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At least 1,171 records · Page 65

A Parallel Trade Study Architecture for Design Optimization of Complex Systems

Design of a successful product requires evaluating many design alternatives in a limited design cycle time. This can be achieved through leveraging design space exploration tools and available computing resources on the network. This paper presents a parallel trade study architecture to integrate trade study clients and computing resources on a network using Web services. The parallel trade study solution is demonstrated to accelerate design of experiments, genetic algorithm optimization, and a cost as an independent variable (CAIV) study for a space system application.

Kim, Hongman↗

Fast Parallel Stochastic Subspace Algorithms for Large-Scale Ambient Oscillation Monitoring

With the installation of synchrophasors widely across the power grid, measurement-based oscillation monitoring algorithms are becoming increasingly useful in identifying the real-time oscillatory modal properties in power systems. When the number of phasor measurement unit (PMU) channels grows, the computational time of many PMU data based algorithms is dominated by the computational burden in processing large-scale dense matrices. In order to overcome this limitation, this paper presents new formulations and computational strategies for speeding up an ambient oscillation monitoring algorithm, namely, stochastic subspace identification (SSI). Based on previous work, two fast singular value decomposition (SVD) approaches are first applied to the SVD evaluation within the SSI algorithm. Next, block structures are exploited so that the large-scale dense matrix computations can be processed in parallel. This helps in memory savings as well as in overall computational time. Experimental results from three sets of archived data of the western interconnection demonstrate that the new approaches can provide significant speedups while retaining modal estimation accuracy. With proposed fast parallel algorithms, the real-time oscillation monitoring of the large-scale system using hundreds of PMU measurements becomes feasible.

97 MATHEMATICS AND COMPUTING↗

Stable large-scale solver for Ginzburg–Landau equations for superconductors

Understanding the interaction of vortices with inclusions in type-II superconductors is a major outstanding challenge both for fundamental science and energy applications. At application-relevant scales, the long-range interactions between a dense configuration of vortices and the dependence of their behavior on external parameters, such as temperature and an applied magnetic field, are all important to the net response of the superconductor. Capturing these features, in general, precludes analytical description of vortex dynamics and has also made numerical simulation prohibitively expensive. Here we report on a highly optimized iterative implicit solver for the time-dependent Ginzburg-Landau equations suitable for investigations of type-II superconductors on massively parallel architectures. Its main purpose is to study vortex dynamics in disordered or geometrically confined mesoscopic systems. In this work, we present the discretization and time integration scheme in detail for two types of boundary conditions. We describe the necessary conditions for a stable and physically accurate integration of the equations of motion. Using an inclusion pattern generator, we can simulate complex pinning landscapes and the effect of geometric confinement. We show that our algorithm, implemented on a GPU, can provide static and dynamic solutions of the Ginzburg-Landau equations for mesoscopically large systems over thousands of time steps in a matter of hours. Using our formulation, studying scientifically-relevant problems is a computationally reasonable task.

Sadovskyy, I. A.↗

Spectral solution of the incompressible Navier-Stokes equations on the Connection Machine 2

The issue of solving the time-dependent incompressible Navier-Stokes equations on the Connection Machine 2 is addressed, for the problem of transition to turbulence of the steady flow in a channel. The spectral algorithm used serially requires O(N(4)) operations when solving the equations on an N x N x N grid; using the massive parallelism of the CM, it becomes an O(N(2)) problem. Preliminary timings of the code, written in LISP, are included and compared with a corresponding code optimized for the Cray-2 for a 128 x 128 x 101 grid.

Tomboulian, Sherryl↗

TuckerMPI: A Parallel C++/MPI Software Package for Large-scale Data Compression via the Tucker Tensor Decomposition

With this study, our goal is compression of massive-scale grid-structured data, such as the multi-terabyte output of a high-fidelity computational simulation. For such data sets, we have developed a new software package called TuckerMPI, a parallel C++/MPI software package for compressing distributed data. The approach is based on treating the data as a tensor, i.e., a multidimensional array, and computing its truncated Tucker decomposition, a higher-order analogue to the truncated singular value decomposition of a matrix. The result is a low-rank approximation of the original tensor-structured data. Compression efficiency is achieved by detecting latent global structure within the data, which we contrast to most compression methods that are focused on local structure. In this work, we describe TuckerMPI, our implementation of the truncated Tucker decomposition, including details of the data distribution and in-memory layouts, the parallel and serial implementations of the key kernels, and analysis of the storage, communication, and computational costs. We test the software on 4.5 and 6.7 terabyte data sets distributed across 100 s of nodes (1,000 s of MPI processes), achieving compression ratios between 100 and 200,000×, which equates to 99--99.999% compression (depending on the desired accuracy) in substantially less time than it would take to even read the same dataset from a parallel file system. Moreover, we show that our method also allows for reconstruction of partial or down-sampled data on a single node, without a parallel computer so long as the reconstructed portion is small enough to fit on a single machine, e.g., in the instance of reconstructing/visualizing a single down-sampled time step or computing summary statistics. The code is available at https://gitlab.com/tensors/TuckerMPI.

97 MATHEMATICS AND COMPUTING↗

Scaling soft matter physics to thousands of graphics processing units in parallel

We describe a multi-graphics processing unit (GPU) implementation of the Ludwig application, which specialises in simulating a variety of complex fluids via lattice Boltzmann fluid dynamics coupled to additional physics describing complex fluid constituents. We describe our methodology in augmenting the original central processing unit (CPU) version with GPU functionality in a maintainable fashion. We present several optimisations that maximise performance on the GPU architecture through tuning for the GPU memory hierarchy. We describe how we implement particles within the fluid in such a way to avoid a major diversion of the CPU and GPU codebases, whilst minimising data transfer at each time step. We detail our halo-exchange communication phase for the code, which exploits overlapping to allow efficient parallel scaling to many GPUs. We present results showing that the application demonstrates excellent scaling to at least 8192 GPUs in parallel, the largest system tested at the time of writing. The GPU version (on NVIDIA K20X GPUs) is around 3.5–5 times faster that the CPU version (on fully utilised AMD Opteron 6274 16-core CPUs), comparing equal numbers of CPUs and GPUs.

Computer Science↗

Parallel implicit unstructured grid Euler solvers

A mesh-vertex finite volume scheme for solving the Euler equations on triangular unstructured meshes is implemented on an MIMD (multiple instruction/multiple data stream) parallel computer. An explicit four-stage Runge-Kutta scheme is used to solve two-dimensional flow problems. A family of implicit schemes is also developed to solve these problems, where the linear system that arises at each time step is solved by a preconditioned GMRES algorithm. Two partitioning strategies are employed, one that partitions triangles and the other that partitions vertices. The choice of the preconditioner in a distributed memory setting is discussed. All the methods are compared both in terms of elapsed times and convergence rates. It is shown that the implicit schemes offer adequate parallelism at the expense of minimal sequential overhead. The use of a global coarse grid to further minimize this overhead is also investigated. The schemes are implemented on a distributed memory parallel computer, the iPSC/860.

Venkatakrishnan, V.↗

Parallel implicit unstructured grid Euler solvers

A mesh-vertex finite volume scheme for solving the Euler equations on triangular unstructured meshes is implemented on a multiple-instruction/multiple-data stream parallel computer. An explicit four-stage Runge-Kutta scheme is used to solve two-dimensional flow problems. A family of implicit schemes is also developed to solve these problems, where the linear system that arises at each time step is solved by a preconditioned GMRES algorithm. Two partitioning strategies are employed: one that partitions triangles and the other that partitions vertices. The choice of the preconditioner in a distributed memory setting is discussed. All of the methods are compared both in terms of elapsed times and convergence rates. It is shown that the implicit schemes offer adequate parallelism at the expense of minimal sequential overhead. The use of a global coarse grid to further minimize this overhead is also investigated. The schemes are implemented on a distributed memory parallel computer, the Intel iPSC/860.

TRT-THEORETICAL↗

Scaled ILU Smoothers for Navier-Stokes Pressure Projection

Incomplete LU (ILU) smoothers are effective in the algebraic multigrid (AMG) V-cycle for reducing high-frequency components of the error. However, the requisite direct triangular solves are comparatively slow on GPUs. Previous work has demonstrated the advantages of Jacobi iteration as an alternative to direct solution of these systems. Depending on the threshold and fill-level parameters chosen, the factors can be highly nonnormal and Jacobi is unlikely to converge in a low number of iterations. We demonstrate that row scaling can reduce the departure from normality, allowing us to replace the inherently sequential solve with a rapidly converging Richardson iteration. There are several advantages beyond the lower compute time. Scaling is performed locally for a diagonal block of the global matrix because it is applied directly to the factor. Further, an ILUT Schur complement smoother maintains a constant GMRES iteration count as the number of MPI ranks increases, and thus parallel strong-scaling is improved. Our algorithms have been incorporated into hypre, and we demonstrate improved time to solution for linear systems arising in the Nalu-Wind and PeleLM pressure solvers. For large problem sizes, GMRES+AMG executes at least five times faster when using iterative triangular solves compared with direct solves on massively parallel GPUs.

algebraic multigrid↗

Space station static and dynamic analyses using parallel methods

Algorithms for high-performance parallel computers are applied to perform static analyses of large-scale Space Station finite-element models (FEMs). Several parallel-vector algorithms under development at NASA Langley are assessed. Sparse matrix solvers were found to be more efficient than banded symmetric or iterative solvers for the static analysis of large-scale applications. In addition, new sparse and 'out-of-core' solvers were found superior to substructure (superelement) techniques which require significant additional cost and time to perform static condensation during global FEM matrix generation as well as the subsequent recovery and expansion. A method to extend the fast parallel static solution techniques to reduce the computation time for dynamic analysis is also described. The resulting static and dynamic algorithms offer design economy for preliminary multidisciplinary design optimization and FEM validation against test modes. The algorithms are being optimized for parallel computers to solve one-million degrees-of-freedom (DOF) FEMs. The high-performance computers at NASA afforded effective software development, testing, efficient and accurate solution with timely system response and graphical interpretation of results rarely found in industry. Based on the author's experience, similar cooperation between industry and government should be encouraged for similar large-scale projects in the future.

Gupta, V.↗

Large-deflection theory for end compression of long rectangular plates rigidly clamped along two edges

The von Karman equations for flat plates are solved beyond the buckling load up to edge strains equal to eight time the buckling strain, for the extreme case of rigid clamping along the edges parallel to the load. Deflections, bending stresses, and membrane stresses are given as a function of end compressive load. The theoretical values of effective width are compared with the values derived for simple support along the edges parallel to the load. The increases in effective width due to rigid clamping drops from about 20 percent near the buckling strain to about 8 percent at an edge strain equal to eight times the buckling strain. Experimental values of effective width in the elastic range reported in NACA Technical Note No. 684 are between the theoretical curves for the extremes of simple support and rigid clamping.

Levy, Samuel↗

Efficient Helicopter Aerodynamic and Aeroacoustic Predictions on Parallel Computers

This paper presents parallel implementations of two codes used in a combined CFD/Kirchhoff methodology to predict the aerodynamics and aeroacoustics properties of helicopters. The rotorcraft Navier-Stokes code, TURNS, computes the aerodynamic flowfield near the helicopter blades and the Kirchhoff acoustics code computes the noise in the far field, using the TURNS solution as input. The overall parallel strategy adds MPI message passing calls to the existing serial codes to allow for communication between processors. As a result, the total code modifications required for parallel execution are relatively small. The biggest bottleneck in running the TURNS code in parallel comes from the LU-SGS algorithm that solves the implicit system of equations. We use a new hybrid domain decomposition implementation of LU-SGS to obtain good parallel performance on the SP-2. TURNS demonstrates excellent parallel speedups for quasi-steady and unsteady three-dimensional calculations of a helicopter blade in forward flight. The execution rate attained by the code on 114 processors is six times faster than the same cases run on one processor of the Cray C-90. The parallel Kirchhoff code also shows excellent parallel speedups and fast execution rates. As a performance demonstration, unsteady acoustic pressures are computed at 1886 far-field observer locations for a sample acoustics problem. The calculation requires over two hundred hours of CPU time on one C-90 processor but takes only a few hours on 80 processors of the SP2. The resultant far-field acoustic field is analyzed with state of-the-art audio and video rendering of the propagating acoustic signals.

Wissink, Andrew M.↗

Video Mosaicking for Inspection of Gas Pipelines

A vision system that includes a specially designed video camera and an image-data-processing computer is under development as a prototype of robotic systems for visual inspection of the interior surfaces of pipes and especially of gas pipelines. The system is capable of providing both forward views and mosaicked radial views that can be displayed in real time or after inspection. To avoid the complexities associated with moving parts and to provide simultaneous forward and radial views, the video camera is equipped with a wide-angle (>165 ) fish-eye lens aimed along the axis of a pipe to be inspected. Nine white-light-emitting diodes (LEDs) placed just outside the field of view of the lens (see Figure 1) provide ample diffuse illumination for a high-contrast image of the interior pipe wall. The video camera contains a 2/3-in. (1.7-cm) charge-coupled-device (CCD) photodetector array and functions according to the National Television Standards Committee (NTSC) standard. The video output of the camera is sent to an off-the-shelf video capture board (frame grabber) by use of a peripheral component interconnect (PCI) interface in the computer, which is of the 400-MHz, Pentium II (or equivalent) class. Prior video-mosaicking techniques are applicable to narrow-field-of-view (low-distortion) images of evenly illuminated, relatively flat surfaces viewed along approximately perpendicular lines by cameras that do not rotate and that move approximately parallel to the viewed surfaces. One such technique for real-time creation of mosaic images of the ocean floor involves the use of visual correspondences based on area correlation, during both the acquisition of separate images of adjacent areas and the consolidation (equivalently, integration) of the separate images into a mosaic image, in order to insure that there are no gaps in the mosaic image. The data-processing technique used for mosaicking in the present system also involves area correlation, but with several notable differences: Because the wide-angle lens introduces considerable distortion, the image data must be processed to effectively unwarp the images (see Figure 2). The computer executes special software that includes an unwarping algorithm that takes explicit account of the cylindrical pipe geometry. To reduce the processing time needed for unwarping, parameters of the geometric mapping between the circular view of a fisheye lens and pipe wall are determined in advance from calibration images and compiled into an electronic lookup table. The software incorporates the assumption that the optical axis of the camera is parallel (rather than perpendicular) to the direction of motion of the camera. The software also compensates for the decrease in illumination with distance from the ring of LEDs.

Magruder, Darby↗

Enhanced Collisional Losses from a Magnetic Mirror Using the Lenard-Bernstein Collision Operator

Collisions are crucial in governing particle and energy transport in plasmas confined in a magnetic mirror trap. Modern gyrokinetic codes model transport in magnetic mirrors, but some utilize approximate model collision operators. This study focuses on a Pastukhov-style method of images calculation of particle and energy confinement times using a Lenard-Bernstein model collision operator. Prior work on parallel particle and energy balances used a different Fokker-Planck plasma collision operator. The method must be extended in non-trivial ways to study the Lenard-Bernstein operator. To assess the effectiveness of our approach, we compare our results with a modern finite element solver. Our findings reveal that the particle confinement time scales like a exp( a 2 ) using the Lenard-Bernstein operator, in contrast to the more accurate scaling that the Coulomb collision operator would yield a 2 exp( a 2 ), where a 2 is approximately proportional to the ambipolar potential. We propose that codes solving for collisional losses in magnetic mirrors utilizing the Lenard-Bernstein or Dougherty collision operator scale their collision frequency of any electrostatically confined species. This study illuminates the collision operator’s intricate role in the Pastukhov-style method of images calculation of collisional confinement.

fusion plasma↗

High-performance epistasis detection in quantitative trait GWAS

epiSNP is a program for identifying pairwise single nucleotide polymorphism (SNP) interactions (epistasis) in quantitative-trait genome-wide association studies (GWAS). A parallel MPI version (EPISNPmpi) was created in 2008 to address this computationally expensive analysis on large data sets with many quantitative traits and SNP markers. However, the falling cost of genotyping has led to an explosion of large-scale GWAS data sets that challenge EPISNPmpi’s ability to compute results in a reasonable amount of time. Therefore, we optimized epiSNP for modern multi-core and highly parallel many-core processors to efficiently handle these large data sets. This paper describes the serial optimizations, dynamic load balancing using MPI-3 RMA operations, and shared-memory parallelization with OpenMP to further enhance load balancing and allow execution on the Intel Xeon Phi coprocessor (MIC). For a large GWAS data set, our optimizations provided a 38.43× speedup over EPISNPmpi on 126 nodes using 2 MICs on TACC’s Stampede Supercomputer. We also describe a Coarray Fortran (CAF) version that demonstrates the suitability of PGAS languages for problems with this computational pattern. We show that the Coarray version performs competitively with the MPI version on the NERSC Edison Cray XC30 supercomputer. Finally, the performance benefits of hyper-threading for this application on Edison (average 1.35× speedup) are demonstrated.

97 MATHEMATICS AND COMPUTING↗

Solar Wind Electron Interaction with the Dayside Lunar Surface and Crustal Magnetic Fields: Evidence for Precursor Effects

Electron distributions measured by Lunar Prospector above the dayside lunar surface in the solar wind often have an energy dependent loss cone, inconsistent with adiabatic magnetic reflection. Energy dependent reflection suggests the presence of downward parallel electric fields below the spacecraft, possibly indicating the presence of a standing electrostatic structure. Many electron distributions contain apparent low energy (<100 eV) upwardgoing conics (58% of the time) and beams (12% of the time), primarily in regions with non-zero crustal magnetic fields, implying the presence of parallel electric fields and/or wave-particle interactions below the spacecraft. Some, but not all, of the observed energy dependence comes from the energy gained during reflection from a moving obstacle; correctly characterizing electron reflection requires the use of the proper reference frame. Nonadiabatic reflection may also play a role, but cannot fully explain observations. In cases with upward-going beams, we observe partial isotropization of incoming solar wind electrons, possibly indicating streaming and/or whistler instabilities. The Moon may therefore influence solar wind plasma well upstream from its surface. Magnetic anomaly interactions and/or non-monotonic near surface potentials provide the most likely candidates to produce the observed precursor effects, which may help ensure quasi-neutrality upstream from the Moon.

Solar↗

Kinetic study of shock formation and particle acceleration in laser-driven quasi-parallel magnetized collisionless shocks

Quasi-parallel magnetized collisionless shocks are believed to be one of the most efficient accelerators in the universe. Compared to quasi-perpendicular shocks, quasi-parallel shocks are more difficult to form in the laboratory and to simulate because of their large spatial scales and long formation times. Our two-dimensional particle-in-cell simulations show that the early stages of quasi-parallel shock formation are achievable in experiments planned for the National Ignition Facility and that particles accelerated by diffusive shock acceleration (DSA) are expected to be observable in the experiment. Repetitive ion acceleration by crossings of the shock front, a key feature of DSA, is seen in the simulations. Other characteristic features of quasi-parallel shocks such as upstream wave excitation by energetic ions are also observed, and energy partition between the ions and the electrons in the downstream of the shock is briefly discussed.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Experiences with the Lanczos method on a parallel computer

A parallel computer implementation of the Lanczos method for the free-vibration analysis of structures is considered, and results for two example problems show substantial time-reduction over the sequential solutions. The major Lanczos calculation tasks are subdivided into subtasks, and parallelism is introduced at the subtask level. A speedup of 7.8 on eight processors was obtained for the decomposition step of the problem involving a 60-m three-longeron space mast, and a speedup of 14.6 on 16 processors was obtained for the decomposition step of the problem involving a blade-stiffened graphite-epoxy panel.

Bostic, Susan W.↗