Carlos III, Madrid (Spain); Unidad de Medicina y Cirugia Experimental, Hospital General Universitario Gregorio Maranon, Madrid (Spain); Udias, J.M. [Grupo de Fisica Nuclear, Departmento Fisica Atomica, Molecular y Nuclear, Universidad Complutense de Madrid (Spain)

2011-08-21

Fully 3D iterative tomographic image reconstruction is computationally very demanding. Graphics Processing Unit (GPU) has been proposed for many years as potential accelerators in complex scientific problems, but it has not been used until the recent advances in the programmability of GPUs that the best available reconstruction codes have started to be implemented to be run on GPUs. This work presents a GPU-based fully 3D PET iterative reconstruction software. This new code may reconstruct sinogram data from several commercially available PET scanners. The most important and time-consuming parts of the code, the forward and backward projection operations, are based on an accurate model of the scanner obtained with the Monte Carlo code PeneloPET and they have been massively parallelized on the GPU. For the PET scanners considered, the GPU-based code is more than 70 times faster than a similar code running on a single core of a fast CPU, obtaining in both cases the same images. The code has been designed to be easily adapted to reconstruct sinograms from any other PET scanner, including scanner prototypes.

Fully 3D GPU PET reconstruction

International Nuclear Information System (INIS)

Herraiz, J.L.; Espana, S.; Cal-Gonzalez, J.; Vaquero, J.J.; Desco, M.; Udias, J.M.

2011-01-01

Fully 3D iterative tomographic image reconstruction is computationally very demanding. Graphics Processing Unit (GPU) has been proposed for many years as potential accelerators in complex scientific problems, but it has not been used until the recent advances in the programmability of GPUs that the best available reconstruction codes have started to be implemented to be run on GPUs. This work presents a GPU-based fully 3D PET iterative reconstruction software. This new code may reconstruct sinogram data from several commercially available PET scanners. The most important and time-consuming parts of the code, the forward and backward projection operations, are based on an accurate model of the scanner obtained with the Monte Carlo code PeneloPET and they have been massively parallelized on the GPU. For the PET scanners considered, the GPU-based code is more than 70 times faster than a similar code running on a single core of a fast CPU, obtaining in both cases the same images. The code has been designed to be easily adapted to reconstruct sinograms from any other PET scanner, including scanner prototypes.

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.

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 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.

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.

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.

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...

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.

Analysis of scalability of high-performance 3D image processing platform for virtual colonoscopy.

Science.gov (United States)

Yoshida, Hiroyuki; Wu, Yin; Cai, Wenli

2014-03-19

One of the key challenges in three-dimensional (3D) medical imaging is to enable the fast turn-around time, which is often required for interactive or real-time response. This inevitably requires not only high computational power but also high memory bandwidth due to the massive amount of data that need to be processed. For this purpose, we previously developed a software platform for high-performance 3D medical image processing, called HPC 3D-MIP platform, which employs increasingly available and affordable commodity computing systems such as the multicore, cluster, and cloud computing systems. To achieve scalable high-performance computing, the platform employed size-adaptive, distributable block volumes as a core data structure for efficient parallelization of a wide range of 3D-MIP algorithms, supported task scheduling for efficient load distribution and balancing, and consisted of a layered parallel software libraries that allow image processing applications to share the common functionalities. We evaluated the performance of the HPC 3D-MIP platform by applying it to computationally intensive processes in virtual colonoscopy. Experimental results showed a 12-fold performance improvement on a workstation with 12-core CPUs over the original sequential implementation of the processes, indicating the efficiency of the platform. Analysis of performance scalability based on the Amdahl's law for symmetric multicore chips showed the potential of a high performance scalability of the HPC 3D-MIP platform when a larger number of cores is available.

Search for charged massive long-lived particles at D0

Science.gov (United States)

Xie, Yunhe

2009-05-01

We report on a new search for charged massive long-lived particles (CMLLP) by the D0 Experiment at Fermilab's Teva- tron. CMLLP are predicted in many theories beyond Standard Model. Time-of-flight information was used in the search for pair-produced CMLLPs, based on the signature of two particles, reconstructed as muons, with speed and invariant mass inconsistent with beam-produced muons. The analysis was done with the data taken by D0 detector in Run II cor- responding to an integrated luminosity of 3 fb-1. Limits on the pair production of CMLLPs are presented quasi-model independently.

Grid-optimized Web 3D applications on wide area network

Science.gov (United States)

Wang, Frank; Helian, Na; Meng, Lingkui; Wu, Sining; Zhang, Wen; Guo, Yike; Parker, Michael Andrew

2008-08-01

Geographical information system has come into the Web Service times now. In this paper, Web3D applications have been developed based on our developed Gridjet platform, which provides a more effective solution for massive 3D geo-dataset sharing in distributed environments. Web3D services enabling web users could access the services as 3D scenes, virtual geographical environment and so on. However, Web3D services should be shared by thousands of essential users that inherently distributed on different geography locations. Large 3D geo-datasets need to be transferred to distributed clients via conventional HTTP, NFS and FTP protocols, which often encounters long waits and frustration in distributed wide area network environments. GridJet was used as the underlying engine between the Web 3D application node and geo-data server that utilizes a wide range of technologies including the one of paralleling the remote file access, which is a WAN/Grid-optimized protocol and provides "local-like" accesses to remote 3D geo-datasets. No change in the way of using software is required since the multi-streamed GridJet protocol remains fully compatible with existing IP infrastructures. Our recent progress includes a real-world test that Web3D applications as Google Earth over the GridJet protocol beats those over the classic ones by a factor of 2-7 where the transfer distance is over 10,000 km.

High-Fidelity RF Gun Simulations with the Parallel 3D Finite Element Particle-In-Cell Code Pic3P

Energy Technology Data Exchange (ETDEWEB)

Candel, A; Kabel, A.; Lee, L.; Li, Z.; Limborg, C.; Ng, C.; Schussman, G.; Ko, K.; /SLAC

2009-06-19

SLAC's Advanced Computations Department (ACD) has developed the first parallel Finite Element 3D Particle-In-Cell (PIC) code, Pic3P, for simulations of RF guns and other space-charge dominated beam-cavity interactions. Pic3P solves the complete set of Maxwell-Lorentz equations and thus includes space charge, retardation and wakefield effects from first principles. Pic3P uses higher-order Finite Elementmethods on unstructured conformal meshes. A novel scheme for causal adaptive refinement and dynamic load balancing enable unprecedented simulation accuracy, aiding the design and operation of the next generation of accelerator facilities. Application to the Linac Coherent Light Source (LCLS) RF gun is presented.

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.

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

Hybrid shared/distributed parallelism for 3D characteristics transport solvers

International Nuclear Information System (INIS)

Dahmani, M.; Roy, R.

2005-01-01

In this paper, we will present a new hybrid parallel model for solving large-scale 3-dimensional neutron transport problems used in nuclear reactor simulations. Large heterogeneous reactor problems, like the ones that occurs when simulating Candu cores, have remained computationally intensive and impractical for routine applications on single-node or even vector computers. Based on the characteristics method, this new model is designed to solve the transport equation after distributing the calculation load on a network of shared memory multi-processors. The tracks are either generated on the fly at each characteristics sweep or stored in sequential files. The load balancing is taken into account by estimating the calculation load of tracks and by distributing batches of uniform load on each node of the network. Moreover, the communication overhead can be predicted after benchmarking the latency and bandwidth using appropriate network test suite. These models are useful for predicting the performance of the parallel applications and to analyze the scalability of the parallel systems. (authors)

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.

The parallel processing system for fast 3D-CT image reconstruction by circular shifting float memory architecture

International Nuclear Information System (INIS)

Wang Shi; Kang Kejun; Wang Jingjin

1996-01-01

Computerized Tomography (CT) is expected to become an inevitable diagnostic technique in the future. However, the long time required to reconstruct an image has been one of the major drawbacks associated with this technique. Parallel process is one of the best way to solve this problem. This paper gives the architecture, hardware and software design of PIRS-4 (4-processor Parallel Image Reconstruction System), which is a parallel processing system for fast 3D-CT image reconstruction by circular shifting float memory architecture. It includes the structure and components of the system, the design of crossbar switch and details of control model, the description of RPBP image reconstruction, the choice of OS (Operate System) and language, the principle of imitating EMS, direct memory R/W of float and programming in the protect model. Finally, the test results are given

Seismic processing using Parallel 3D FMM

OpenAIRE

Borlaug, Idar

2007-01-01

This thesis develops and tests 3D Fast Marching Method (FMM) algorithm and apply these to seismic simulations. The FMM is a general method for monotonically advancing fronts, originally developed by Sethian. It calculates the first arrival time for an advancing front or wave. FMM methods are used for a variety of applications including, fatigue cracks in materials, lymph node segmentation in CT images, computing skeletons and centerlines in 3D objects and for finding salt formations in seismi...

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.

3-D Hybrid Simulation of Quasi-Parallel Bow Shock and Its Effects on the Magnetosphere

International Nuclear Information System (INIS)

Lin, Y.; Wang, X.Y.

2005-01-01

A three-dimensional (3-D) global-scale hybrid simulation is carried out for the structure of the quasi-parallel bow shock, in particular the foreshock waves and pressure pulses. The wave evolution and interaction with the dayside magnetosphere are discussed. It is shown that diamagnetic cavities are generated in the turbulent foreshock due to the ion beam plasma interaction, and these compressional pulses lead to strong surface perturbations at the magnetopause and Alfven waves/field line resonance in the magnetosphere

Advanced 3-D Ultrasound Imaging

DEFF Research Database (Denmark)

Rasmussen, Morten Fischer

The main purpose of the PhD project was to develop methods that increase the 3-D ultrasound imaging quality available for the medical personnel in the clinic. Acquiring a 3-D volume gives the medical doctor the freedom to investigate the measured anatomy in any slice desirable after the scan has...... been completed. This allows for precise measurements of organs dimensions and makes the scan more operator independent. Real-time 3-D ultrasound imaging is still not as widespread in use in the clinics as 2-D imaging. A limiting factor has traditionally been the low image quality achievable using...... a channel limited 2-D transducer array and the conventional 3-D beamforming technique, Parallel Beamforming. The first part of the scientific contributions demonstrate that 3-D synthetic aperture imaging achieves a better image quality than the Parallel Beamforming technique. Data were obtained using both...

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.

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

A parallel 3-D discrete wavelet transform architecture using pipelined lifting scheme approach for video coding

Science.gov (United States)

Hegde, Ganapathi; Vaya, Pukhraj

2013-10-01

This article presents a parallel architecture for 3-D discrete wavelet transform (3-DDWT). The proposed design is based on the 1-D pipelined lifting scheme. The architecture is fully scalable beyond the present coherent Daubechies filter bank (9, 7). This 3-DDWT architecture has advantages such as no group of pictures restriction and reduced memory referencing. It offers low power consumption, low latency and high throughput. The computing technique is based on the concept that lifting scheme minimises the storage requirement. The application specific integrated circuit implementation of the proposed architecture is done by synthesising it using 65 nm Taiwan Semiconductor Manufacturing Company standard cell library. It offers a speed of 486 MHz with a power consumption of 2.56 mW. This architecture is suitable for real-time video compression even with large frame dimensions.

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...

Flexbar 3.0 - SIMD and multicore parallelization.

Science.gov (United States)

Roehr, Johannes T; Dieterich, Christoph; Reinert, Knut

2017-09-15

High-throughput sequencing machines can process many samples in a single run. For Illumina systems, sequencing reads are barcoded with an additional DNA tag that is contained in the respective sequencing adapters. The recognition of barcode and adapter sequences is hence commonly needed for the analysis of next-generation sequencing data. Flexbar performs demultiplexing based on barcodes and adapter trimming for such data. The massive amounts of data generated on modern sequencing machines demand that this preprocessing is done as efficiently as possible. We present Flexbar 3.0, the successor of the popular program Flexbar. It employs now twofold parallelism: multi-threading and additionally SIMD vectorization. Both types of parallelism are used to speed-up the computation of pair-wise sequence alignments, which are used for the detection of barcodes and adapters. Furthermore, new features were included to cover a wide range of applications. We evaluated the performance of Flexbar based on a simulated sequencing dataset. Our program outcompetes other tools in terms of speed and is among the best tools in the presented quality benchmark. https://github.com/seqan/flexbar. johannes.roehr@fu-berlin.de or knut.reinert@fu-berlin.de. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

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.

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

SERENDIPITOUS DISCOVERY OF A MASSIVE cD GALAXY AT z = 1.096: IMPLICATIONS FOR THE EARLY FORMATION AND LATE EVOLUTION OF cD GALAXIES

Energy Technology Data Exchange (ETDEWEB)

Liu, F. S. [College of Physical Science and Technology, Shenyang Normal University, Shenyang 110034 (China); Guo Yicheng; Koo, David C.; Trump, Jonathan R.; Barro, Guillermo; Yesuf, Hassen; Faber, S. M.; Cheung, Edmond [UCO/Lick Observatory, Department of Astronomy and Astrophysics, University of California, Santa Cruz, CA 95064 (United States); Giavalisco, M. [Department of Astronomy, University of Massachusetts, Amherst, MA 01003 (United States); Cassata, P. [Aix Marseille Universite, CNRS, LAM-Laboratoire d' Astrophysique de Marseille, F-13388 Marseille (France); Koekemoer, A. M.; Grogin, Norman A. [Space Telescope Science Institute, 3700 San Martin Boulevard, Baltimore, MD 21218 (United States); Pentericci, L.; Castellano, M. [INAF Osservatorio Astronomico di Roma, Via Frascati 33, I-00040 Monteporzio (RM) (Italy); Mao, Shude [National Astronomical Observatories, Chinese Academy of Sciences, A20 Datun Road, Beijing 100012 (China); Xia, X. Y. [Tianjin Astrophysics Center, Tianjin Normal University, Tianjin 300387 (China); Hathi, Nimish P. [Observatories of the Carnegie Institution for Science, Pasadena, CA 91101 (United States); Huang, Kuang-Han [Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218 (United States); Kocevski, Dale [Department of Physics and Astronomy, University of Kentucky, Lexington, KY 40506-0055 (United States); McGrath, Elizabeth J., E-mail: fengshan@ucolick.org [Department of Physics and Astronomy, Colby College, Mayflower Hill Drive, Waterville, ME 0490 (United States); and others

2013-06-01

We have made a serendipitous discovery of a massive ({approx}5 Multiplication-Sign 10{sup 11} M{sub Sun }) cD galaxy at z = 1.096 in a candidate-rich cluster in the Hubble Ultra Deep Field (HUDF) area of GOODS-South. This brightest cluster galaxy (BCG) is the most distant cD galaxy confirmed to date. Ultra-deep HST/WFC3 images reveal an extended envelope starting from {approx}10 kpc and reaching {approx}70 kpc in radius along the semimajor axis. The spectral energy distributions indicate that both its inner component and outer envelope are composed of an old, passively evolving (specific star formation rate <10{sup -4} Gyr{sup -1}) stellar population. The cD galaxy lies on the same mass-size relation as the bulk of quiescent galaxies at similar redshifts. The cD galaxy has a higher stellar mass surface density ({approx}M{sub *}/R{sub 50}{sup 2}) but a similar velocity dispersion ({approx}{radical}(M{sub *}/R{sub 50})) to those of more massive, nearby cDs. If the cD galaxy is one of the progenitors of today's more massive cDs, its size (R{sub 50}) and stellar mass have had to increase on average by factors of 3.4 {+-} 1.1 and 3.3 {+-} 1.3 over the past {approx}8 Gyr, respectively. Such increases in size and stellar mass without being accompanied by significant increases in velocity dispersion are consistent with evolutionary scenarios driven by both major and minor dissipationless (dry) mergers. If such cD envelopes originate from dry mergers, our discovery of even one example proves that some BCGs entered the dry merger phase at epochs earlier than z = 1. Our data match theoretical models which predict that the continuance of dry mergers at z < 1 can result in structures similar to those of massive cD galaxies seen today. Moreover, our discovery is a surprise given that the extreme depth of the HUDF is essential to reveal such an extended cD envelope at z > 1 and, yet, the HUDF covers only a minuscule region of sky ({approx}3.1 Multiplication-Sign 10{sup -8

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

A parallel implementation of 3D Zernike moment analysis

OpenAIRE

Berjón Díez, Daniel; Arnaldo Duart, Sergio; Morán Burgos, Francisco

2011-01-01

Zernike polynomials are a well known set of functions that find many applications in image or pattern characterization because they allow to construct shape descriptors that are invariant against translations, rotations or scale changes. The concepts behind them can be extended to higher dimension spaces, making them also fit to describe volumetric data. They have been less used than their properties might suggest due to their high computational cost. We present a parallel implementation of 3...

Algebraic multigrid preconditioning within parallel finite-element solvers for 3-D electromagnetic modelling problems in geophysics

Science.gov (United States)

Koldan, Jelena; Puzyrev, Vladimir; de la Puente, Josep; Houzeaux, Guillaume; Cela, José María

2014-06-01

We present an elaborate preconditioning scheme for Krylov subspace methods which has been developed to improve the performance and reduce the execution time of parallel node-based finite-element (FE) solvers for 3-D electromagnetic (EM) numerical modelling in exploration geophysics. This new preconditioner is based on algebraic multigrid (AMG) that uses different basic relaxation methods, such as Jacobi, symmetric successive over-relaxation (SSOR) and Gauss-Seidel, as smoothers and the wave front algorithm to create groups, which are used for a coarse-level generation. We have implemented and tested this new preconditioner within our parallel nodal FE solver for 3-D forward problems in EM induction geophysics. We have performed series of experiments for several models with different conductivity structures and characteristics to test the performance of our AMG preconditioning technique when combined with biconjugate gradient stabilized method. The results have shown that, the more challenging the problem is in terms of conductivity contrasts, ratio between the sizes of grid elements and/or frequency, the more benefit is obtained by using this preconditioner. Compared to other preconditioning schemes, such as diagonal, SSOR and truncated approximate inverse, the AMG preconditioner greatly improves the convergence of the iterative solver for all tested models. Also, when it comes to cases in which other preconditioners succeed to converge to a desired precision, AMG is able to considerably reduce the total execution time of the forward-problem code-up to an order of magnitude. Furthermore, the tests have confirmed that our AMG scheme ensures grid-independent rate of convergence, as well as improvement in convergence regardless of how big local mesh refinements are. In addition, AMG is designed to be a black-box preconditioner, which makes it easy to use and combine with different iterative methods. Finally, it has proved to be very practical and efficient in the

A Parallel Sweeping Preconditioner for Heterogeneous 3D Helmholtz Equations

KAUST Repository

Poulson, Jack

2013-05-02

A parallelization of a sweeping preconditioner for three-dimensional Helmholtz equations without large cavities is introduced and benchmarked for several challenging velocity models. The setup and application costs of the sequential preconditioner are shown to be O(γ2N4/3) and O(γN logN), where γ(ω) denotes the modestly frequency-dependent number of grid points per perfectly matched layer. Several computational and memory improvements are introduced relative to using black-box sparse-direct solvers for the auxiliary problems, and competitive runtimes and iteration counts are reported for high-frequency problems distributed over thousands of cores. Two open-source packages are released along with this paper: Parallel Sweeping Preconditioner (PSP) and the underlying distributed multifrontal solver, Clique. © 2013 Society for Industrial and Applied Mathematics.

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.

Scalable Multi-Platform Distribution of Spatial 3d Contents

Science.gov (United States)

Klimke, J.; Hagedorn, B.; Döllner, J.

2013-09-01

Virtual 3D city models provide powerful user interfaces for communication of 2D and 3D geoinformation. Providing high quality visualization of massive 3D geoinformation in a scalable, fast, and cost efficient manner is still a challenging task. Especially for mobile and web-based system environments, software and hardware configurations of target systems differ significantly. This makes it hard to provide fast, visually appealing renderings of 3D data throughout a variety of platforms and devices. Current mobile or web-based solutions for 3D visualization usually require raw 3D scene data such as triangle meshes together with textures delivered from server to client, what makes them strongly limited in terms of size and complexity of the models they can handle. In this paper, we introduce a new approach for provisioning of massive, virtual 3D city models on different platforms namely web browsers, smartphones or tablets, by means of an interactive map assembled from artificial oblique image tiles. The key concept is to synthesize such images of a virtual 3D city model by a 3D rendering service in a preprocessing step. This service encapsulates model handling and 3D rendering techniques for high quality visualization of massive 3D models. By generating image tiles using this service, the 3D rendering process is shifted from the client side, which provides major advantages: (a) The complexity of the 3D city model data is decoupled from data transfer complexity (b) the implementation of client applications is simplified significantly as 3D rendering is encapsulated on server side (c) 3D city models can be easily deployed for and used by a large number of concurrent users, leading to a high degree of scalability of the overall approach. All core 3D rendering techniques are performed on a dedicated 3D rendering server, and thin-client applications can be compactly implemented for various devices and platforms.

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

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)

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.

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

Design for scalability in 3D computer graphics architectures

DEFF Research Database (Denmark)

Holten-Lund, Hans Erik

2002-01-01

This thesis describes useful methods and techniques for designing scalable hybrid parallel rendering architectures for 3D computer graphics. Various techniques for utilizing parallelism in a pipelines system are analyzed. During the Ph.D study a prototype 3D graphics architecture named Hybris has...

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.

Black string in dRGT massive gravity

Energy Technology Data Exchange (ETDEWEB)

Tannukij, Lunchakorn [Mahidol University, Department of Physics, Faculty of Science, Bangkok (Thailand); Hanyang University, Department of Physics, Seoul (Korea, Republic of); Naresuan University, The Institute for Fundamental Study, Phitsanulok (Thailand); Wongjun, Pitayuth [Naresuan University, The Institute for Fundamental Study, Phitsanulok (Thailand); Ministry of Education, Thailand Center of Excellence in Physics, Bangkok (Thailand); Ghosh, Suchant G. [Jamia Millia Islamia, Centre of Theoretical Physics, New Delhi (India); University of Kwazulu-Natal, Astrophysics and Cosmology Research Unit, School of Mathematical Sciences, Durban (South Africa)

2017-12-15

We present a cylindrically symmetric solution, both charged and uncharged, which is known as a black string solution to the nonlinear ghost-free massive gravity found by de Rham, Gabadadze, and Tolley (dRGT). This ''dRGT black string'' can be thought of as a generalization of the black string solution found by Lemos. Moreover, the dRGT black string solution includes other classes of black string solution such as the monopole-black string ones since the graviton mass contributes to the global monopole term as well as the cosmological-constant term. To investigate the solution, we compute mass, temperature, and entropy of the dRGT black string. We found that the existence of the graviton mass drastically affects the thermodynamics of the black string. Furthermore, the Hawking-Page phase transition is found to be possible for the dRGT black string as well as the charged dRGT black string. The dRGT black string solution is thermodynamically stable for r > r{sub c} with negative thermodynamical potential and positive heat capacity while it is unstable for r < r{sub c} where the potential is positive. (orig.)

3D Body Scanning Measurement System Associated with RF Imaging, Zero-padding and Parallel Processing

Directory of Open Access Journals (Sweden)

Kim Hyung Tae

2016-04-01

Full Text Available This work presents a novel signal processing method for high-speed 3D body measurements using millimeter waves with a general processing unit (GPU and zero-padding fast Fourier transform (ZPFFT. The proposed measurement system consists of a radio-frequency (RF antenna array for a penetrable measurement, a high-speed analog-to-digital converter (ADC for significant data acquisition, and a general processing unit for fast signal processing. The RF waves of the transmitter and the receiver are converted to real and imaginary signals that are sampled by a high-speed ADC and synchronized with the kinematic positions of the scanner. Because the distance between the surface and the antenna is related to the peak frequency of the conjugate signals, a fast Fourier transform (FFT is applied to the signal processing after the sampling. The sampling time is finite owing to a short scanning time, and the physical resolution needs to be increased; further, zero-padding is applied to interpolate the spectra of the sampled signals to consider a 1/m floating point frequency. The GPU and parallel algorithm are applied to accelerate the speed of the ZPFFT because of the large number of additional mathematical operations of the ZPFFT. 3D body images are finally obtained by spectrograms that are the arrangement of the ZPFFT in a 3D space.

Crossover from 2d to 3d in anisotropic Kondo lattices

International Nuclear Information System (INIS)

Reyes, D.; Continentino, M.A.

2008-01-01

We study the crossover from two to three dimensions in Kondo lattices (KLM) using the Kondo necklace model (KNM). In order to diagonalize the KNM, we use a representation for the localized and conduction electron spins in terms of bond operators and a decoupling for the relevant Green's functions. Both models have a quantum critical point at a finite value of the ratio (J/t) between the Kondo coupling (J) and the hopping (t). In 2d there is no line of finite temperature antiferromagnetic (AF) transitions while for d≥3 this line is given by, T N ∝|g| 1/(d-1) [D. Reyes, M.A. Continentino, Phys. Rev. B 76 (2007) 075114]. The crossover from 2d to 3d is investigated by turning on the electronic hopping (t -perpendicular ) of conduction electrons between different planes. The phase diagram as a function of temperature T, J/t -parallel and ξ=t -perpendicular /t -parallel , where t -parallel is the hopping within the planes is calculated

3D seismic modeling and reverse‐time migration with the parallel Fourier method using non‐blocking collective communications

KAUST Repository

Chu, Chunlei

2009-01-01

The major performance bottleneck of the parallel Fourier method on distributed memory systems is the network communication cost. In this study, we investigate the potential of using non‐blocking all‐to‐all communications to solve this problem by overlapping computation and communication. We present the runtime comparison of a 3D seismic modeling problem with the Fourier method using non‐blocking and blocking calls, respectively, on a Linux cluster. The data demonstrate that a performance improvement of up to 40% can be achieved by simply changing blocking all‐to‐all communication calls to non‐blocking ones to introduce the overlapping capability. A 3D reverse‐time migration result is also presented as an extension to the modeling work based on non‐blocking collective communications.

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.

Parallel 3D Simulation of Seismic Wave Propagation in the Structure of Nobi Plain, Central Japan

Science.gov (United States)

Kotani, A.; Furumura, T.; Hirahara, K.

2003-12-01

We performed large-scale parallel simulations of the seismic wave propagation to understand the complex wave behavior in the 3D basin structure of the Nobi Plain, which is one of the high population cities in central Japan. In this area, many large earthquakes occurred in the past, such as the 1891 Nobi earthquake (M8.0), the 1944 Tonankai earthquake (M7.9) and the 1945 Mikawa earthquake (M6.8). In order to mitigate the potential disasters for future earthquakes, 3D subsurface structure of Nobi Plain has recently been investigated by local governments. We referred to this model together with bouguer anomaly data to construct a detail 3D basin structure model for Nobi plain, and conducted computer simulations of ground motions. We first evaluated the ground motions for two small earthquakes (M4~5); one occurred just beneath the basin edge at west, and the other occurred at south. The ground motions from these earthquakes were well recorded by the strong motion networks; K-net, Kik-net, and seismic intensity instruments operated by local governments. We compare the observed seismograms with simulations to validate the 3D model. For the 3D simulation we sliced the 3D model into a number of layers to assign to many processors for concurrent computing. The equation of motions are solved using a high order (32nd) staggered-grid FDM in horizontal directions, and a conventional (4th-order) FDM in vertical direction with the MPI inter-processor communications between neighbor region. The simulation model is 128km by 128km by 43km, which is discritized at variable grid size of 62.5-125m in horizontal directions and of 31.25-62.5m in vertical direction. We assigned a minimum shear wave velocity is Vs=0.4km/s, at the top of the sedimentary basin. The seismic sources for the small events are approximated by double-couple point source and we simulate the seismic wave propagation at maximum frequency of 2Hz. We used the Earth Simulator (JAMSTEC, Yokohama Inst) to conduct such

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.

3D 14N/1H Double Quantum/1H Single Quantum Correlation Solid-State NMR for Probing Parallel and Anti-Parallel Beta-Sheet Arrangement of Oligo-Peptides at Natural Abundance.

Science.gov (United States)

Hong, You-Lee; Asakura, Tetsuo; Nishiyama, Yusuke

2018-05-08

β-sheet structure of oligo- and poly-peptides can be formed in anti-parallel (AP)- and parallel (P)-structure, which is the important feature to understand the structures. In principle, P- and AP-β-sheet structures can be identified by the presence (AP) and absence (P) of the interstrand 1HNH/1HNH correlations on a diagonal in 2D 1H double quantum (DQ)/1H single quantum (SQ) spectrum due to the different interstrand 1HNH/1HNH distances between these two arrangements. However, the 1HNH/1HNH peaks overlap to the 1HNH3+/1HNH3+ peaks, which always give cross peaks regardless of the β-sheet arrangement. The 1HNH3+/1HNH3+ peaks disturb the observation of the presence/absence of 1HNH/1HNH correlations and the assignment of 1HNH and 1HNH3+ is not always available. Here, 3D 14N/1H DQ/1H SQ correlation solid-state NMR experiments at fast magic angle spinning (70 kHz) are introduced to distinguish AP and P β-sheet structure. The 14N dimension allows the separate observation of 1HNH/1HNH peaks from 1HNH3+/1HNH3+ peaks with clear assignment of 1HNH and 1HNH3+. In addition, the high natural abundance of 1H and 14N enables 3D 14N/1H DQ/1H SQ experiments of oligo-alanines (Ala3-6) in four hours without any isotope labelling. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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.

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)

Experiences Using Hybrid MPI/OpenMP in the Real World: Parallelization of a 3D CFD Solver for Multi-Core Node Clusters

Directory of Open Access Journals (Sweden)

Gabriele Jost

2010-01-01

Full Text Available Today most systems in high-performance computing (HPC feature a hierarchical hardware design: shared-memory nodes with several multi-core CPUs are connected via a network infrastructure. When parallelizing an application for these architectures it seems natural to employ a hierarchical programming model such as combining MPI and OpenMP. Nevertheless, there is the general lore that pure MPI outperforms the hybrid MPI/OpenMP approach. In this paper, we describe the hybrid MPI/OpenMP parallelization of IR3D (Incompressible Realistic 3-D code, a full-scale real-world application, which simulates the environmental effects on the evolution of vortices trailing behind control surfaces of underwater vehicles. We discuss performance, scalability and limitations of the pure MPI version of the code on a variety of hardware platforms and show how the hybrid approach can help to overcome certain limitations.

SERENDIPITOUS DISCOVERY OF A MASSIVE cD GALAXY AT z = 1.096: IMPLICATIONS FOR THE EARLY FORMATION AND LATE EVOLUTION OF cD GALAXIES

International Nuclear Information System (INIS)

Liu, F. S.; Guo Yicheng; Koo, David C.; Trump, Jonathan R.; Barro, Guillermo; Yesuf, Hassen; Faber, S. M.; Cheung, Edmond; Giavalisco, M.; Cassata, P.; Koekemoer, A. M.; Grogin, Norman A.; Pentericci, L.; Castellano, M.; Mao, Shude; Xia, X. Y.; Hathi, Nimish P.; Huang, Kuang-Han; Kocevski, Dale; McGrath, Elizabeth J.

2013-01-01

We have made a serendipitous discovery of a massive (∼5 × 10 11 M ☉ ) cD galaxy at z = 1.096 in a candidate-rich cluster in the Hubble Ultra Deep Field (HUDF) area of GOODS-South. This brightest cluster galaxy (BCG) is the most distant cD galaxy confirmed to date. Ultra-deep HST/WFC3 images reveal an extended envelope starting from ∼10 kpc and reaching ∼70 kpc in radius along the semimajor axis. The spectral energy distributions indicate that both its inner component and outer envelope are composed of an old, passively evolving (specific star formation rate –4 Gyr –1 ) stellar population. The cD galaxy lies on the same mass-size relation as the bulk of quiescent galaxies at similar redshifts. The cD galaxy has a higher stellar mass surface density (∼M * /R 50 2 ) but a similar velocity dispersion (∼√(M * /R 50 )) to those of more massive, nearby cDs. If the cD galaxy is one of the progenitors of today's more massive cDs, its size (R 50 ) and stellar mass have had to increase on average by factors of 3.4 ± 1.1 and 3.3 ± 1.3 over the past ∼8 Gyr, respectively. Such increases in size and stellar mass without being accompanied by significant increases in velocity dispersion are consistent with evolutionary scenarios driven by both major and minor dissipationless (dry) mergers. If such cD envelopes originate from dry mergers, our discovery of even one example proves that some BCGs entered the dry merger phase at epochs earlier than z = 1. Our data match theoretical models which predict that the continuance of dry mergers at z 1 and, yet, the HUDF covers only a minuscule region of sky (∼3.1 × 10 –8 ). Adding that cDs are rare, our serendipitous discovery hints that such cDs may be more common than expected, perhaps even ubiquitous. Images reaching HUDF depths of more area (especially with cluster BCGs at z > 1) are needed to confirm this conjecture.

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...

Optimal data replication: A new approach to optimizing parallel EM algorithms on a mesh-connected multiprocessor for 3D PET image reconstruction

International Nuclear Information System (INIS)

Chen, C.M.; Lee, S.Y.

1995-01-01

The EM algorithm promises an estimated image with the maximal likelihood for 3D PET image reconstruction. However, due to its long computation time, the EM algorithm has not been widely used in practice. While several parallel implementations of the EM algorithm have been developed to make the EM algorithm feasible, they do not guarantee an optimal parallelization efficiency. In this paper, the authors propose a new parallel EM algorithm which maximizes the performance by optimizing data replication on a mesh-connected message-passing multiprocessor. To optimize data replication, the authors have formally derived the optimal allocation of shared data, group sizes, integration and broadcasting of replicated data as well as the scheduling of shared data accesses. The proposed parallel EM algorithm has been implemented on an iPSC/860 with 16 PEs. The experimental and theoretical results, which are consistent with each other, have shown that the proposed parallel EM algorithm could improve performance substantially over those using unoptimized data replication

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

Qademah Fault 3D Survey

KAUST Repository

Hanafy, Sherif M.

2014-01-01

Objective: Collect 3D seismic data at Qademah Fault location to 1. 3D traveltime tomography 2. 3D surface wave migration 3. 3D phase velocity 4. Possible reflection processing Acquisition Date: 26 – 28 September 2014 Acquisition Team: Sherif, Kai, Mrinal, Bowen, Ahmed Acquisition Layout: We used 288 receiver arranged in 12 parallel lines, each line has 24 receiver. Inline offset is 5 m and crossline offset is 10 m. One shot is fired at each receiver location. We use the 40 kgm weight drop as seismic source, with 8 to 15 stacks at each shot location.

3D Massive MIMO Systems: Modeling and Performance Analysis

KAUST Repository

Nadeem, Qurrat-Ul-Ain; Kammoun, Abla; Debbah, Merouane; Alouini, Mohamed-Slim

2015-01-01

necessitates the characterization of 3D channels. We present an information-theoretic channel model for MIMO systems that supports the elevation dimension. The model is based on the principle of maximum entropy, which enables us to determine the distribution

3D Laser Imprint Using a Smoother Ray-Traced Power Deposition Method

Science.gov (United States)

Schmitt, Andrew J.

2017-10-01

Imprinting of laser nonuniformities in directly-driven icf targets is a challenging problem to accurately simulate with large radiation-hydro codes. One of the most challenging aspects is the proper construction of the complex and rapidly changing laser interference structure driving the imprint using the reduced laser propagation models (usually ray-tracing) found in these codes. We have upgraded the modelling capability in our massively-parallel fastrad3d code by adding a more realistic EM-wave interference structure. This interference model adds an axial laser speckle to the previous transverse-only laser structure, and can be impressed on our improved smoothed 3D raytrace package. This latter package, which connects rays to form bundles and performs power deposition calculations on the bundles, is intended to decrease ray-trace noise (which can mask or add to imprint) while using fewer rays. We apply this improved model to 3D simulations of recent imprint experiments performed on the Omega-EP laser and the Nike laser that examined the reduction of imprinting due to very thin high-Z target coatings. We report on the conditions in which this new model makes a significant impact on the development of laser imprint. Supported by US DoE/NNSA.

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

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)

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

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.

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

On massive gravitons in 2+1 dimensions

NARCIS (Netherlands)

Bergshoeff, Eric; Hohm, Olaf; Townsend, Paul; Lazkoz, R; Vera, R

2010-01-01

The Fierz-Pauli (FP) free field theory for massive spin-2 particles can be extended, in a spacetime of (1+2) dimensions (3D), to a generally covariant parity-preserving interacting field theory, in at least two ways. One is "new massive gravity" (NMG), with an action that involves curvature-squared

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

Reentrant phase transitions of higher-dimensional AdS black holes in dRGT massive gravity

International Nuclear Information System (INIS)

Zou, De-Cheng; Yue, Ruihong; Zhang, Ming

2017-01-01

We study the P-V criticality and phase transition in the extended phase space of anti-de Sitter (AdS) black holes in higher-dimensional de Rham, Gabadadze and Tolley (dRGT) massive gravity, treating the cosmological constant as pressure and the corresponding conjugate quantity is interpreted as thermodynamic volume. Besides the usual small/large black hole phase transitions, the interesting thermodynamic phenomena of reentrant phase transitions (RPTs) are observed for black holes in all d ≥ 6-dimensional spacetime when the coupling coefficients c_im"2 of massive potential satisfy some certain conditions. (orig.)

The spectrum of massive excitations of 3d 3-state Potts model and universality

International Nuclear Information System (INIS)

Falcone, R.; Fiore, R.; Gravina, M.; Papa, A.

2007-01-01

We consider the mass spectrum of the 3d 3-state Potts model in the broken phase (a) near the second order Ising critical point in the temperature-magnetic field plane and (b) near the weakly first order transition point at zero magnetic field. In the case (a), we compare the mass spectrum with the prediction from universality of mass ratios in the 3d Ising class; in the case (b), we determine a mass ratio to be compared with the corresponding one in the spectrum of screening masses of the (3+1)d SU(3) pure gauge theory at finite temperature in the deconfined phase near the transition. The agreement in the comparison in the case (a) would represent a non-trivial test of validity of the conjecture of spectrum universality. A positive answer to the comparison in the case (b) would suggest the possibility to extend this conjecture to weakly first order phase transitions

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.

Simulation of current generation in a 3-D plasma model

International Nuclear Information System (INIS)

Tsung, F.S.; Dawson, J.M.

1996-01-01

Two wires carrying current in the same direction will attract each other, and two wires carrying current in the opposite direction will repel each other. Now, consider a test charge in a plasma. If the test charge carries current parallel to the plasma, then it will be pulled toward the plasma core, and if the test charge carries current anti-parallel to the plasma, then it will be pushed to the edge. The electromagnetic coupling between the plasma and a test charge (i.e., the A parallel circ v parallel term in the test charge's Hamiltonian) breaks the symmetry in the parallel direction, and gives rise to a diffusion coefficient which is dependent on the particle's parallel velocity. This is the basis for the open-quotes preferential lossclose quotes mechanism described in the work by Nunan et al. In our previous 2+1/2 D work, in both cylindrical and toroidal geometries, showed that if the plasma column is centrally fueled, then an initial current increases steadily. The results in straight, cylindrical plasmas showed that self generated parallel current arises without trapped particle or neoclassical diffusion, as assumed by the bootstrap theory. It suggests that the fundamental mechanism seems to be the conservation of particles canonical momenta in the direction of the ignorable coordinate. We have extended the simulation to 3D to verify the model put forth. A scalable 3D EM-PIC code, with a localized field-solver, has been implemented to run on a large class of parallel computers. On the 512-node SP2 at Cornell Theory Center, we have benchmarked the 2+1/2 D calculations using 32 grids in the previously ignored direction, and a 100-fold increase in the number of particles. Our preliminary results show good agreements between the 2+1/2 D and the 3D calculations. We will present our 3D results at the meeting

Uncertainty Analysis of RELAP5-3D

Energy Technology Data Exchange (ETDEWEB)

Alexandra E Gertman; Dr. George L Mesina

2012-07-01

As world-wide energy consumption continues to increase, so does the demand for the use of alternative energy sources, such as Nuclear Energy. Nuclear Power Plants currently supply over 370 gigawatts of electricity, and more than 60 new nuclear reactors have been commissioned by 15 different countries. The primary concern for Nuclear Power Plant operation and lisencing has been safety. The safety of the operation of Nuclear Power Plants is no simple matter- it involves the training of operators, design of the reactor, as well as equipment and design upgrades throughout the lifetime of the reactor, etc. To safely design, operate, and understand nuclear power plants, industry and government alike have relied upon the use of best-estimate simulation codes, which allow for an accurate model of any given plant to be created with well-defined margins of safety. The most widely used of these best-estimate simulation codes in the Nuclear Power industry is RELAP5-3D. Our project focused on improving the modeling capabilities of RELAP5-3D by developing uncertainty estimates for its calculations. This work involved analyzing high, medium, and low ranked phenomena from an INL PIRT on a small break Loss-Of-Coolant Accident as wall as an analysis of a large break Loss-Of- Coolant Accident. Statistical analyses were performed using correlation coefficients. To perform the studies, computer programs were written that modify a template RELAP5 input deck to produce one deck for each combination of key input parameters. Python scripting enabled the running of the generated input files with RELAP5-3D on INL’s massively parallel cluster system. Data from the studies was collected and analyzed with SAS. A summary of the results of our studies are presented.

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.

Dalle applicazioni professionali al 3D per tutti

Directory of Open Access Journals (Sweden)

Domenico Santarsiero

2008-03-01

Full Text Available From professional applications to 3D for everyone The applications of 3D technology are constantly maturing and so are the solutions designed to satisfy the needs of various professionals. The development of extremely user oriented solutions, which encouraged the use of 3D technology by a wide range of users, have evolved alongside a market in which final user skills are fundamental. The origins of this trend are particularly evident in the massive diffusion of geospatial web applications.

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

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.

Multirate-based fast parallel algorithms for 2-D DHT-based real-valued discrete Gabor transform.

Science.gov (United States)

Tao, Liang; Kwan, Hon Keung

2012-07-01

Novel algorithms for the multirate and fast parallel implementation of the 2-D discrete Hartley transform (DHT)-based real-valued discrete Gabor transform (RDGT) and its inverse transform are presented in this paper. A 2-D multirate-based analysis convolver bank is designed for the 2-D RDGT, and a 2-D multirate-based synthesis convolver bank is designed for the 2-D inverse RDGT. The parallel channels in each of the two convolver banks have a unified structure and can apply the 2-D fast DHT algorithm to speed up their computations. The computational complexity of each parallel channel is low and is independent of the Gabor oversampling rate. All the 2-D RDGT coefficients of an image are computed in parallel during the analysis process and can be reconstructed in parallel during the synthesis process. The computational complexity and time of the proposed parallel algorithms are analyzed and compared with those of the existing fastest algorithms for 2-D discrete Gabor transforms. The results indicate that the proposed algorithms are the fastest, which make them attractive for real-time image processing.

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

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...

NIF Ignition Target 3D Point Design

Energy Technology Data Exchange (ETDEWEB)

Jones, O; Marinak, M; Milovich, J; Callahan, D

2008-11-05

We have developed an input file for running 3D NIF hohlraums that is optimized such that it can be run in 1-2 days on parallel computers. We have incorporated increasing levels of automation into the 3D input file: (1) Configuration controlled input files; (2) Common file for 2D and 3D, different types of capsules (symcap, etc.); and (3) Can obtain target dimensions, laser pulse, and diagnostics settings automatically from NIF Campaign Management Tool. Using 3D Hydra calculations to investigate different problems: (1) Intrinsic 3D asymmetry; (2) Tolerance to nonideal 3D effects (e.g. laser power balance, pointing errors); and (3) Synthetic diagnostics.

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.

The new Exponential Directional Iterative (EDI) 3-D Sn scheme for parallel adaptive differencing

International Nuclear Information System (INIS)

Sjoden, G.E.

2005-01-01

The new Exponential Directional Iterative (EDI) discrete ordinates (Sn) scheme for 3-D Cartesian Coordinates is presented. The EDI scheme is a logical extension of the positive, efficient Exponential Directional Weighted (EDW) Sn scheme currently used as the third level of the adaptive spatial differencing algorithm in the PENTRAN parallel discrete ordinates solver. Here, the derivation and advantages of the EDI scheme are presented; EDI uses EDW-rendered exponential coefficients as initial starting values to begin a fixed point iteration of the exponential coefficients. One issue that required evaluation was an iterative cutoff criterion to prevent the application of an unstable fixed point iteration; although this was needed in some cases, it was readily treated with a default to EDW. Iterative refinement of the exponential coefficients in EDI typically converged in fewer than four fixed point iterations. Moreover, EDI yielded more accurate angular fluxes compared to the other schemes tested, particularly in streaming conditions. Overall, it was found that the EDI scheme was up to an order of magnitude more accurate than the EDW scheme on a given mesh interval in streaming cases, and is potentially a good candidate as a fourth-level differencing scheme in the PENTRAN adaptive differencing sequence. The 3-D Cartesian computational cost of EDI was only about 20% more than the EDW scheme, and about 40% more than Diamond Zero (DZ). More evaluation and testing are required to determine suitable upgrade metrics for EDI to be fully integrated into the current adaptive spatial differencing sequence in PENTRAN. (author)

Reentrant phase transitions of higher-dimensional AdS black holes in dRGT massive gravity

Energy Technology Data Exchange (ETDEWEB)

Zou, De-Cheng; Yue, Ruihong [Yangzhou University, College of Physical Science and Technology, Yangzhou (China); Zhang, Ming [Xi' an Aeronautical University, Faculty of Science, Xi' an (China)

2017-04-15

We study the P-V criticality and phase transition in the extended phase space of anti-de Sitter (AdS) black holes in higher-dimensional de Rham, Gabadadze and Tolley (dRGT) massive gravity, treating the cosmological constant as pressure and the corresponding conjugate quantity is interpreted as thermodynamic volume. Besides the usual small/large black hole phase transitions, the interesting thermodynamic phenomena of reentrant phase transitions (RPTs) are observed for black holes in all d ≥ 6-dimensional spacetime when the coupling coefficients c{sub i}m{sup 2} of massive potential satisfy some certain conditions. (orig.)

FANS-3D Users Guide (ESTEP Project ER 201031)

Science.gov (United States)

2016-08-01

TECHNICAL DOCUMENT 3293 August 2016 FANS -3D User’s Guide (ESTEP Project ER-201031) Pei-Fang Wang SSC Pacific Hamn-Ching...1.1 THEORY AND NUMERICAL ALGORITHM OF FANS CODE ............................................. 1 2. FANS -3D SOFTWARE DOCUMENTATION AND EXECUTION...5 3. FANS -3D CODE PARALLELIZATION

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.

Programmable level-1 trigger with 3D-Flow processor array

International Nuclear Information System (INIS)

Crosetto, D.

1994-01-01

The 3D-Flow parallel processing system is a new concept in processor architecture, system architecture, and assembly architecture. Compared to the electronics used in present systems, this approach reduces the cost and complexity of the hardware and allows easy assembly, disassembly, incremental upgrading, and maintenance of different interconnection topologies. The 3D-Flow parallel-processing system benefits high energy physics (HEP) by allowing: (1) common less costly hardware to be used in different experiments. (2) new uses of existing installations. (3) tuning of trigger based on the first analyzed data, and (4) selection of desired events directly from raw data. The goal of this parallel-processing architecture is to acquire multiple data in parallel (up to 100 million frames per second) and to process them at high speed, accomplishing digital filtering on the input data, pattern recognition (particle identification), data moving, and data formatting. The main features of the system are its programmability, scalability, high-speed communication, and low cost. The compactness of the 3D-Flow parallel-processing system in concert with the processor architecture allows processor interconnections to be mapped into the geometry of sensors (detectors in HEP) without large interconnection signal delay, enabling real-time pattern recognition. The overall 3D-Flow project has passed a major design review at Fermilab (Reviewers included experts in computers, triggering, system assembly, and electronics)

25-Hydroxyvitamin D-3 affects vitamin D status similar to vitamin D-3 in pigs - but the meat produced has a lower content of vitamin D

DEFF Research Database (Denmark)

Jakobsen, Jette; Maribo, H.; Bysted, Anette

2007-01-01

In food databases, the specific contents of vitamin D-3 and 25-hydroxyvitamin D-3 in food have been implemented in the last 10 years. No consensus has yet been established on the relative activity between the components. Therefore, the objective of the present study was to assess the relative...... activity of 25-hydroxyvitamin D-3 compared to vitamin D-3. The design was a parallel study in pigs (n 24), which from an age of 12 weeks until slaughter 11 weeks later were fed approximately 55 mu g vitamin D/d, as vitamin D-3, in a mixture of vitamin D-3 and 25-hydroxyvitamin D-3, or 25-hydroxyvitamin D-3....... The end-points measured were plasma 25-hydroxyvitamin D-3, and in the liver and loin the content of vitamin D-3 and 25-hydroxyvitamin D-3 Vitamin D-3 and 25-hydroxyvitamin D3 in the feed did not affect 25-hydroxyvitamin D-3 in the plasma, liver or loin differently, while a significant effect was shown...

3D neutron transport modelization

International Nuclear Information System (INIS)

Warin, X.

1996-12-01

Some nodal methods to solve the transport equation in 3D are presented. Two nodal methods presented at an OCDE congress are described: a first one is a low degree one called RTN0; a second one is a high degree one called BDM1. The two methods can be made faster with a totally consistent DSA. Some results of parallelization show that: 98% of the time is spent in sweeps; transport sweeps are easily parallelized. (K.A.)

Outer Electrospun Polycaprolactone Shell Induces Massive Foreign Body Reaction and Impairs Axonal Regeneration through 3D Multichannel Chitosan Nerve Guides

Directory of Open Access Journals (Sweden)

Sven Duda

2014-01-01

Full Text Available We report on the performance of composite nerve grafts with an inner 3D multichannel porous chitosan core and an outer electrospun polycaprolactone shell. The inner chitosan core provided multiple guidance channels for regrowing axons. To analyze the in vivo properties of the bare chitosan cores, we separately implanted them into an epineural sheath. The effects of both graft types on structural and functional regeneration across a 10 mm rat sciatic nerve gap were compared to autologous nerve transplantation (ANT. The mechanical biomaterial properties and the immunological impact of the grafts were assessed with histological techniques before and after transplantation in vivo. Furthermore during a 13-week examination period functional tests and electrophysiological recordings were performed and supplemented by nerve morphometry. The sheathing of the chitosan core with a polycaprolactone shell induced massive foreign body reaction and impairment of nerve regeneration. Although the isolated novel chitosan core did allow regeneration of axons in a similar size distribution as the ANT, the ANT was superior in terms of functional regeneration. We conclude that an outer polycaprolactone shell should not be used for the purpose of bioartificial nerve grafting, while 3D multichannel porous chitosan cores could be candidate scaffolds for structured nerve grafts.

Outer electrospun polycaprolactone shell induces massive foreign body reaction and impairs axonal regeneration through 3D multichannel chitosan nerve guides.

Science.gov (United States)

Duda, Sven; Dreyer, Lutz; Behrens, Peter; Wienecke, Soenke; Chakradeo, Tanmay; Glasmacher, Birgit; Haastert-Talini, Kirsten

2014-01-01

We report on the performance of composite nerve grafts with an inner 3D multichannel porous chitosan core and an outer electrospun polycaprolactone shell. The inner chitosan core provided multiple guidance channels for regrowing axons. To analyze the in vivo properties of the bare chitosan cores, we separately implanted them into an epineural sheath. The effects of both graft types on structural and functional regeneration across a 10 mm rat sciatic nerve gap were compared to autologous nerve transplantation (ANT). The mechanical biomaterial properties and the immunological impact of the grafts were assessed with histological techniques before and after transplantation in vivo. Furthermore during a 13-week examination period functional tests and electrophysiological recordings were performed and supplemented by nerve morphometry. The sheathing of the chitosan core with a polycaprolactone shell induced massive foreign body reaction and impairment of nerve regeneration. Although the isolated novel chitosan core did allow regeneration of axons in a similar size distribution as the ANT, the ANT was superior in terms of functional regeneration. We conclude that an outer polycaprolactone shell should not be used for the purpose of bioartificial nerve grafting, while 3D multichannel porous chitosan cores could be candidate scaffolds for structured nerve grafts.

Medium generated gap in gravity and a 3D gauge theory

Science.gov (United States)

Gabadadze, Gregory; Older, Daniel

2018-05-01

It is well known that a physical medium that sets a Lorentz frame generates a Lorentz-breaking gap for a graviton. We examine such generated "mass" terms in the presence of a fluid medium whose ground state spontaneously breaks spatial translation invariance in d =D +1 spacetime dimensions, and for a solid in D =2 spatial dimensions. By requiring energy positivity and subluminal propagation, certain constraints are placed on the equation of state of the medium. In the case of D =2 spatial dimensions, classical gravity can be recast as a Chern-Simons gauge theory, and motivated by this we recast the massive theory of gravity in AdS3 as a massive Chern-Simons gauge theory with an unusual mass term. We find that in the flat space limit the Chern-Simons theory has a novel gauge invariance that mixes the kinetic and mass terms, and enables the massive theory with a noncompact internal group to be free of ghosts and tachyons.

Supersymmetric D3/D7 for holographic flavors on curved space

International Nuclear Information System (INIS)

Karch, Andreas; Robinson, Brandon; Uhlemann, Christoph F.

2015-01-01

We derive a new class of supersymmetric D3/D7 brane configurations, which allow to holographically describe N=4 SYM coupled to massive N=2 flavor degrees of freedom on spaces of constant curvature. We systematically solve the κ-symmetry condition for D7-brane embeddings into AdS_4-sliced AdS_5×S"5, and find supersymmetric embeddings in a simple closed form. Up to a critical mass, these embeddings come in surprisingly diverse families, and we present a first study of their (holographic) phenomenology. We carry out the holographic renormalization, compute the one-point functions and attempt a field-theoretic interpretation of the different families. To complete the catalog of supersymmetric D3/D7 configurations, we construct analogous embeddings for flavored N=4 SYM on S"4 and dS_4.

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.

Quasi-local conserved charges of spin-3 topologically massive gravity

Directory of Open Access Journals (Sweden)

M.R. Setare

2016-08-01

Full Text Available In this paper we obtain conserved charges of spin-3 topologically massive gravity by using a quasi-local formalism. We find a general formula to calculate conserved charge of the spin-3 topologically massive gravity which corresponds to a Killing vector field ξ. We show that this general formula reduces to the previous one for the ordinary spin-3 gravity presented in [18] when we take into account only transformation under diffeomorphism, without considering generalized Lorentz gauge transformation (i.e. λξ=0, and by taking 1μ→0. Then we obtain a general formula for the entropy of black hole solutions of the spin-3 topologically massive gravity. Finally we apply our formalism to calculate energy, angular momentum and entropy of a special black hole solution and we find that obtained results are consistent with previous results in the limiting cases. Moreover our results for energy, angular momentum and entropy are consistent with the first law of black hole mechanics.

3-D inversion of airborne electromagnetic data parallelized and accelerated by local mesh and adaptive soundings

Science.gov (United States)

Yang, Dikun; Oldenburg, Douglas W.; Haber, Eldad

2014-03-01

Airborne electromagnetic (AEM) methods are highly efficient tools for assessing the Earth's conductivity structures in a large area at low cost. However, the configuration of AEM measurements, which typically have widely distributed transmitter-receiver pairs, makes the rigorous modelling and interpretation extremely time-consuming in 3-D. Excessive overcomputing can occur when working on a large mesh covering the entire survey area and inverting all soundings in the data set. We propose two improvements. The first is to use a locally optimized mesh for each AEM sounding for the forward modelling and calculation of sensitivity. This dedicated local mesh is small with fine cells near the sounding location and coarse cells far away in accordance with EM diffusion and the geometric decay of the signals. Once the forward problem is solved on the local meshes, the sensitivity for the inversion on the global mesh is available through quick interpolation. Using local meshes for AEM forward modelling avoids unnecessary computing on fine cells on a global mesh that are far away from the sounding location. Since local meshes are highly independent, the forward modelling can be efficiently parallelized over an array of processors. The second improvement is random and dynamic down-sampling of the soundings. Each inversion iteration only uses a random subset of the soundings, and the subset is reselected for every iteration. The number of soundings in the random subset, determined by an adaptive algorithm, is tied to the degree of model regularization. This minimizes the overcomputing caused by working with redundant soundings. Our methods are compared against conventional methods and tested with a synthetic example. We also invert a field data set that was previously considered to be too large to be practically inverted in 3-D. These examples show that our methodology can dramatically reduce the processing time of 3-D inversion to a practical level without losing resolution

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

3D neutron transport modelization

Energy Technology Data Exchange (ETDEWEB)

Warin, X.

1996-12-01

Some nodal methods to solve the transport equation in 3D are presented. Two nodal methods presented at an OCDE congress are described: a first one is a low degree one called RTN0; a second one is a high degree one called BDM1. The two methods can be made faster with a totally consistent DSA. Some results of parallelization show that: 98% of the time is spent in sweeps; transport sweeps are easily parallelized. (K.A.). 10 refs.

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

Fast parallel approach for 2-D DHT-based real-valued discrete Gabor transform.

Science.gov (United States)

Tao, Liang; Kwan, Hon Keung

2009-12-01

Two-dimensional fast Gabor transform algorithms are useful for real-time applications due to the high computational complexity of the traditional 2-D complex-valued discrete Gabor transform (CDGT). This paper presents two block time-recursive algorithms for 2-D DHT-based real-valued discrete Gabor transform (RDGT) and its inverse transform and develops a fast parallel approach for the implementation of the two algorithms. The computational complexity of the proposed parallel approach is analyzed and compared with that of the existing 2-D CDGT algorithms. The results indicate that the proposed parallel approach is attractive for real time image processing.

3D numerical simulations of multiphase continental rifting

Science.gov (United States)

Naliboff, J.; Glerum, A.; Brune, S.

2017-12-01

Observations of rifted margin architecture suggest continental breakup occurs through multiple phases of extension with distinct styles of deformation. The initial rifting stages are often characterized by slow extension rates and distributed normal faulting in the upper crust decoupled from deformation in the lower crust and mantle lithosphere. Further rifting marks a transition to higher extension rates and coupling between the crust and mantle lithosphere, with deformation typically focused along large-scale detachment faults. Significantly, recent detailed reconstructions and high-resolution 2D numerical simulations suggest that rather than remaining focused on a single long-lived detachment fault, deformation in this phase may progress toward lithospheric breakup through a complex process of fault interaction and development. The numerical simulations also suggest that an initial phase of distributed normal faulting can play a key role in the development of these complex fault networks and the resulting finite deformation patterns. Motivated by these findings, we will present 3D numerical simulations of continental rifting that examine the role of temporal increases in extension velocity on rifted margin structure. The numerical simulations are developed with the massively parallel finite-element code ASPECT. While originally designed to model mantle convection using advanced solvers and adaptive mesh refinement techniques, ASPECT has been extended to model visco-plastic deformation that combines a Drucker Prager yield criterion with non-linear dislocation and diffusion creep. To promote deformation localization, the internal friction angle and cohesion weaken as a function of accumulated plastic strain. Rather than prescribing a single zone of weakness to initiate deformation, an initial random perturbation of the plastic strain field combined with rapid strain weakening produces distributed normal faulting at relatively slow rates of extension in both 2D and

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

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.

Zwei-Dreibein Gravity : A Two-Frame-Field Model of 3D Massive Gravity

NARCIS (Netherlands)

Bergshoeff, Eric A.; de Haan, Sjoerd; Hohm, Olaf; Merbis, Wout; Townsend, Paul K.

2013-01-01

We present a generally covariant and parity-invariant two-frame field ("zwei-dreibein") action for gravity in three space-time dimensions that propagates two massive spin-2 modes, unitarily, and we use Hamiltonian methods to confirm the absence of unphysical degrees of freedom. We show how

Parallel FE Electron-Photon Transport Analysis on 2-D Unstructured Mesh

International Nuclear Information System (INIS)

Drumm, C.R.; Lorenz, J.

1999-01-01

A novel solution method has been developed to solve the coupled electron-photon transport problem on an unstructured triangular mesh. Instead of tackling the first-order form of the linear Boltzmann equation, this approach is based on the second-order form in conjunction with the conventional multi-group discrete-ordinates approximation. The highly forward-peaked electron scattering is modeled with a multigroup Legendre expansion derived from the Goudsmit-Saunderson theory. The finite element method is used to treat the spatial dependence. The solution method is unique in that the space-direction dependence is solved simultaneously, eliminating the need for the conventional inner iterations, a method that is well suited for massively parallel computers

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

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

Wireless Rover Meets 3D Design and Product Development

Science.gov (United States)

Deal, Walter F., III; Hsiung, Steve C.

2016-01-01

Today there are a number of 3D printing technologies that are low cost and within the budgets of middle and high school programs. Educational technology companies offer a variety of 3D printing technologies and parallel curriculum materials to enable technology and engineering teachers to easily add 3D learning activities to their programs.…

3-D OBJECT RECOGNITION FROM POINT CLOUD DATA

Directory of Open Access Journals (Sweden)

W. Smith

2012-09-01

Full Text Available The market for real-time 3-D mapping includes not only traditional geospatial applications but also navigation of unmanned autonomous vehicles (UAVs. Massively parallel processes such as graphics processing unit (GPU computing make real-time 3-D object recognition and mapping achievable. Geospatial technologies such as digital photogrammetry and GIS offer advanced capabilities to produce 2-D and 3-D static maps using UAV data. The goal is to develop real-time UAV navigation through increased automation. It is challenging for a computer to identify a 3-D object such as a car, a tree or a house, yet automatic 3-D object recognition is essential to increasing the productivity of geospatial data such as 3-D city site models. In the past three decades, researchers have used radiometric properties to identify objects in digital imagery with limited success, because these properties vary considerably from image to image. Consequently, our team has developed software that recognizes certain types of 3-D objects within 3-D point clouds. Although our software is developed for modeling, simulation and visualization, it has the potential to be valuable in robotics and UAV applications. The locations and shapes of 3-D objects such as buildings and trees are easily recognizable by a human from a brief glance at a representation of a point cloud such as terrain-shaded relief. The algorithms to extract these objects have been developed and require only the point cloud and minimal human inputs such as a set of limits on building size and a request to turn on a squaring option. The algorithms use both digital surface model (DSM and digital elevation model (DEM, so software has also been developed to derive the latter from the former. The process continues through the following steps: identify and group 3-D object points into regions; separate buildings and houses from trees; trace region boundaries; regularize and simplify boundary polygons; construct complex

3-D Object Recognition from Point Cloud Data

Science.gov (United States)

Smith, W.; Walker, A. S.; Zhang, B.

2011-09-01

The market for real-time 3-D mapping includes not only traditional geospatial applications but also navigation of unmanned autonomous vehicles (UAVs). Massively parallel processes such as graphics processing unit (GPU) computing make real-time 3-D object recognition and mapping achievable. Geospatial technologies such as digital photogrammetry and GIS offer advanced capabilities to produce 2-D and 3-D static maps using UAV data. The goal is to develop real-time UAV navigation through increased automation. It is challenging for a computer to identify a 3-D object such as a car, a tree or a house, yet automatic 3-D object recognition is essential to increasing the productivity of geospatial data such as 3-D city site models. In the past three decades, researchers have used radiometric properties to identify objects in digital imagery with limited success, because these properties vary considerably from image to image. Consequently, our team has developed software that recognizes certain types of 3-D objects within 3-D point clouds. Although our software is developed for modeling, simulation and visualization, it has the potential to be valuable in robotics and UAV applications. The locations and shapes of 3-D objects such as buildings and trees are easily recognizable by a human from a brief glance at a representation of a point cloud such as terrain-shaded relief. The algorithms to extract these objects have been developed and require only the point cloud and minimal human inputs such as a set of limits on building size and a request to turn on a squaring option. The algorithms use both digital surface model (DSM) and digital elevation model (DEM), so software has also been developed to derive the latter from the former. The process continues through the following steps: identify and group 3-D object points into regions; separate buildings and houses from trees; trace region boundaries; regularize and simplify boundary polygons; construct complex roofs. Several case

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...

A 3D Two-node and One-node HCMFD Algorithm for Pin-wise Reactor Analysis

International Nuclear Information System (INIS)

Kim, Jaeha; Kim, Yonghee

2016-01-01

To maximize the parallel computational efficiency, an iterative local-global strategy is adopted in the HCMFD algorithm. The global eigenvalue problem is solved by one-node CMFD, and the local fixed-source problems are solved by two-node CMFD based on the pin-wise nodal solutions. In such local-global scheme, the computational cost is mostly concentrated in solving the local problems while they can be solved in parallel so that a parallel computing can effectively be applied. Previously, the feasibility of the HCMFD algorithm was evaluated only in a 2-D scheme. In this paper, the 3D HCMFD algorithm with some possible variations in treating the axial direction is introduced. The HCMFD algorithm was successfully extended to a 3-D core analysis without any numerical instability even though the axial mesh size in local problems is quite different from the x-y node size. We have shown that 3D pin-wise core analysis can be done very effectively with the HCMFD framework. Additionally, it was demonstrated that parallel efficiency of the new 3D HCMFD scheme can be quite high on a simple OpenMP parallel architecture. It is concluded that the 3D HCMFD will enable an efficient pin-wise 3D core analysis

Real time 3D structural and Doppler OCT imaging on graphics processing units

Science.gov (United States)

Sylwestrzak, Marcin; Szlag, Daniel; Szkulmowski, Maciej; Gorczyńska, Iwona; Bukowska, Danuta; Wojtkowski, Maciej; Targowski, Piotr

2013-03-01

In this report the application of graphics processing unit (GPU) programming for real-time 3D Fourier domain Optical Coherence Tomography (FdOCT) imaging with implementation of Doppler algorithms for visualization of the flows in capillary vessels is presented. Generally, the time of the data processing of the FdOCT data on the main processor of the computer (CPU) constitute a main limitation for real-time imaging. Employing additional algorithms, such as Doppler OCT analysis, makes this processing even more time consuming. Lately developed GPUs, which offers a very high computational power, give a solution to this problem. Taking advantages of them for massively parallel data processing, allow for real-time imaging in FdOCT. The presented software for structural and Doppler OCT allow for the whole processing with visualization of 2D data consisting of 2000 A-scans generated from 2048 pixels spectra with frame rate about 120 fps. The 3D imaging in the same mode of the volume data build of 220 × 100 A-scans is performed at a rate of about 8 frames per second. In this paper a software architecture, organization of the threads and optimization applied is shown. For illustration the screen shots recorded during real time imaging of the phantom (homogeneous water solution of Intralipid in glass capillary) and the human eye in-vivo is presented.

DICE/ColDICE: 6D collisionless phase space hydrodynamics using a lagrangian tesselation

Science.gov (United States)

Sousbie, Thierry

2018-01-01

DICE is a C++ template library designed to solve collisionless fluid dynamics in 6D phase space using massively parallel supercomputers via an hybrid OpenMP/MPI parallelization. ColDICE, based on DICE, implements a cosmological and physical VLASOV-POISSON solver for cold systems such as dark matter (CDM) dynamics.

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.

Parallel 3-D numerical simulation of dielectric barrier discharge plasma actuators

Science.gov (United States)

Houba, Tomas

Dielectric barrier discharge plasma actuators have shown promise in a range of applications including flow control, sterilization and ozone generation. Developing numerical models of plasma actuators is of great importance, because a high-fidelity parallel numerical model allows new design configurations to be tested rapidly. Additionally, it provides a better understanding of the plasma actuator physics which is useful for further innovation. The physics of plasma actuators is studied numerically. A loosely coupled approach is utilized for the coupling of the plasma to the neutral fluid. The state of the art in numerical plasma modeling is advanced by the development of a parallel, three-dimensional, first-principles model with detailed air chemistry. The model incorporates 7 charged species and 18 reactions, along with a solution of the electron energy equation. To the author's knowledge, a parallel three-dimensional model of a gas discharge with a detailed air chemistry model and the solution of electron energy is unique. Three representative geometries are studied using the gas discharge model. The discharge of gas between two parallel electrodes is used to validate the air chemistry model developed for the gas discharge code. The gas discharge model is then applied to the discharge produced by placing a dc powered wire and grounded plate electrodes in a channel. Finally, a three-dimensional simulation of gas discharge produced by electrodes placed inside a riblet is carried out. The body force calculated with the gas discharge model is loosely coupled with a fluid model to predict the induced flow inside the riblet.

3D documenatation of the petalaindera: digital heritage preservation methods using 3D laser scanner and photogrammetry

Science.gov (United States)

Sharif, Harlina Md; Hazumi, Hazman; Hafizuddin Meli, Rafiq

2018-01-01

3D imaging technologies have undergone massive revolution in recent years. Despite this rapid development, documentation of 3D cultural assets in Malaysia is still very much reliant upon conventional techniques such as measured drawings and manual photogrammetry. There is very little progress towards exploring new methods or advanced technologies to convert 3D cultural assets into 3D visual representation and visualization models that are easily accessible for information sharing. In recent years, however, the advent of computer vision (CV) algorithms make it possible to reconstruct 3D geometry of objects by using image sequences from digital cameras, which are then processed by web services and freeware applications. This paper presents a completed stage of an exploratory study that investigates the potentials of using CV automated image-based open-source software and web services to reconstruct and replicate cultural assets. By selecting an intricate wooden boat, Petalaindera, this study attempts to evaluate the efficiency of CV systems and compare it with the application of 3D laser scanning, which is known for its accuracy, efficiency and high cost. The final aim of this study is to compare the visual accuracy of 3D models generated by CV system, and 3D models produced by 3D scanning and manual photogrammetry for an intricate subject such as the Petalaindera. The final objective is to explore cost-effective methods that could provide fundamental guidelines on the best practice approach for digital heritage in Malaysia.

Formation and pre-MS Evolution of Massive Stars with Growing Accretion

Science.gov (United States)

Maeder, A.; Behrend, R.

2002-10-01

We briefly describe the three existing scenarios for forming massive stars and emphasize that the arguments often used to reject the accretion scenario for massive stars are misleading. It is usually not accounted for the fact that the turbulent pressure associated to large turbulent velocities in clouds necessarily imply relatively high accretion rates for massive stars. We show the basic difference between the formation of low and high mass stars based on the values of the free fall time and of the Kelvin-Helmholtz timescale, and define the concept of birthline for massive stars. Due to D-burning, the radius and location of the birthline in the HR diagram, as well as the lifetimes are very sensitive to the accretion rate dM/dt(accr). If a form dM/dt(accr) propto A(M/Msun)phi is adopted, the observations in the HR diagram and the lifetimes support a value of A approx 10-5 Msun/yr and a value of phi > 1. Remarkably, such a law is consistent with the relation found by Churchwell and Henning et al. between the outflow rates and the luminosities of ultracompact HII regions, if we assume that a fraction 0.15 to 0.3 of the global inflow is accreted. The above relation implies high dM/dt(accr) approx 10-3 Msun/yr for the most massive stars. The physical possibility of such high dM/dt(accr) is supported by current numerical models. Finally, we give simple analytical arguments in favour of the growth of dM/dt(accr) with the already accreted mass. We also suggest that due to Bondi-Hoyle accretion, the formation of binary stars is largely favoured among massive stars in the accretion scenario.

FROMS3D: New Software for 3-D Visualization of Fracture Network System in Fractured Rock Masses

Science.gov (United States)

Noh, Y. H.; Um, J. G.; Choi, Y.

2014-12-01

A new software (FROMS3D) is presented to visualize fracture network system in 3-D. The software consists of several modules that play roles in management of borehole and field fracture data, fracture network modelling, visualization of fracture geometry in 3-D and calculation and visualization of intersections and equivalent pipes between fractures. Intel Parallel Studio XE 2013, Visual Studio.NET 2010 and the open source VTK library were utilized as development tools to efficiently implement the modules and the graphical user interface of the software. The results have suggested that the developed software is effective in visualizing 3-D fracture network system, and can provide useful information to tackle the engineering geological problems related to strength, deformability and hydraulic behaviors of the fractured rock masses.

A massive, quiescent galaxy at a redshift of 3.717

Science.gov (United States)

Glazebrook, Karl; Schreiber, Corentin; Labbé, Ivo; Nanayakkara, Themiya; Kacprzak, Glenn G.; Oesch, Pascal A.; Papovich, Casey; Spitler, Lee R.; Straatman, Caroline M. S.; Tran, Kim-Vy H.; Yuan, Tiantian

2017-04-01

Finding massive galaxies that stopped forming stars in the early Universe presents an observational challenge because their rest-frame ultraviolet emission is negligible and they can only be reliably identified by extremely deep near-infrared surveys. These surveys have revealed the presence of massive, quiescent early-type galaxies appearing as early as redshift z ≈ 2, an epoch three billion years after the Big Bang. Their age and formation processes have now been explained by an improved generation of galaxy-formation models, in which they form rapidly at z ≈ 3-4, consistent with the typical masses and ages derived from their observations. Deeper surveys have reported evidence for populations of massive, quiescent galaxies at even higher redshifts and earlier times, using coarsely sampled photometry. However, these early, massive, quiescent galaxies are not predicted by the latest generation of theoretical models. Here we report the spectroscopic confirmation of one such galaxy at redshift z = 3.717, with a stellar mass of 1.7 × 1011 solar masses. We derive its age to be nearly half the age of the Universe at this redshift and the absorption line spectrum shows no current star formation. These observations demonstrate that the galaxy must have formed the majority of its stars quickly, within the first billion years of cosmic history in a short, extreme starburst. This ancestral starburst appears similar to those being found by submillimetre-wavelength surveys. The early formation of such massive systems implies that our picture of early galaxy assembly requires substantial revision.

Massive Kaluza-Klein theories and their spontaneously broken symmetries

International Nuclear Information System (INIS)

Hohm, O.

2006-07-01

In this thesis we investigate the effective actions for massive Kaluza-Klein states, focusing on the massive modes of spin-3/2 and spin-2 fields. To this end we determine the spontaneously broken gauge symmetries associated to these 'higher-spin' states and construct the unbroken phase of the Kaluza-Klein theory. We show that for the particular background AdS 3 x S 3 x S 3 a consistent coupling of the first massive spin-3/2 multiplet requires an enhancement of local supersymmetry, which in turn will be partially broken in the Kaluza-Klein vacuum. The corresponding action is constructed as a gauged maximal supergravity in D=3. Subsequently, the symmetries underlying an infinite tower of massive spin-2 states are analyzed in case of a Kaluza-Klein compactification of four-dimensional gravity to D=3. It is shown that the resulting gravity-spin-2 theory is given by a Chern-Simons action of an affine algebra and also allows a geometrical interpretation in terms of 'algebra-valued' differential geometry. The global symmetry group is determined, which contains an affine extension of the Ehlers group. We show that the broken phase can in turn be constructed via gauging a certain subgroup of the global symmetry group. Finally, deformations of the Kaluza-Klein theory on AdS 3 x S 3 x S 3 and the corresponding symmetry breakings are analyzed as possible applications for the AdS/CFT correspondence. (Orig.)

3D magnetospheric parallel hybrid multi-grid method applied to planet–plasma interactions

Energy Technology Data Exchange (ETDEWEB)

Leclercq, L., E-mail: ludivine.leclercq@latmos.ipsl.fr [LATMOS/IPSL, UVSQ Université Paris-Saclay, UPMC Univ. Paris 06, CNRS, Guyancourt (France); Modolo, R., E-mail: ronan.modolo@latmos.ipsl.fr [LATMOS/IPSL, UVSQ Université Paris-Saclay, UPMC Univ. Paris 06, CNRS, Guyancourt (France); Leblanc, F. [LATMOS/IPSL, UPMC Univ. Paris 06 Sorbonne Universités, UVSQ, CNRS, Paris (France); Hess, S. [ONERA, Toulouse (France); Mancini, M. [LUTH, Observatoire Paris-Meudon (France)

2016-03-15

We present a new method to exploit multiple refinement levels within a 3D parallel hybrid model, developed to study planet–plasma interactions. This model is based on the hybrid formalism: ions are kinetically treated whereas electrons are considered as a inertia-less fluid. Generally, ions are represented by numerical particles whose size equals the volume of the cells. Particles that leave a coarse grid subsequently entering a refined region are split into particles whose volume corresponds to the volume of the refined cells. The number of refined particles created from a coarse particle depends on the grid refinement rate. In order to conserve velocity distribution functions and to avoid calculations of average velocities, particles are not coalesced. Moreover, to ensure the constancy of particles' shape function sizes, the hybrid method is adapted to allow refined particles to move within a coarse region. Another innovation of this approach is the method developed to compute grid moments at interfaces between two refinement levels. Indeed, the hybrid method is adapted to accurately account for the special grid structure at the interfaces, avoiding any overlapping grid considerations. Some fundamental test runs were performed to validate our approach (e.g. quiet plasma flow, Alfven wave propagation). Lastly, we also show a planetary application of the model, simulating the interaction between Jupiter's moon Ganymede and the Jovian plasma.

Iterative methods for 3D implicit finite-difference migration using the complex Padé approximation

International Nuclear Information System (INIS)

Costa, Carlos A N; Campos, Itamara S; Costa, Jessé C; Neto, Francisco A; Schleicher, Jörg; Novais, Amélia

2013-01-01

Conventional implementations of 3D finite-difference (FD) migration use splitting techniques to accelerate performance and save computational cost. However, such techniques are plagued with numerical anisotropy that jeopardises the correct positioning of dipping reflectors in the directions not used for the operator splitting. We implement 3D downward continuation FD migration without splitting using a complex Padé approximation. In this way, the numerical anisotropy is eliminated at the expense of a computationally more intensive solution of a large-band linear system. We compare the performance of the iterative stabilized biconjugate gradient (BICGSTAB) and that of the multifrontal massively parallel direct solver (MUMPS). It turns out that the use of the complex Padé approximation not only stabilizes the solution, but also acts as an effective preconditioner for the BICGSTAB algorithm, reducing the number of iterations as compared to the implementation using the real Padé expansion. As a consequence, the iterative BICGSTAB method is more efficient than the direct MUMPS method when solving a single term in the Padé expansion. The results of both algorithms, here evaluated by computing the migration impulse response in the SEG/EAGE salt model, are of comparable quality. (paper)

POU4F3 mutation screening in Japanese hearing loss patients: Massively parallel DNA sequencing-based analysis identified novel variants associated with autosomal dominant hearing loss.

Directory of Open Access Journals (Sweden)

Tomohiro Kitano

Full Text Available A variant in a transcription factor gene, POU4F3, is responsible for autosomal dominant nonsyndromic hereditary hearing loss, DFNA15. To date, 14 variants, including a whole deletion of POU4F3, have been reported to cause HL in various ethnic groups. In the present study, genetic screening for POU4F3 variants was carried out for a large series of Japanese hearing loss (HL patients to clarify the prevalence and clinical characteristics of DFNA15 in the Japanese population. Massively parallel DNA sequencing of 68 target candidate genes was utilized in 2,549 unrelated Japanese HL patients (probands to identify genomic variations responsible for HL. The detailed clinical features in patients with POU4F3 variants were collected from medical charts and analyzed. Novel 12 POU4F3 likely pathogenic variants (six missense variants, three frameshift variants, and three nonsense variants were successfully identified in 15 probands (2.5% among 602 families exhibiting autosomal dominant HL, whereas no variants were detected in the other 1,947 probands with autosomal recessive or inheritance pattern unknown HL. To obtain the audiovestibular configuration of the patients harboring POU4F3 variants, we collected audiograms and vestibular symptoms of the probands and their affected family members. Audiovestibular phenotypes in a total of 24 individuals from the 15 families possessing variants were characterized by progressive HL, with a large variation in the onset age and severity with or without vestibular symptoms observed. Pure-tone audiograms indicated the most prevalent configuration as mid-frequency HL type followed by high-frequency HL type, with asymmetry observed in approximately 20% of affected individuals. Analysis of the relationship between age and pure-tone average suggested that individuals with truncating variants showed earlier onset and slower progression of HL than did those with non-truncating variants. The present study showed that variants

Parallel algorithms for 2-D cylindrical transport equations of Eigenvalue problem

International Nuclear Information System (INIS)

Wei, J.; Yang, S.

2013-01-01

In this paper, aimed at the neutron transport equations of eigenvalue problem under 2-D cylindrical geometry on unstructured grid, the discrete scheme of Sn discrete ordinate and discontinuous finite is built, and the parallel computation for the scheme is realized on MPI systems. Numerical experiments indicate that the designed parallel algorithm can reach perfect speedup, it has good practicality and scalability. (authors)

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.

MAP3D: a media processor approach for high-end 3D graphics

Science.gov (United States)

Darsa, Lucia; Stadnicki, Steven; Basoglu, Chris

1999-12-01

Equator Technologies, Inc. has used a software-first approach to produce several programmable and advanced VLIW processor architectures that have the flexibility to run both traditional systems tasks and an array of media-rich applications. For example, Equator's MAP1000A is the world's fastest single-chip programmable signal and image processor targeted for digital consumer and office automation markets. The Equator MAP3D is a proposal for the architecture of the next generation of the Equator MAP family. The MAP3D is designed to achieve high-end 3D performance and a variety of customizable special effects by combining special graphics features with high performance floating-point and media processor architecture. As a programmable media processor, it offers the advantages of a completely configurable 3D pipeline--allowing developers to experiment with different algorithms and to tailor their pipeline to achieve the highest performance for a particular application. With the support of Equator's advanced C compiler and toolkit, MAP3D programs can be written in a high-level language. This allows the compiler to successfully find and exploit any parallelism in a programmer's code, thus decreasing the time to market of a given applications. The ability to run an operating system makes it possible to run concurrent applications in the MAP3D chip, such as video decoding while executing the 3D pipelines, so that integration of applications is easily achieved--using real-time decoded imagery for texturing 3D objects, for instance. This novel architecture enables an affordable, integrated solution for high performance 3D graphics.

4d quantum geometry from 3d supersymmetric gauge theory and holomorphic block

International Nuclear Information System (INIS)

Han, Muxin

2016-01-01

A class of 3d N=2 supersymmetric gauge theories are constructed and shown to encode the simplicial geometries in 4-dimensions. The gauge theories are defined by applying the Dimofte-Gaiotto-Gukov construction http://dx.doi.org/10.1007/s00220-013-1863-2 in 3d-3d correspondence to certain graph complement 3-manifolds. Given a gauge theory in this class, the massive supersymmetric vacua of the theory contain the classical geometries on a 4d simplicial complex. The corresponding 4d simplicial geometries are locally constant curvature (either dS or AdS), in the sense that they are made by gluing geometrical 4-simplices of the same constant curvature. When the simplicial complex is sufficiently refined, the simplicial geometries can approximate all possible smooth geometries on 4-manifold. At the quantum level, we propose that a class of holomorphic blocks defined in http://dx.doi.org/10.1007/JHEP12(2014)177 from the 3d N=2 gauge theories are wave functions of quantum 4d simplicial geometries. In the semiclassical limit, the asymptotic behavior of holomorphic block reproduces the classical action of 4d Einstein-Hilbert gravity in the simplicial context.

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 3D domain decomposition approach for the identification of spatially varying elastic material parameters

KAUST Repository

Moussawi, Ali; Lubineau, Gilles; Xu, Jiangping; Pan, Bing

2015-01-01

Summary: The post-treatment of (3D) displacement fields for the identification of spatially varying elastic material parameters is a large inverse problem that remains out of reach for massive 3D structures. We explore here the potential

2-D and 3-D computations of curved accelerator magnets

International Nuclear Information System (INIS)

Turner, L.R.

1991-01-01

In order to save computer memory, a long accelerator magnet may be computed by treating the long central region and the end regions separately. The dipole magnets for the injector synchrotron of the Advanced Photon Source (APS), now under construction at Argonne National Laboratory (ANL), employ magnet iron consisting of parallel laminations, stacked with a uniform radius of curvature of 33.379 m. Laplace's equation for the magnetic scalar potential has a different form for a straight magnet (x-y coordinates), a magnet with surfaces curved about a common center (r-θ coordinates), and a magnet with parallel laminations like the APS injector dipole. Yet pseudo 2-D computations for the three geometries give basically identical results, even for a much more strongly curved magnet. Hence 2-D (x-y) computations of the central region and 3-D computations of the end regions can be combined to determine the overall magnetic behavior of the magnets. 1 ref., 6 figs

An ESPRIT-Based Approach for 2-D Localization of Incoherently Distributed Sources in Massive MIMO Systems

Science.gov (United States)

Hu, Anzhong; Lv, Tiejun; Gao, Hui; Zhang, Zhang; Yang, Shaoshi

2014-10-01

In this paper, an approach of estimating signal parameters via rotational invariance technique (ESPRIT) is proposed for two-dimensional (2-D) localization of incoherently distributed (ID) sources in large-scale/massive multiple-input multiple-output (MIMO) systems. The traditional ESPRIT-based methods are valid only for one-dimensional (1-D) localization of the ID sources. By contrast, in the proposed approach the signal subspace is constructed for estimating the nominal azimuth and elevation direction-of-arrivals and the angular spreads. The proposed estimator enjoys closed-form expressions and hence it bypasses the searching over the entire feasible field. Therefore, it imposes significantly lower computational complexity than the conventional 2-D estimation approaches. Our analysis shows that the estimation performance of the proposed approach improves when the large-scale/massive MIMO systems are employed. The approximate Cram\\'{e}r-Rao bound of the proposed estimator for the 2-D localization is also derived. Numerical results demonstrate that albeit the proposed estimation method is comparable with the traditional 2-D estimators in terms of performance, it benefits from a remarkably lower computational complexity.

Parallel fabrication of macroporous scaffolds.

Science.gov (United States)

Dobos, Andrew; Grandhi, Taraka Sai Pavan; Godeshala, Sudhakar; Meldrum, Deirdre R; Rege, Kaushal

2018-07-01

Scaffolds generated from naturally occurring and synthetic polymers have been investigated in several applications because of their biocompatibility and tunable chemo-mechanical properties. Existing methods for generation of 3D polymeric scaffolds typically cannot be parallelized, suffer from low throughputs, and do not allow for quick and easy removal of the fragile structures that are formed. Current molds used in hydrogel and scaffold fabrication using solvent casting and porogen leaching are often single-use and do not facilitate 3D scaffold formation in parallel. Here, we describe a simple device and related approaches for the parallel fabrication of macroporous scaffolds. This approach was employed for the generation of macroporous and non-macroporous materials in parallel, in higher throughput and allowed for easy retrieval of these 3D scaffolds once formed. In addition, macroporous scaffolds with interconnected as well as non-interconnected pores were generated, and the versatility of this approach was employed for the generation of 3D scaffolds from diverse materials including an aminoglycoside-derived cationic hydrogel ("Amikagel"), poly(lactic-co-glycolic acid) or PLGA, and collagen. Macroporous scaffolds generated using the device were investigated for plasmid DNA binding and cell loading, indicating the use of this approach for developing materials for different applications in biotechnology. Our results demonstrate that the device-based approach is a simple technology for generating scaffolds in parallel, which can enhance the toolbox of current fabrication techniques. © 2018 Wiley Periodicals, Inc.

Parallel CFD simulation of flow in a 3D model of vibrating human vocal folds

Czech Academy of Sciences Publication Activity Database

Šidlof, Petr; Horáček, Jaromír; Řidký, V.

2013-01-01

Roč. 80, č. 1 (2013), s. 290-300 ISSN 0045-7930 R&D Projects: GA ČR(CZ) GAP101/11/0207 Institutional research plan: CEZ:AV0Z20760514 Keywords : numerical simulation * vocal folds * glottal airflow * inite volume method * parallel CFD Subject RIV: BI - Acoustics Impact factor: 1.532, year: 2013 http://www.sciencedirect.com/science?_ob=ArticleListURL&_method=list&_ArticleListID=-268060849&_sort=r&_st=13&view=c&_acct=C000034318&_version=1&_urlVersion=0&_userid=640952&md5=7c5b5539857ee9a02af5e690585b3126&searchtype=a

Parallelization of elliptic solver for solving 1D Boussinesq model

Science.gov (United States)

Tarwidi, D.; Adytia, D.

2018-03-01

In this paper, a parallel implementation of an elliptic solver in solving 1D Boussinesq model is presented. Numerical solution of Boussinesq model is obtained by implementing a staggered grid scheme to continuity, momentum, and elliptic equation of Boussinesq model. Tridiagonal system emerging from numerical scheme of elliptic equation is solved by cyclic reduction algorithm. The parallel implementation of cyclic reduction is executed on multicore processors with shared memory architectures using OpenMP. To measure the performance of parallel program, large number of grids is varied from 28 to 214. Two test cases of numerical experiment, i.e. propagation of solitary and standing wave, are proposed to evaluate the parallel program. The numerical results are verified with analytical solution of solitary and standing wave. The best speedup of solitary and standing wave test cases is about 2.07 with 214 of grids and 1.86 with 213 of grids, respectively, which are executed by using 8 threads. Moreover, the best efficiency of parallel program is 76.2% and 73.5% for solitary and standing wave test cases, respectively.

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

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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.

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.

Iterative and iterative-noniterative integral solutions in 3-loop massive QCD calculations

International Nuclear Information System (INIS)

Ablinger, J.; Radu, C.S.; Schneider, C.; Behring, A.; Imamoglu, E.; Van Hoeij, M.; Von Manteuffel, A.; Raab, C.G.

2017-11-01

Various of the single scale quantities in massless and massive QCD up to 3-loop order can be expressed by iterative integrals over certain classes of alphabets, from the harmonic polylogarithms to root-valued alphabets. Examples are the anomalous dimensions to 3-loop order, the massless Wilson coefficients and also different massive operator matrix elements. Starting at 3-loop order, however, also other letters appear in the case of massive operator matrix elements, the so called iterative non-iterative integrals, which are related to solutions based on complete elliptic integrals or any other special function with an integral representation that is definite but not a Volterra-type integral. After outlining the formalism leading to iterative non-iterative integrals,we present examples for both of these cases with the 3-loop anomalous dimension γ (2) qg and the structure of the principle solution in the iterative non-interative case of the 3-loop QCD corrections to the ρ-parameter.

Iterative and iterative-noniterative integral solutions in 3-loop massive QCD calculations

Energy Technology Data Exchange (ETDEWEB)

Ablinger, J.; Radu, C.S.; Schneider, C. [Johannes Kepler Univ., Linz (Austria). Research Inst. for Symbolic Computation (RISC); Behring, A. [RWTH Aachen Univ. (Germany). Inst. fuer Theoretische Teilchenphysik und Kosmologie; Bluemlein, J.; Freitas, A. de [Deutsches Elektronen-Synchrotron (DESY), Zeuthen (Germany); Imamoglu, E.; Van Hoeij, M. [Florida State Univ., Tallahassee, FL (United States). Dept. of Mathematics; Von Manteuffel, A. [Michigan State Univ., East Lansing, MI (United States). Dept. of Physics and Astronomy; Raab, C.G. [Johannes Kepler Univ., Linz (Austria). Inst. for Algebra

2017-11-15

Various of the single scale quantities in massless and massive QCD up to 3-loop order can be expressed by iterative integrals over certain classes of alphabets, from the harmonic polylogarithms to root-valued alphabets. Examples are the anomalous dimensions to 3-loop order, the massless Wilson coefficients and also different massive operator matrix elements. Starting at 3-loop order, however, also other letters appear in the case of massive operator matrix elements, the so called iterative non-iterative integrals, which are related to solutions based on complete elliptic integrals or any other special function with an integral representation that is definite but not a Volterra-type integral. After outlining the formalism leading to iterative non-iterative integrals,we present examples for both of these cases with the 3-loop anomalous dimension γ{sup (2)}{sub qg} and the structure of the principle solution in the iterative non-interative case of the 3-loop QCD corrections to the ρ-parameter.

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.

Massive Kaluza-Klein theories and their spontaneously broken symmetries

Energy Technology Data Exchange (ETDEWEB)

Hohm, O.

2006-07-15

In this thesis we investigate the effective actions for massive Kaluza-Klein states, focusing on the massive modes of spin-3/2 and spin-2 fields. To this end we determine the spontaneously broken gauge symmetries associated to these 'higher-spin' states and construct the unbroken phase of the Kaluza-Klein theory. We show that for the particular background AdS{sub 3} x S{sup 3} x S{sup 3} a consistent coupling of the first massive spin-3/2 multiplet requires an enhancement of local supersymmetry, which in turn will be partially broken in the Kaluza-Klein vacuum. The corresponding action is constructed as a gauged maximal supergravity in D=3. Subsequently, the symmetries underlying an infinite tower of massive spin-2 states are analyzed in case of a Kaluza-Klein compactification of four-dimensional gravity to D=3. It is shown that the resulting gravity-spin-2 theory is given by a Chern-Simons action of an affine algebra and also allows a geometrical interpretation in terms of 'algebra-valued' differential geometry. The global symmetry group is determined, which contains an affine extension of the Ehlers group. We show that the broken phase can in turn be constructed via gauging a certain subgroup of the global symmetry group. Finally, deformations of the Kaluza-Klein theory on AdS{sub 3} x S{sup 3} x S{sup 3} and the corresponding symmetry breakings are analyzed as possible applications for the AdS/CFT correspondence. (Orig.)

Development of the PARVMEC Code for Rapid Analysis of 3D MHD Equilibrium

Science.gov (United States)

Seal, Sudip; Hirshman, Steven; Cianciosa, Mark; Wingen, Andreas; Unterberg, Ezekiel; Wilcox, Robert; ORNL Collaboration

2015-11-01

The VMEC three-dimensional (3D) MHD equilibrium has been used extensively for designing stellarator experiments and analyzing experimental data in such strongly 3D systems. Recent applications of VMEC include 2D systems such as tokamaks (in particular, the D3D experiment), where application of very small (delB/B ~ 10-3) 3D resonant magnetic field perturbations render the underlying assumption of axisymmetry invalid. In order to facilitate the rapid analysis of such equilibria (for example, for reconstruction purposes), we have undertaken the task of parallelizing the VMEC code (PARVMEC) to produce a scalable and temporally rapidly convergent equilibrium code for use on parallel distributed memory platforms. The parallelization task naturally splits into three distinct parts 1) radial surfaces in the fixed-boundary part of the calculation; 2) two 2D angular meshes needed to compute the Green's function integrals over the plasma boundary for the free-boundary part of the code; and 3) block tridiagonal matrix needed to compute the full (3D) pre-conditioner near the final equilibrium state. Preliminary results show that scalability is achieved for tasks 1 and 3, with task 2 still nearing completion. The impact of this work on the rapid reconstruction of D3D plasmas using PARVMEC in the V3FIT code will be discussed. Work supported by U.S. DOE under Contract DE-AC05-00OR22725 with UT-Battelle, LLC.

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)

OpenSWPC: an open-source integrated parallel simulation code for modeling seismic wave propagation in 3D heterogeneous viscoelastic media

Science.gov (United States)

Maeda, Takuto; Takemura, Shunsuke; Furumura, Takashi

2017-07-01

We have developed an open-source software package, Open-source Seismic Wave Propagation Code (OpenSWPC), for parallel numerical simulations of seismic wave propagation in 3D and 2D (P-SV and SH) viscoelastic media based on the finite difference method in local-to-regional scales. This code is equipped with a frequency-independent attenuation model based on the generalized Zener body and an efficient perfectly matched layer for absorbing boundary condition. A hybrid-style programming using OpenMP and the Message Passing Interface (MPI) is adopted for efficient parallel computation. OpenSWPC has wide applicability for seismological studies and great portability to allowing excellent performance from PC clusters to supercomputers. Without modifying the code, users can conduct seismic wave propagation simulations using their own velocity structure models and the necessary source representations by specifying them in an input parameter file. The code has various modes for different types of velocity structure model input and different source representations such as single force, moment tensor and plane-wave incidence, which can easily be selected via the input parameters. Widely used binary data formats, the Network Common Data Form (NetCDF) and the Seismic Analysis Code (SAC) are adopted for the input of the heterogeneous structure model and the outputs of the simulation results, so users can easily handle the input/output datasets. All codes are written in Fortran 2003 and are available with detailed documents in a public repository.[Figure not available: see fulltext.

A parallel algorithm for transient solid dynamics simulations with contact detection

International Nuclear Information System (INIS)

Attaway, S.; Hendrickson, B.; Plimpton, S.; Gardner, D.; Vaughan, C.; Heinstein, M.; Peery, J.

1996-01-01

Solid dynamics simulations with Lagrangian finite elements are used to model a wide variety of problems, such as the calculation of impact damage to shipping containers for nuclear waste and the analysis of vehicular crashes. Using parallel computers for these simulations has been hindered by the difficulty of searching efficiently for material surface contacts in parallel. A new parallel algorithm for calculation of arbitrary material contacts in finite element simulations has been developed and implemented in the PRONTO3D transient solid dynamics code. This paper will explore some of the issues involved in developing efficient, portable, parallel finite element models for nonlinear transient solid dynamics simulations. The contact-detection problem poses interesting challenges for efficient implementation of a solid dynamics simulation on a parallel computer. The finite element mesh is typically partitioned so that each processor owns a localized region of the finite element mesh. This mesh partitioning is optimal for the finite element portion of the calculation since each processor must communicate only with the few connected neighboring processors that share boundaries with the decomposed mesh. However, contacts can occur between surfaces that may be owned by any two arbitrary processors. Hence, a global search across all processors is required at every time step to search for these contacts. Load-imbalance can become a problem since the finite element decomposition divides the volumetric mesh evenly across processors but typically leaves the surface elements unevenly distributed. In practice, these complications have been limiting factors in the performance and scalability of transient solid dynamics on massively parallel computers. In this paper the authors present a new parallel algorithm for contact detection that overcomes many of these limitations

HeinzelCluster: accelerated reconstruction for FORE and OSEM3D.

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