Large Scale Integral Equation Modeling Using Scalable Parallel Processing
(See abstract).
speed matrix solvers↗
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An implicit numerical scheme for the simulation of internal viscous flows on unstructured grids
The Navier-Stokes equations are solved numerically for two-dimensional steady viscous laminar flows. The grids are generated based on the method of Delaunay triangulation. A finite-volume approach is used to discretize the conservation law form of the compressible flow equations written in terms of primitive variables. A preconditioning matrix is added to the equations so that low Mach number flows can be solved economically. The equations are time marched using either an implicit Gauss-Seidel iterative procedure or a solver based on a conjugate gradient like method. A four color scheme is employed to vectorize the block Gauss-Seidel relaxation procedure. This increases the memory requirements minimally and decreases the computer time spent solving the resulting system of equations substantially. A factor of 7.6 speed up in the matrix solver is typical for the viscous equations. Numerical results are obtained for inviscid flow over a bump in a channel at subsonic and transonic conditions for validation with structured solvers. Viscous results are computed for developing flow in a channel, a symmetric sudden expansion, periodic tandem cylinders in a cross-flow, and a four-port valve. Comparisons are made with available results obtained by other investigators.
Jorgenson, Philip C. E.↗
Parallel Computation of the Jacobian Matrix for Nonlinear Equation Solvers Using MATLAB
Demonstrating speedup for parallel code on a multicore shared memory PC can be challenging in MATLAB due to underlying parallel operations that are often opaque to the user. This can limit potential for improvement of serial code even for the so-called embarrassingly parallel applications. One such application is the computation of the Jacobian matrix inherent to most nonlinear equation solvers. Computation of this matrix represents the primary bottleneck in nonlinear solver speed such that commercial finite element (FE) and multi-body-dynamic (MBD) codes attempt to minimize computations. A timing study using MATLAB's Parallel Computing Toolbox was performed for numerical computation of the Jacobian. Several approaches for implementing parallel code were investigated while only the single program multiple data (spmd) method using composite objects provided positive results. Parallel code speedup is demonstrated but the goal of linear speedup through the addition of processors was not achieved due to PC architecture.
Rose, Geoffrey K.↗
Pushing memory bandwidth limitations through efficient implementations of Block-Krylov space solvers on GPUs
Lattice quantum chromodynamics simulations in nuclear physics have benefited from a tremendous number of algorithmic advances such as multigrid and eigenvector deflation. These improve the time to solution but do not alleviate the intrinsic memory-bandwidth constraints of the matrix-vector operation dominating iterative solvers. Batching this operation for multiple vectors and exploiting cache and register blocking can yield a super-linear speed up. Block-Krylov solvers can naturally take advantage of such batched matrix-vector operations, further reducing the iterations to solution by sharing the Krylov space between solves. However, practical implementations typically suffer from the quadratic scaling in the number of vector-vector operations. Here, using the QUDA library, we present an implementation of a block-CG solver on NVIDIA GPUs which reduces the memory-bandwidth complexity of vector-vector operations from quadratic to linear. We present results for the HISQ discretization, showing a 5x speedup compared to highly-optimized independent Krylov solves on NVIDIA's SaturnV cluster.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
Linearized frequency domain Landau-Lifshitz-Gilbert equation formulation
We present a general finite element linearized Landau-Lifshitz-Gilbert equation (LLGE) solver for magnetic systems under weak time-harmonic excitation field. The linearized LLGE is obtained by assuming a small deviation around the equilibrium state of the magnetic system. Inserting such expansion into LLGE and keeping only first order terms gives the linearized LLGE, which gives a frequency domain solution for the complex magnetization amplitudes under an external time-harmonic applied field of a given frequency. We solve the linear system with an iterative solver using generalized minimal residual method. We construct a preconditioner matrix to effectively solve the linear system. The validity, effectiveness, speed, and scalability of the linear solver are demonstrated via numerical examples.
36 MATERIALS SCIENCE↗
High-order fully implicit solver for all-speed fluid dynamics: AUSM ride from nearly incompressible variable-density flows to shock dynamics
We introduce a novel Newton–Krylov (NK)-based fully implicit algorithm for solving fluid flows in a wide range of flow conditions—from variable density nearly incompressible to supersonic shock dynamics. The key enabling feature of our all-speed solver is the ability to efficiently solve conservation laws by choosing a set of independent variables that produce a well-conditioned Jacobian matrix for the linear iterations of the global nonlinear iterative solver. In particular, instead of choosing to discretize the conservative variables (density, momentum, total energy), which is traditionally used in Eulerian high-speed compressible fluid dynamics, we demonstrate superior performance by discretizing the primitive variables—pressure–velocity–temperature in the very low-Mach flow limits or density–velocity–temperature/entropy in the shock dynamics range. Moreover, our method allows us to avoid direct inversion of the mass matrix in discrete time derivatives, which is usually an additional source for stiffness, especially pronounced when going to very high-order schemes with non-orthogonal basis functions. Here, we show robust solutions obtained for discontinuous finite element discretization up to seventh-order accuracy. Another important aspect of the solution algorithm is the Advection Upstream Splitting Method (AUSM), adopted to compute numerical fluxes within our reconstructed discontinuous Galerkin (rDG) spatial discretization scheme. The use of the low-Mach modification of the hyperbolic flux operator is found to be necessary for enabling robust simulations of very stiff liquids and metals for Mach numbers below M=10 -5 , which is well known to be very computationally challenging for compressible solvers. We demonstrate that our fully implicit rDG-NK solver with the AUSM + -up flux treatment produces efficient and high-resolution numerical solutions at all speeds, ranging from vanishing Mach numbers to transonic and supersonic, without substantial modifications of the solution procedures. (At high speed, we add limiting and use a simpler preconditioning of the Krylov solver.) Numerical examples include nearly incompressible constant-property flow past a backward-facing step with heat transfer, low-Mach variable-property channel flow of water at supercritical state, phase change and melt pool dynamics for laser spot welding and selective laser melting in additive manufacturing, and Mach 3 flow in a wind tunnel with a step.
97 MATHEMATICS AND COMPUTING↗
Optimizing Sparse Matrix-Multiple Vectors Multiplication for Nuclear Configuration Interaction Calculations
Obtaining highly accurate predictions on the properties of light atomic nuclei using the configuration interaction (CI) approach requires computing a few extremal Eigen pairs of the many-body nuclear Hamiltonian matrix. In the Many-body Fermion Dynamics for nuclei (MFDn) code, a block Eigen solver is used for this purpose. Due to the large size of the sparse matrices involved, a significant fraction of the time spent on the Eigen value computations is associated with the multiplication of a sparse matrix (and the transpose of that matrix) with multiple vectors (SpMM and SpMM-T). Existing implementations of SpMM and SpMM-T significantly underperform expectations. Thus, in this paper, we present and analyze optimized implementations of SpMM and SpMM-T. We base our implementation on the compressed sparse blocks (CSB) matrix format and target systems with multi-core architectures. We develop a performance model that allows us to understand and estimate the performance characteristics of our SpMM kernel implementations, and demonstrate the efficiency of our implementation on a series of real-world matrices extracted from MFDn. In particular, we obtain 3-4 speedup on the requisite operations over good implementations based on the commonly used compressed sparse row (CSR) matrix format. The improvements in the SpMM kernel suggest we may attain roughly a 40% speed up in the overall execution time of the block Eigen solver used in MFDn.
97 MATHEMATICS AND COMPUTING↗
Numerical Computation of a Continuous-thrust State Transition Matrix Incorporating Accurate Hardware and Ephemeris Models
A significant body of work exists showing that providing a nonlinear programming (NLP) solver with expressions for the problem constraint gradient substantially increases the speed of program execution and can also improve the robustness of convergence, especially for local optimizers. Calculation of these derivatives is often accomplished through the computation of spacecraft's state transition matrix (STM). If the two-body gravitational model is employed as is often done in the context of preliminary design, closed form expressions for these derivatives may be provided. If a high fidelity dynamics model, that might include perturbing forces such as the gravitational effect from multiple third bodies and solar radiation pressure is used then these STM's must be computed numerically. We present a method for the power hardward model and a full ephemeris model. An adaptive-step embedded eight order Dormand-Prince numerical integrator is discussed and a method for the computation of the time of flight derivatives in this framework is presented. The use of these numerically calculated derivatieves offer a substantial improvement over finite differencing in the context of a global optimizer. Specifically the inclusion of these STM's into the low thrust missiondesign tool chain in use at NASA Goddard Spaceflight Center allows for an increased preliminary mission design cadence.
Low Thrust↗
Developement of an Optimum Interpolation Analysis Method for the CYBER 205
A state-of-the-art technique to assimilate the diverse observational database obtained during FGGE, and thus create initial conditions for numerical forecasts is described. The GLA optimum interpolation (OI) analysis method analyzes pressure, winds, and temperature at sea level, mixing ratio at six mandatory pressure levels up to 300 mb, and heights and winds at twelve levels up to 50 mb. Conversion to the CYBER 205 required a major re-write of the Amdahl OI code to take advantage of the CYBER vector processing capabilities. Structured programming methods were used to write the programs and this has resulted in a modular, understandable code. Among the contributors to the increased speed of the CYBER code are a vectorized covariance-calculation routine, an extremely fast matrix equation solver, and an innovative data search and sort technique.
Nestler, M. S.↗
Preconditioned conjugate-gradient methods for low-speed flow calculations
An investigation is conducted into the viability of using a generalized Conjugate Gradient-like method as an iterative solver to obtain steady-state solutions of very low-speed fluid flow problems. Low-speed flow at Mach 0.1 over a backward-facing step is chosen as a representative test problem. The unsteady form of the two dimensional, compressible Navier-Stokes equations is integrated in time using discrete time-steps. The Navier-Stokes equations are cast in an implicit, upwind finite-volume, flux split formulation. The new iterative solver is used to solve a linear system of equations at each step of the time-integration. Preconditioning techniques are used with the new solver to enhance the stability and convergence rate of the solver and are found to be critical to the overall success of the solver. A study of various preconditioners reveals that a preconditioner based on the Lower-Upper Successive Symmetric Over-Relaxation iterative scheme is more efficient than a preconditioner based on Incomplete L-U factorizations of the iteration matrix. The performance of the new preconditioned solver is compared with a conventional Line Gauss-Seidel Relaxation (LGSR) solver. Overall speed-up factors of 28 (in terms of global time-steps required to converge to a steady-state solution) and 20 (in terms of total CPU time on one processor of a CRAY-YMP) are found in favor of the new preconditioned solver, when compared with the LGSR solver.
Ajmani, Kumud↗
Preconditioned Conjugate Gradient methods for low speed flow calculations
An investigation is conducted into the viability of using a generalized Conjugate Gradient-like method as an iterative solver to obtain steady-state solutions of very low-speed fluid flow problems. Low-speed flow at Mach 0.1 over a backward-facing step is chosen as a representative test problem. The unsteady form of the two dimensional, compressible Navier-Stokes equations are integrated in time using discrete time-steps. The Navier-Stokes equations are cast in an implicit, upwind finite-volume, flux split formulation. The new iterative solver is used to solve a linear system of equations at each step of the time-integration. Preconditioning techniques are used with the new solver to enhance the stability and the convergence rate of the solver and are found to be critical to the overall success of the solver. A study of various preconditioners reveals that a preconditioner based on the lower-upper (L-U)-successive symmetric over-relaxation iterative scheme is more efficient than a preconditioner based on incomplete L-U factorizations of the iteration matrix. The performance of the new preconditioned solver is compared with a conventional line Gauss-Seidel relaxation (LGSR) solver. Overall speed-up factors of 28 (in terms of global time-steps required to converge to a steady-state solution) and 20 (in terms of total CPU time on one processor of a CRAY-YMP) are found in favor of the new preconditioned solver, when compared with the LGSR solver.
Ajmani, Kumud↗
Overview of Transonic to Hypersonic Stage Separation Tool Development for Multi-Stage-to-Orbit Concepts
An overview of research efforts at NASA in support of the stage separation and ascent aerothermodynamics research program is presented. The objective of this work is to develop a synergistic suite of experimental, computational, and engineering tools and methods to apply to vehicle separation across the transonic to hypersonic speed regimes. Proximity testing of a generic bimese wing-body configuration is on-going in the transonic (Mach numbers 0.6, 1.05, and 1.1), supersonic (Mach numbers 2.3, 3.0, and 4.5) and hypersonic (Mach numbers 6 and 10) speed regimes in four wind tunnel facilities at the NASA Langley Research Center. An overset grid, Navier-Stokes flow solver has been enhanced and demonstrated on a matrix of proximity cases and on a dynamic separation simulation of the bimese configuration. Steady-state predictions with this solver were in excellent agreement with wind tunnel data at Mach 3 as were predictions via a Cartesian-grid Euler solver. Experimental and computational data have been used to evaluate multi-body enhancements to the widely-used Aerodynamic Preliminary Analysis System, an engineering methodology, and to develop a new software package, SepSim, for the simulation and visualization of vehicle motions in a stage separation scenario. Web-based software will be used for archiving information generated from this research program into a database accessible to the user community. Thus, a framework has been established to study stage separation problems using coordinated experimental, computational, and engineering tools.
Murphy, Kelly J.↗
Exponential time differencing for the tracer equations appearing in primitive equation ocean models
The tracer equations are part of the primitive equations used in ocean modeling and describe the transport of tracers, such as temperature, salinity or chemicals, in the ocean. Depending on the number of tracers considered, several equations may be added to and coupled to the dynamics system. In many relevant situations, the time-step requirements of explicit methods imposed by the transport and mixing in the vertical direction are more restrictive than those for the horizontal, and this may cause the need to use very small time steps if a fully explicit method is employed. To overcome this issue, we propose an exponential time differencing (ETD) solver where the vertical terms (transport and diffusion) are treated with a matrix exponential, whereas the horizontal terms are dealt with in an explicit way. In this work, we investigate numerically the computational speed-ups that can be obtained over other semi-implicit methods, and we analyze the advantages of the method in the case of multiple tracers.
42 ENGINEERING↗
BiGlobal Secondary Instabilities of Roughness-Induced Transient Growth
Roughness-induced transient disturbances distort laminar boundary layers and can lead to premature transition if the roughness is of sufficient height and shape. If transition does occur, it does so through a high-frequency "secondary" instability of the roughness wake. A BiGlobal secondaryinstability code has been developed to solve the stability problem downstream of roughness. The code implements multiple solvers for incompressible/compressible, inviscid/viscous, and temporal/spatial stability. High-order finite differences, sparse matrix linear algebra, LU decomposition, and Arnoldi iterations are used to solve the resulting generalized eigenvalue problem. The code has been used to evaluate the stability properties of experimental roughness-induced transient growth on a flat-plate at low-speed and a slightly blunted cone at M∞= 6. The resulting mode shapes, growth rates, and spatial N-factors show excellent agreement with experimental data. The viscous mode shapes show the best agreement with the experimental disturbance profiles. Yet, execution time can be reduced by an order-of-magnitude by using the inviscid solvers with only modest differences in growth rates.
BiGlobal↗
Optimal control study for the Space Station Solar Dynamic power module
The authors present the design of an optimal control system for the Space Station Freedom's Solar Dynamic Fine Pointing and Tracking (SDFPT) module. A very large state model of six rigid body modes and 272 flexible modes is used in conjunction with classical LQG optimal control to produce a full-order controller which satisfies the requirements. The results obtained are compared with those of a classically designed PID (proportional plus integral plus derivative) controller that was implemented for a six-rigid-body-mode forty-flexible-mode model. A major difficulty with designing LQG controllers for large models is solving the Riccati equation that arises from the optimal formulation. A Riccati solver based on a Pade approximation to the matrix sign function is used. A symmetric version of this algorithm is derived for the special class of Hamiltonion matrices, thereby yielding, for large problems, a nearly twofold speed increase over a previous algorithm.
Papadopoulos, P. M.↗
Sparse, iterative simulation methods for one-dimensional laminar flames
Sparse, iterative simulation methods for one-dimensional laminar flames are proposed. The resulting steady and unsteady flame solvers exploit approximate Jacobians to greatly reduce the computational cost associated with matrix operations. The constant, non-unity Lewis number assumption is introduced to further reduce the computational cost. The solvers are also parallelized to reduce time-to-solution on distributed memory computer systems. Computed laminar flame speeds and species profiles for a range of chemical mechanisms (from 10 to 2878 species) are compared against a well-validated commercial code and are found to be consistent within solver tolerances. The computation times of both the unsteady and steady solutions increase only linearly with the number of species, which is a significant improvement over the quadratic or cubic scaling of existing steady-state flame solvers. For the largest mechanism tested, the steady-state flame solver is two orders of magnitude faster than commonly-used codes. The use of an approximate Jacobian is shown to reduce the rate of convergence for the steady-state solver, but does not significantly affect the domain of convergence. The steady-state solver with approximate Jacobian is thus well suited for computationally efficient laminar flame speed sweeps with large kinetic mechanisms.
42 ENGINEERING↗
A Parallel Solver for Graph Laplacians
Problems from graph drawing, spectral clustering, network flow and graph partitioning can all be expressed in terms of graph Laplacian matrices. There are a variety of practical approaches to solving these problems in serial. However, as problem sizes increase and single core speeds stagnate, parallelism is essential to solve such problems quickly. We present an unsmoothed aggregation multigrid method for solving graph Laplacians in a distributed memory setting. We introduce new parallel aggregation and low degree elimination algorithms targeted specifically at irregular degree graphs. These algorithms are expressed in terms of sparse matrix-vector products using generalized sum and product operations. This formulation is amenable to linear algebra using arbitrary distributions and allows us to operate on a 2D sparse matrix distribution, which is necessary for parallel scalability. Our solver outperforms the natural parallel extension of the current state of the art in an algorithmic comparison. We demonstrate scalability to 576 processes and graphs with up to 1.7 billion edges.
Konolige, Tristan↗
Parallel-vector unsymmetric Eigen-Solver on high performance computers
The popular QR algorithm for solving all eigenvalues of an unsymmetric matrix is reviewed. Among the basic components in the QR algorithm, it was concluded from this study, that the reduction of an unsymmetric matrix to a Hessenberg form (before applying the QR algorithm itself) can be done effectively by exploiting the vector speed and multiple processors offered by modern high-performance computers. Numerical examples of several test cases have indicated that the proposed parallel-vector algorithm for converting a given unsymmetric matrix to a Hessenberg form offers computational advantages over the existing algorithm. The time saving obtained by the proposed methods is increased as the problem size increased.
Nguyen, Duc T.↗