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At least 19 records

Linear and Nonlinear Solvers for Simulating Multiphase Flow within Large-Scale Engineered Subsurface Systems

Simulation of multiphase flow in the subsurface is well-known to be computationally challenging. While there have been many studies that have explored approaches to overcoming these challenges, they often utilize relatively simple case studies. In this paper, we focus on the unique numerical challenges posed by modeling large-scale engineered subsurface systems, characterized by discrete features embedded in a heterogeneous natural subsurface setting. The man-made features such as shafts, tunnels, and barriers often cause multiple challenges in modeling the domain for multiphase porous media flow. This flow scenario can have a wide range of applications such as nuclear waste repositories, enhanced recovery of a petroleum reservoir, geothermal engineering, and carbon sequestration. An example of these severe numerical challenges is the case of performance assessment (PA) for Waste Isolation Pilot Plant (WIPP), the only operating deep geological repository in the US, which simulates extreme material properties of bedded salt rock formation and extreme contrast due to open excavation next to the formation. The models have extremes not only of permeability and porosity but also of the constitutive models needed for multiphase flow; additionally, they have process models like salt creep closure reducing porosity over time, fracturing in clay and anhydrite interbeds of the bedded salt, gas generation from the waste materials, and unintentional human borehole intrusions in some scenarios. Numerical simulations require the solution of coupled systems of nonlinear PDEs; in our work, we use the open-source simulator PFLOTRAN which is based on Finite Volume discretization. The solution of the nonlinear equations requires use of the Newton-Raphson iteration at each time step, which entails the solution of the linearized Jacobian system at each iteration. The effects of all the processes (i.e., large number of unknowns, highly nonlinear constitutive relations, large contrasts in material properties in short distances) lead to an ill-conditioned Jacobian matrix that severely challenges traditional linear solver, i.e., stabilized biconjugate gradient with block Jacobi incomplete LU preconditioner (BCGS-ILU) leading to non-convergence for traditional Newton-Raphson nonlinear solver causing unacceptably long computation time for each model. This paper presents linear solvers such as constrained pressure residual (CPR) two-stage preconditioner with alternate-block-factorization (ABF) and quasi- implicit pressure and explicit saturation (QIMPES) decouplers and flexible generalized residual solver (FGMRES). The new general-purpose nonlinear solver, Newton trust-region dogleg Cauchy (NTRDC), is also introduced to resolve extreme nonlinearities in the models. We demonstrate the effectiveness of each method relative to the default BCGS-Newton solver. The two best cases had nearly 50 times speed-up and achieved completion of a simulation in 14 hours that never completed due to non-convergence with the default solver. We also investigate the strong scalability of each method and discuss some of the deficiencies found for Block Jacobi preconditioner using parallel domain decomposition, and node packing effects of modern processor architecture.

Preconditioner, Nonlinear, Porous media, Multiphas↗

Large-scale computation of incompressible viscous flow by least-squares finite element method

The least-squares finite element method (LSFEM) based on the velocity-pressure-vorticity formulation is applied to large-scale/three-dimensional steady incompressible Navier-Stokes problems. This method can accommodate equal-order interpolations and results in symmetric, positive definite algebraic system which can be solved effectively by simple iterative methods. The first-order velocity-Bernoulli function-vorticity formulation for incompressible viscous flows is also tested. For three-dimensional cases, an additional compatibility equation, i.e., the divergence of the vorticity vector should be zero, is included to make the first-order system elliptic. The simple substitution of the Newton's method is employed to linearize the partial differential equations, the LSFEM is used to obtain discretized equations, and the system of algebraic equations is solved using the Jacobi preconditioned conjugate gradient method which avoids formation of either element or global matrices (matrix-free) to achieve high efficiency. To show the validity of this scheme for large-scale computation, we give numerical results for 2D driven cavity problem at Re = 10000 with 408 x 400 bilinear elements. The flow in a 3D cavity is calculated at Re = 100, 400, and 1,000 with 50 x 50 x 50 trilinear elements. The Taylor-Goertler-like vortices are observed for Re = 1,000.

Jiang, Bo-Nan↗

A least-squares finite element method for 3D incompressible Navier-Stokes equations

The least-squares finite element method (LSFEM) based on the velocity-pressure-vorticity formulation is applied to three-dimensional steady incompressible Navier-Stokes problems. This method can accommodate equal-order interpolations, and results in symmetric, positive definite algebraic system. An additional compatibility equation, i.e., the divergence of vorticity vector should be zero, is included to make the first-order system elliptic. The Newton's method is employed to linearize the partial differential equations, the LSFEM is used to obtain discretized equations, and the system of algebraic equations is solved using the Jacobi preconditioned conjugate gradient method which avoids formation of either element or global matrices (matrix-free) to achieve high efficiency. The flow in a half of 3D cubic cavity is calculated at Re = 100, 400, and 1,000 with 50 x 52 x 25 trilinear elements. The Taylor-Gortler-like vortices are observed at Re = 1,000.

Jiang, Bo-Nan↗

Finite Element Methods for real-time Haptic Feedback of Soft-Tissue Models in Virtual Reality Simulators

We have applied the linear elastic finite element method to compute haptic force feedback and domain deformations of soft tissue models for use in virtual reality simulators. Our results show that, for virtual object models of high-resolution 3D data (>10,000 nodes), haptic real time computations (>500 Hz) are not currently possible using traditional methods. Current research efforts are focused in the following areas: 1) efficient implementation of fully adaptive multi-resolution methods and 2) multi-resolution methods with specialized basis functions to capture the singularity at the haptic interface (point loading). To achieve real time computations, we propose parallel processing of a Jacobi preconditioned conjugate gradient method applied to a reduced system of equations resulting from surface domain decomposition. This can effectively be achieved using reconfigurable computing systems such as field programmable gate arrays (FPGA), thereby providing a flexible solution that allows for new FPGA implementations as improved algorithms become available. The resulting soft tissue simulation system would meet NASA Virtual Glovebox requirements and, at the same time, provide a generalized simulation engine for any immersive environment application, such as biomedical/surgical procedures or interactive scientific applications.

Frank, Andreas O.↗

HFEM3D

Software solves the three-dimensional Poisson equation div(k(grad(u)) = f, by the finite element method for the case when material properties, k, are distributed over hierarchy of edges, facets and tetrahedra in the finite element mesh. Method is described in Weiss, CJ, Finite element analysis for model parameters distributed on a hierarchy of geometric simplices, Geophysics, v82, E155-167, doi:10.1190/GEO2017-0058.1 (2017). A standard finite element method for solving Poisson’s equation is augmented by including in the 3D stiffness matrix additional 2D and 1D stiffness matrices representing the contributions from material properties associated with mesh faces and edges, respectively. The resulting linear system is solved iteratively using the conjugate gradient method with Jacobi preconditioning. To minimize computer storage for program execution, the linear solver computes matrix-vector contractions element-by-element over the mesh, without explicit storage of the global stiffness matrix. Program output vtk compliant for visualization and rendering by 3rd party software. Program uses dynamic memory allocation and as such there are no hard limits on problem size outside of those imposed by the operating system and configuration on which the software is run. Dimension, N, of the finite element solution vector is constrained by the the addressable space in 32-vs-64 bit operating systems. Total storage requirements for the problem. Total working space required for the program is approximately 13*N double precision words.

Weiss, Chester J↗

Replicated Computational Results (RCR) Report for “Adaptive Precision Block-Jacobi for High Performance Preconditioning in the Ginkgo Linear Algebra Software”

The article by Flegar et al. titled “Adaptive Precision Block-Jacobi for High Performance Preconditioning in the Ginkgo Linear Algebra Software” presents a novel, practical implementation of an adaptive precision block-Jacobi preconditioner. Performance results using state-of-the-art GPU architectures for the block-Jacobi preconditioner generation and application demonstrate the practical usability of the method, compared to a traditional full-precision block-Jacobi preconditioner. A production-ready implementation is provided in the Ginkgo numerical linear algebra library. In this report, the Ginkgo library is reinstalled and performance results are generated to perform a comparison to the original results when using Ginkgo’s Conjugate Gradient solver with either the full or the adaptive precision block-Jacobi preconditioner for a suite of test problems on an NVIDIA GPU accelerator. After completing this process, the published results are deemed reproducible.

97 MATHEMATICS AND COMPUTING↗

Replicated Computational Results (RCR) Report for "Adaptive Precision Block-Jacobi for High Performance Preconditioning in the Ginkgo Linear Algebra Software''

In, a practical implementation of a novel adaptive precision block-Jacobi preconditioner is introduced. In particular, the authors present a heavily-tuned GPU implementation of the adaptive precision block-Jacobi preconditioner within the Ginkgo numerical linear algebra library. The performance of the methodology and implementation is demonstrated using the proposed preconditioning scheme within Ginkgo’s high-performance Conjugate Gradient (CG) implementation on an NVIDIA Volta GPU. In this report, we replicate a subset of the computational results presented in. The focus is generating results from Fig. 9 to evaluate the performance of using Ginkgo’s CG solver integrated with either the full or the adaptive precision block-Jacobi preconditioner applied to a variety of test cases

97 MATHEMATICS AND COMPUTING↗

A high accuracy/resolution spectral element/Fourier–Galerkin method for the simulation of shoaling non-linear internal waves and turbulence in long domains with variable bathymetry

A high-order hybrid continuous-Galerkin numerical method, designed for the simulation of non-linear, non -hydrostatic internal waves and turbulence in long computational domains with complex bathymetry, is presented. The spatial discretization in the non-periodic wave-propagating directions, utilizes the nodal spectral element method. Such a high-order element-based discretization allows the highly accurate representation of complex domain geometry along with the flexibility of concentrating resolution in areas of interest. Under the assumption of the normal-to-isobath propagation of non-linear internal waves, a third periodic direction is incorporated via a Fourier-Galerkin discretization. The distinct non-hydrostatic nature of non-linear internal waves and, any instabilities and turbulence therein, necessitates the numerically challenging solution of the pressure Poisson problem. A defining feature of this work is the application of a domain decomposition approach, combined with block-Jacobi/deflation-based preconditioning to the pressure Poisson problem. Such a combined approach is particularly suitable for the long high aspect-ratio complex domains of interest and enables the efficient high-accuracy reproduction of the non-hydrostatic dynamics of non-linear internal waves. Implementation details are also described in the context of the stability of the solver and its parallelization strategy. A series of benchmarks of increasing complexity demonstrate the robustness of the flow solver. The benchmarks culminate with the three-dimensional simulation of a convectively breaking mode-one non-linear internal wave over a realistic South-China-Sea bathymetric transect and background current/stratification profiles.

Deflation↗

REACTIVE TRANSPORT MODELING USING A PARALLEL FULLY-COUPLED SIMULATOR BASED ON PRECONDITIONED JACOBIAN-FREE NEWTON-KRYLOV

Systems of multicomponent reactive transport in porous media that are large, highly nonlinear, and tightly coupled due to complex nonlinear reactions and strong solution-media interactions are often described by a system of coupled nonlinear partial differential algebraic equations (PDAEs). A preconditioned Jacobian-Free Newton-Krylov (JFNK) solution approach is applied to solve the PDAEs in a fully coupled, fully implicit manner. The advantage of the JFNK method is that it avoids explicitly computing and storing the Jacobian matrix during Newton nonlinear iterations for computational efficiency considerations. This solution approach is also enhanced by physics-based blocking preconditioning and multigrid algorithm for efficient inversion of preconditioners. Based on the solution approach, we have developed a reactive transport simulator named RAT. Numerical results are presented to demonstrate the efficiency and massive scalability of the simulator for reactive transport problems involving strong solution-mineral interactions and fast kinetics. It has been applied to study the highly nonlinearly coupled reactive transport system of a promising in situ environmental remediation that involves urea hydrolysis and calcium carbonate precipitation.

58 GEOSCIENCES↗

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↗

Incomplete Sparse Approximate Inverses for Parallel Preconditioning

In this study, we propose a new preconditioning method that can be seen as a generalization of block-Jacobi methods, or as a simplification of the sparse approximate inverse (SAI) preconditioners. The “Incomplete Sparse Approximate Inverses” (ISAI) is in particular efficient in the solution of sparse triangular linear systems of equations. Those arise, for example, in the context of incomplete factorization preconditioning. ISAI preconditioners can be generated via an algorithm providing fine-grained parallelism, which makes them attractive for hardware with a high concurrency level. Finally, in a study covering a large number of matrices, we identify the ISAI preconditioner as an attractive alternative to exact triangular solves in the context of incomplete factorization preconditioning.

97 MATHEMATICS AND COMPUTING↗

Research on Computational Fluid Dynamics and Turbulence

Preconditioning matrices for Chebyshev derivative operators in several space dimensions; the Jacobi matrix technique in computational fluid dynamics; and Chebyshev techniques for periodic problems are discussed.

Source record↗

A Robust Locally Preconditioned Semi-Coarsening Multigrid Algorithm for the 2-D Navier-Stokes Equations

The goal of this thesis is to develop an efficient and robust locally preconditioned semi-coarsening multigrid algorithm for the two-dimensional Navier-Stokes equations. This thesis examines the performance of the multigrid algorithm with local preconditioning for an upwind-discretization of the Navier-Stokes equations. A block Jacobi iterative scheme is used because of its high frequency error mode damping ability. At low Mach numbers, the performance of a flux preconditioner is investigated. The flux preconditioner utilizes a new limiting technique based on local information that was developed by Siu. Full-coarsening and-semi-coarsening are examined as well as the multigrid V-cycle and full multigrid. The numerical tests were performed on a NACA 0012 airfoil at a range of Mach numbers. The tests show that semi-coarsening with flux preconditioning is the most efficient and robust combination of coarsening strategy, and iterative scheme - especially at low Mach numbers.

Cain, Michael D.↗

Time integration algorithms for the two-dimensional Euler equations on unstructured meshes

Explicit and implicit time integration algorithms for the two-dimensional Euler equations on unstructured grids are presented. Both cell-centered and cell-vertex finite volume upwind schemes utilizing Roe's approximate Riemann solver are developed. For the cell-vertex scheme, a four-stage Runge-Kutta time integration, a fourstage Runge-Kutta time integration with implicit residual averaging, a point Jacobi method, a symmetric point Gauss-Seidel method and two methods utilizing preconditioned sparse matrix solvers are presented. For the cell-centered scheme, a Runge-Kutta scheme, an implicit tridiagonal relaxation scheme modeled after line Gauss-Seidel, a fully implicit lower-upper (LU) decomposition, and a hybrid scheme utilizing both Runge-Kutta and LU methods are presented. A reverse Cuthill-McKee renumbering scheme is employed for the direct solver to decrease CPU time by reducing the fill of the Jacobian matrix. A comparison of the various time integration schemes is made for both first-order and higher order accurate solutions using several mesh sizes, higher order accuracy is achieved by using multidimensional monotone linear reconstruction procedures. The results obtained for a transonic flow over a circular arc suggest that the preconditioned sparse matrix solvers perform better than the other methods as the number of elements in the mesh increases.

Slack, David C.↗

Comparison of Implicit Schemes for the Incompressible Navier-Stokes Equations

For a computational flow simulation tool to be useful in a design environment, it must be very robust and efficient. To develop such a tool for incompressible flow applications, a number of different implicit schemes are compared for several two-dimensional flow problems in the current study. The schemes include Point-Jacobi relaxation, Gauss-Seidel line relaxation, incomplete lower-upper decomposition, and the generalized minimum residual method preconditioned with each of the three other schemes. The efficiency of the schemes is measured in terms of the computing time required to obtain a steady-state solution for the laminar flow over a backward-facing step, the flow over a NACA 4412 airfoil, and the flow over a three-element airfoil using overset grids. The flow solver used in the study is the INS2D code that solves the incompressible Navier-Stokes equations using the method of artificial compressibility and upwind differencing of the convective terms. The results show that the generalized minimum residual method preconditioned with the incomplete lower-upper factorization outperforms all other methods by at least a factor of 2.

Rogers, Stuart E.↗