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At least 343 records · Page 19

Alternating Anderson–Richardson method: An efficient alternative to preconditioned Krylov methods for large, sparse linear systems

Here, we present the Alternating Anderson–Richardson (AAR) method: an efficient and scalable alternative to preconditioned Krylov solvers for the solution of large, sparse linear systems on high performance computing platforms. Specifically, we generalize the recently proposed Alternating Anderson–Jacobi (AAJ) method (Pratapa et al., 2016) to include preconditioning, discuss efficient parallel implementation, and provide serial MATLAB and parallel C/C++ implementations. In serial applications to nonsymmetric systems, we find that AAR is comparably robust to GMRES, using the same preconditioning, while often outperforming it in time to solution; and find AAR to be more robust than Bi-CGSTAB for the problems considered. In parallel applications to the Helmholtz and Poisson equations, we find that AAR shows superior strong and weak scaling to GMRES, Bi-CGSTAB, and Conjugate Gradient (CG) methods, using the same preconditioning, with consistently shorter times to solution at larger processor counts. Finally, in massively parallel applications to the Poisson equation, on up to 110,592 processors, we find that AAR shows superior strong and weak scaling to CG, with shorter minimum time to solution. We thus find that AAR offers a robust and efficient alternative to current state-of-the-art solvers, with increasing advantages as the number of processors grows.

97 MATHEMATICS AND COMPUTING↗

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↗

Jacobian-free Newton–Krylov method for the simulation of non-thermal plasma discharges with high-order time integration and physics-based preconditioning

A preconditioning framework for the numerical simulation of non-thermal streamer discharges is developed using the Jacobian-free Newton-Krylov (JFNK) method. A reduced plasma fluid model is considered, consisting of electrons, one positive ion, one negative ion, and the electrostatic potential. Here, the plasma kinetics model includes ionization, electron-ion recombination, electron attachment, electron detachment, and ion-ion recombination. The governing equations are made dimensionless, discretized in space with finite differences, and integrated in time with a fully implicit method based on high-order backward differentiation formulas. The preconditioning framework is based on a linearized form of the governing equations and physics-based operator splitting. The efficiency of the preconditioning strategy is assessed through two test cases: streamer propagation between parallel plates and an axisymmetric pin-to-pin discharge. The fully implicit approach overcomes traditional restrictions in the time step size due to processes such as electron drift, electron diffusion, and dielectric relaxation. Excellent performance is observed through relevant statistics of the JFNK solver, although the number of linear iterations increases for the pin-to-pin discharge when nonlinear numerical boundary conditions are imposed at the electrodes. Performance studies show scalability with O(100-1000) processors for O(10M) unknowns with ample room for optimization.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Milestone 49 Report: Batched Sparse LA Phase 5 Implementation

Batched sparse linear algebra operations in general, and solvers in particular, have become the major algorithmic development activity and foremost performance engineering effort in the numerical software libraries work on modern hardware with accelerators such as GPUs. Many applications, ECP and non-ECP alike, require simultaneous solutions of many small linear systems of equations that are structurally sparse in one form or another. In order to move towards high hardware utilization levels, it is important to provide these applications with appropriate interface designs to be both functionally efficient and performance portable and give full access to the appropriate batched sparse solvers running on modern hardware accelerators prevalent across DOE supercomputing sites since the inception of ECP. To this end, we present here a summary of recent advances on the interface designs in use by HPC software libraries supporting batched sparse linear algebra and the development of sparse batched kernel codes for solvers and preconditioners. We also address the potential interoperability opportunities to keep the corresponding software portable between the major hardware accelerators from AMD, Intel, and NVIDIA, while maintaining the appropriate disclosure levels conforming to the active NDA agreements. The presented interface specifications include a mix of batched band, sparse iterative, and sparse direct solvers with their accompanying functionality that is already required by the application codes or we anticipated to be needed in the near future. This report summarizes progress in Kokkos Kernels and the xSDK libraries MAGMA, Ginkgo, hypre, PETSc, and SuperLU.

97 MATHEMATICS AND COMPUTING↗

Sparse Approximate Multifrontal Factorization with Butterfly Compression for High-Frequency Wave Equations

In this work, we present a fast and approximate multifrontal solver for large-scale sparse linear systems arising from finite-difference, finite-volume or finite-element discretization of high-frequency wave equations. The proposed solver leverages the butterfly algorithm and its hierarchical matrix extension for compressing and factorizing large frontal matrices via graph-distance guided entry evaluation or randomized matrix-vector multiplication-based schemes. Complexity analysis and numerical experiments demonstrate $\mathcal{O}(N\log^2 N)$ computation and $\mathcal{O}(N)$ memory complexity when applied to an $N\times N$ sparse system arising from 3D high-frequency Helmholtz and Maxwell problems.

97 MATHEMATICS AND COMPUTING↗

Numerical Modeling of Spray Combustion with an Unstructured-Grid Method

The present unstructured-grid method follows strictly the basic finite volume forms of the conservation laws of the governing equations for the entire flow domain. High-order spatially accurate formulation has been employed for the numerical solutions of the Navier-Stokes equations. A two-equation k-epsilon turbulence model is also incorporated in the unstructured-grid solver. The convergence of the resulted linear algebraic equation is accelerated with preconditioned Conjugate Gradient method. A statistical spray combustion model has been incorporated into the present unstructured-grid solver. In this model, spray is represented by discrete particles, rather than by continuous distributions. A finite number of computational particles are used to predict a sample of total population of particles. Particle trajectories are integrated using their momentum and motion equations and particles exchange mass, momentum and energy with the gas within the computational cell in which they are located. The interaction calculations are performed simultaneously and eliminate global iteration for the two-phase momentum exchange. A transient spray flame in a high pressure combustion chamber is predicted and then the solution of liquid-fuel combusting flow with a rotating cup atomizer is presented and compared with the experimental data. The major conclusion of this investigation is that the unstructured-grid method can be employed to study very complicated flow fields of turbulent spray combustion. Grid adaptation can be easily achieved in any flow domain such as droplet evaporation and combustion zone. Future applications of the present model can be found in the full three-dimensional study of flow fields of gas turbine and liquid propulsion engine combustion chambers with multi-injectors.

Shang, H. M.↗

Improvements in Iterative Convergence of FUN3D Solutions

This paper presents a hierarchical adaptive nonlinear iteration method (HANIM) implemented in the NASA computational fluid dynamics code, FUN3D, to improve robustness and computational efficiency. In contrast to the legacy FUN3D iterative solver that relies on an approximate Jacobian, a simple multicolor Gauss-Seidel point-implicit iteration scheme, and linear Courant-Friedrichs-Lewy number (CFL) ramping, HANIM is based upon a hierarchy of modules including preconditioner, generalized conjugate residual, realizability check, nonlinear control, and CFL adaption modules. HANIM performance is systematically compared with the performance of the legacy solver of FUN3D and a baseline solver based on a preconditioner alone. Iterative solutions are compared for three benchmark cases: a subsonic separated flow around a hemisphere cylinder, a supersonic flow through a long duct, and a subsonic flow over the NASA wing-fuselage juncture model. Two Reynolds-averaged Navier-Stokes turbulence models are used in these computations, namely, the negative variant of the linear one-equation Spalart-Allmaras model and its nonlinear extension based on quadratic constitutive relations.

CFD↗

A Scalable Semi-Implicit Barotropic Mode Solver for the MPAS-Ocean

A scalable semi-implicit barotropic mode solver for the ocean component of the model for prediction across scales has been implemented as a competitor to an existing explicit-subcycling scheme to allow faster and more stable simulations while not sacrificing accuracy. The semi-implicit solver adopts the pipelined preconditioned bi-conjugate gradient stabilization algorithm as an iterative solver in conjunction with the restricted additive Schwarz preconditioner that accelerates the convergence rate of the iterative solver. The preconditioner is constructed from a linearized barotropic system that also reorders the system for optimal performance, while the semi-implicit solver deals with the fully nonlinear barotropic system that requires reassembly of the coefficient matrix for every time step. Several numerical experiments, from simple one-dimensional tests to three-dimensional real-world tests, demonstrate that the semi-implicit solver has almost the same accuracy and better parallel scalability compared with the existing scheme while allowing faster and more stable simulations. Furthermore, the semi-implicit solver accelerates the barotropic mode up to 2.9 times faster than the existing scheme on 16,320 processors, leading to an overall runtime speedup of 1.9.

97 MATHEMATICS AND COMPUTING↗

ELSI — An open infrastructure for electronic structure solvers

Routine applications of electronic structure theory to molecules and periodic systems need to compute the electron density from given Hamiltonian and, in case of non-orthogonal basis sets, overlap matrices. System sizes can range from few to thousands or, in some examples, millions of atoms. Different discretization schemes (basis sets) and different system geometries (finite non-periodic vs. infinite periodic boundary conditions) yield matrices with different structures. The ELectronic Structure Infrastructure (ELSI) project provides an open-source software interface to facilitate the implementation and optimal use of high-performance solver libraries covering cubic scaling eigensolvers, linear scaling density-matrix-based algorithms, and other reduced scaling methods in between. In this paper, we present recent improvements and developments inside ELSI, mainly covering (1) new solvers connected to the interface, (2) matrix layout and communication adapted for parallel calculations of periodic and/or spin-polarized systems, (3) routines for density matrix extrapolation in geometry optimization and molecular dynamics calculations, and (4) general utilities such as parallel matrix I/O and JSON output. The ELSI interface has been integrated into four electronic structure code projects (DFTB+, DGDFT, FHI-aims, SIESTA), allowing us to rigorously benchmark the performance of the solvers on an equal footing. Based on results of a systematic set of large-scale benchmarks performed with Kohn–Sham density-functional theory and density-functional tight-binding theory, we identify factors that strongly affect the efficiency of the solvers, and propose a decision layer that assists with the solver selection process. As a result, we describe a reverse communication interface encoding matrix-free iterative solver strategies that are amenable, e.g., for use with planewave basis sets.

97 MATHEMATICS AND COMPUTING↗

Parallel three-dimensional simulations of quasi-static elastoplastic solids

Hypo-elastoplasticity is a flexible framework for modeling the mechanics of many hard materials under small elastic deformation and large plastic deformation. Under typical loading rates, most laboratory tests of these materials happen in the quasi-static limit, but there are few existing numerical methods tailor-made for this physical regime. Here, we extend to three dimensions a recent projection method for simulating quasi-static hypo-elastoplastic materials. The method is based on a mathematical correspondence to the incompressible Navier–Stokes equations, where the projection method of Chorin (1968) is an established numerical technique. We develop and utilize a three-dimensional parallel geometric multigrid solver employed to solve a linear system for the quasi-static projection. Our method is tested through simulation of three-dimensional shear band nucleation and growth, a precursor to failure in many materials. As an example system, we employ a physical model of a bulk metallic glass based on the shear transformation zone theory, but the method can be applied to any elastoplasticity model. We consider several examples of three-dimensional shear banding, and examine shear band formation in physically realistic materials with heterogeneous initial conditions under both simple shear deformation and boundary conditions inspired by friction welding.

97 MATHEMATICS AND COMPUTING↗

Neural network acceleration of large-scale structure theory calculations

Here, we make use of neural networks to accelerate the calculation of power spectra required for the analysis of galaxy clustering and weak gravitational lensing data. For modern perturbation theory codes, evaluation time for a single cosmology and redshift can take on the order of two seconds. In combination with the comparable time required to compute linear predictions using a Boltzmann solver, these calculations are the bottleneck for many contemporary large-scale structure analyses. Here, we construct neural network-based surrogate models for Lagrangian perturbation theory (LPT) predictions of matter power spectra, real and redshift space galaxy power spectra, and galaxy-matter cross power spectra that attain ~ 0.1% (at one sigma) accuracy over a broad range of scales in a ωCDM parameter space. The neural network surrogates can be evaluated in approximately one millisecond, a factor of 1000 times faster than the full Boltzmann code and LPT computations. In a simulated full-shape redshift space galaxy power spectrum analysis, we demonstrate that the posteriors obtained using our surrogates are accurate compared to those obtained using the full LPT model. We make our surrogate models public at https://github.com/sfschen/EmulateLSS, so that others may take advantage of the speed gains they provide to enable rapid iteration on analysis settings, something that is essential in complex contemporary large-scale structure analyses.

79 ASTRONOMY AND ASTROPHYSICS↗

Focused wave interactions with floating structures: a blind comparative study

The paper presents results from the Collaborative Computational Project in Wave Structure Interaction (CCP-WSI) Blind Test Series 2. Without prior access to the physical data, participants, with numerical methods ranging from low-fidelity linear models to fully non-linear Navier-Stokes (NS) solvers, simulate the interaction between focused wave events and two separate, taut-moored, floating structures: a hemispherical-bottomed cylinder and a cylinder with a moonpool. The ‘blind’ numerical predictions for heave, surge, pitch and mooring load, are compared against physical measurements. Dynamic time warping is used to quantify the predictive capability of participating methods. In general, NS solvers and hybrid methods give more accurate predictions; however, heave amplitude is predicted reasonably well by all methods; and a WEC-Sim implementation, with CFD-informed viscous terms, demonstrates comparable predictive capability to even the stronger NS solvers. Large variations in the solutions are observed (even among similar methods), highlighting a need for standardisation in the numerical modelling of WSI problems.

42 ENGINEERING↗

Workshop Report on Basic Research Needs for Scientific Machine Learning: Core Technologies for Artificial Intelligence

Scientific Machine Learning (SciML) and Artificial Intelligence (AI) will have broad use and transformative effects across the Department of Energy. Accordingly, the January 2018 Basic Research Needs workshop identified six Priority Research Directions (PRDs). The first three PRDs describe foundational research themes that correspond to the need for domain-awareness (PRD #1), interpretability (PRD #2), and robustness (PRD #3). The other three PRDs describe capability research themes and correspond to the three major use cases for massive scientific data analysis (PRD #4), machine learning-enhanced modeling and simulation (PRD #5), and intelligent automation and decision-support for complex systems (PRD #6). The Priority Research Directions provide a sound basis for a coherent, long-term research and development strategy in SciML and AI. Over the last decade, DOE investments in applied mathematics have laid the groundwork for the type of basic research that will underpin key advances in the six PRDs. Such advances will build on the work from leading researchers in optimization, linear algebra, high-performance solvers and algorithms, multiscale modeling and simulation, complex systems research, uncertainty quantification, and the new basic research areas that will emerge from the pursuit of transformative technologies.

97 MATHEMATICS AND COMPUTING↗

Brochure on Basic Research Needs for Scientific Machine Learning: Core Technologies for Artificial Intelligence [Slides]

Scientific Machine Learning (SciML) and Artificial Intelligence (AI) will have broad use and transformative effects across the Department of Energy. Accordingly, the January 2018 Basic Research Needs workshop identified six Priority Research Directions (PRDs). The first three PRDs describe foundational research themes that correspond to the need for domain-awareness (PRD #1), interpretability (PRD #2), and robustness (PRD #3). The other three PRDs describe capability research themes and correspond to the three major use cases for massive scientific data analysis (PRD #4), machine learning-enhanced modeling and simulation (PRD #5), and intelligent automation and decision-support for complex systems (PRD #6). The Priority Research Directions provide a sound basis for a coherent, long-term research and development strategy in SciML and AI. Over the last decade, DOE investments in applied mathematics have laid the groundwork for the type of basic research that will underpin key advances in the six PRDs. Such advances will build on the work from leading researchers in optimization, linear algebra, high-performance solvers and algorithms, multiscale modeling and simulation, complex systems research, uncertainty quantification, and the new basic research areas that will emerge from the pursuit of transformative technologies.

97 MATHEMATICS AND COMPUTING↗

A multigrid method for the Euler equations

A multigrid algorithm has been developed for the numerical solution of the steady two-dimensional Euler equations. Flux vector splitting and one-sided differencing are employed to define the spatial discretization. Newton's method is used to solve the nonlinear equations, and a multigrid solver is used on each linear problem. The relaxation scheme for the linear problems is symmetric Gauss-Seidel. Standard restriction and interpolation operators are employed. Local mode analysis is used to predict the convergence rate of the multigrid process on the linear problems. Computed results for transonic flows over airfoils are presented.

Jespersen, D. C.↗

Computation of the flow field in a centrifugal impeller with splitter blades

To support the design effort of the Space Transportation Main Engine (STME) Fuel Pump Stage, viscous flow calculations were performed in a centrifugal impeller with splitter blades. These calculations were carried out with a Navier-Stokes solver (MINT), which employs a linearized block-implicit Alternating Direction Implicit (ADI) procedure to iteratively solve a finite difference form of the system of conservation equations of mass, momentum, and energy in body-fitted coordinates. A computational grid was generated algebraically for the 'channel' between two main blades of the impeller and extended both upstream of the impeller inlet and downstream of the impeller exit so that the appropriate boundary conditions could be applied. The results of the calculations show that although the overall level of flow distortion near the impeller exit is not very large, there is a noticeable difference between the flow patterns in the two 'passages' (one passage between the pressure side of the splitter blade and the suction side of the next full blade).

Dejong, Frederik J.↗

Tangle-Free Finite Element Mesh Motion for Ablation Problems

Mesh motion is the process by which a computational domain is updated in time to reflect physical changes in the material the domain represents. Such a technique is needed in the study of the thermal response of ablative materials, which erode when strong heating is applied to the boundary. Traditionally, the thermal solver is coupled with a linear elastic or biharmonic system whose sole purpose is to update mesh node locations in response to altering boundary heating. Simple mesh motion algorithms rely on boundary surface normals. In such schemes, evolution in time will eventually cause the mesh to intersect and "tangle" with itself, causing failure. Furthermore, such schemes are greatly limited in the problems geometries on which they will be successful. This paper presents a comprehensive and sophisticated scheme that tailors the directions of motion based on context. By choosing directions for each node smartly, the inevitable tangle can be completely avoided and mesh motion on complex geometries can be modeled accurately.

Droba, Justin↗