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At least 163 records · Page 9

Parallel performance investigations of an unstructured mesh Navier-Stokes solver

A Reynolds-averaged Navier-Stokes solver based on unstructured mesh techniques for analysis of high-lift configurations is described. The method makes use of an agglomeration multigrid solver for convergence acceleration. Implicit line-smoothing is employed to relieve the stiffness associated with highly stretched meshes. A GMRES technique is also implemented to speed convergence at the expense of additional memory usage. The solver is cache efficient and fully vectorizable, and is parallelized using a two-level hybrid MPI-OpenMP implementation suitable for shared and/or distributed memory architectures, as well as clusters of shared memory machines. Convergence and scalability results are illustrated for various high-lift cases.

Mavriplis, Dimitri J.↗

Semi-implicit continuum kinetic modeling of weakly collisional parallel transport in a magnetic mirror

We present implicit-explicit (IMEX) kinetic simulations of weakly collisional parallel plasma transport in magnetic mirror configurations using the continuum code COGENT. The numerical scheme employs a Jacobian-free Newton–Krylov method with algebraic multigrid preconditioning to overcome the severe time step limitations imposed by strong mirror forces in fully explicit schemes. Applied to parameters relevant to the Wisconsin HTS Axisymmetric Mirror experiment, the IMEX approach enables time steps up to 2.5×10 4 times larger than those permitted by explicit methods, resulting in a 2500× speedup in 1D–2V simulations of parallel transport with kinetic ions and Boltzmann electrons. Additionally, a reduced bounce-averaged model for a square mirror is implemented to support the computationally intensive fully kinetic simulations. The bounce-averaged formulation is used to evaluate the numerical convergence of the velocity-space discretization algorithms and to assess the role of the collision model by comparing simulations employing the nonlinear Fokker–Planck and the simplified Lenard–Bernstein–Dougherty collision operators.

Collision theories↗

Solving Upwind-Biased Discretizations: Multigrid Solver Using Semicoarsening - 2

This paper studies a novel multigrid approach to the solution for a second order upwind biased discretization of the convection equation in two dimensions. This approach is based on semi-coarsening and well balanced explicit correction terms added to coarse-grid operators to maintain on coarse-grid the same cross-characteristic interaction as on the target (fine) grid. Colored relaxation schemes are used on all the levels allowing a very efficient parallel implementation. The results of the numerical tests can be summarized as follows: 1) The residual asymptotic convergence rate of the proposed V(0, 2) multigrid cycle is about 3 per cycle. This convergence rate far surpasses the theoretical limit (4/3) predicted for standard multigrid algorithms using full coarsening. The reported efficiency does not deteriorate with increasing the cycle, depth (number of levels) and/or refining the target-grid mesh spacing. 2) The full multi-grid algorithm (FMG) with two V(0, 2) cycles on the target grid and just one V(0, 2) cycle on all the coarse grids always provides an approximate solution with the algebraic error less than the discretization error. Estimates of the total work in the FMG algorithm are ranged between 18 and 30 minimal work units (depending on the target (discretizatioin). Thus, the overall efficiency of the FMG solver closely approaches (if does not achieve) the goal of the textbook multigrid efficiency. 3) A novel approach to deriving a discrete solution approximating the true continuous solution with a relative accuracy given in advance is developed. An adaptive multigrid algorithm (AMA) using comparison of the solutions on two successive target grids to estimate the accuracy of the current target-grid solution is defined. A desired relative accuracy is accepted as an input parameter. The final target grid on which this accuracy can be achieved is chosen automatically in the solution process. the actual relative accuracy of the discrete solution approximation obtained by AMA is always better than the required accuracy; the computational complexity of the AMA algorithm is (nearly) optimal (comparable with the complexity of the FMG algorithm applied to solve the problem on the optimally spaced target grid).

Diskin, Boris↗

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↗

Simulating coupled surface–subsurface flows with ParFlow v3.5.0: capabilities, applications, and ongoing development of an open-source, massively parallel, integrated hydrologic model

Surface flow and subsurface flow constitute a naturally linked hydrologic continuum that has not traditionally been simulated in an integrated fashion. Recognizing the interactions between these systems has encouraged the development of integrated hydrologic models (IHMs) capable of treating surface and subsurface systems as a single integrated resource. IHMs are dynamically evolving with improvements in technology, and the extent of their current capabilities are often only known to the developers and not general users. This article provides an overview of the core functionality, capability, applications, and ongoing development of one open-source IHM, ParFlow. ParFlow is a parallel, integrated, hydrologic model that simulates surface and subsurface flows. ParFlow solves the Richards equation for three-dimensional variably saturated groundwater flow and the two-dimensional kinematic wave approximation of the shallow water equations for overland flow. The model employs a conservative centered finite-difference scheme and a conservative finite-volume method for subsurface flow and transport, respectively. ParFlow uses multigrid-preconditioned Krylov and Newton–Krylov methods to solve the linear and nonlinear systems within each time step of the flow simulations. The code has demonstrated very efficient parallel solution capabilities. ParFlow has been coupled to geochemical reaction, land surface (e.g., the Common Land Model), and atmospheric models to study the interactions among the subsurface, land surface, and atmosphere systems across different spatial scales. This overview focuses on the current capabilities of the code, the core simulation engine, and the primary couplings of the subsurface model to other codes, taking a high-level perspective.

58 GEOSCIENCES↗

Diffusion Synthetic Acceleration for Heterogeneous Domains, Compatible with Voids

A standard approach to solving the S N transport equations is to use source iteration with diffusion synthetic acceleration (DSA). Although this approach is widely used and effective on many problems, there remain some practical issues with DSA preconditioning, particularly on highly heterogeneous domains. For large-scale parallel simulation, it is critical that both (a) preconditioned source iteration converges rapidly and (b) the action of the DSA preconditioner can be applied using fast, scalable solvers, such as algebraic multigrid (AMG). For heterogeneous domains, these two interests can be at odds. In particular, there exist DSA diffusion discretizations that can be solved rapidly using AMG, but they do not always yield robust/fast convergence of the larger source iteration. Conversely, there exist robust DSA discretizations where source iteration converges rapidly on difficult heterogeneous problems, but fast parallel solvers like AMG tend to struggle applying the action of such operators. Moreover, very few current methods for the solution of deterministic transport are compatible with voids. This paper develops a new heterogeneous DSA preconditioner based on only preconditioning the optically thick subdomains. The resulting method proves robust on a variety of heterogeneous transport problems, including a linearized hohlraum mesh related to inertial confinement fusion. Moreover, the action of the preconditioner is easily computed using O(1) AMG iterations, convergence of the transport iteration typically requires 2 to 5× fewer iterations than current state-of-the-art “full” DSA, and the proposed method is trivially compatible with voids. On the hohlraum problem, rapid convergence is obtained by preconditioning less than 3% of the mesh elements with five to ten AMG iterations.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

A Conforming Multigrid Method for the Pure Traction Problem of Linear Elasticity: Mixed Formulation

A multigrid method using conforming P-1 finite element is developed for the two-dimensional pure traction boundary value problem of linear elasticity. The convergence is uniform even as the material becomes nearly incompressible. A heuristic argument for acceleration of the multigrid method is discussed as well. Numerical results with and without this acceleration as well as performance estimates on a parallel computer are included.

Lee, Chang-Ock↗

Tokamak disruption simulation

UT contribution in this Tokamak Disruption Simulation (TDS) is to develop a parallel high‐order hybridized Discontinuous Galerkin (HDG) methods for large‐s cale MHD simulations. The following are the major goals: 1) Construction of HDG methods for linearized MHD, 2) Rigorous analysis for the HDG formulations for linearized MHD, 3) 2D and 3D simulations to verify the convergent of the HDG methods for linearized MHD, 4) multigrid solvers/preconditioners for HDG formulations, 5) HDG for reconnection problems, 6) Divergence cleaning with HDG, 7) HDG formulations for nonlinear MHD, 8) Picard fixed point HDG approach, 9) IMEX HDG‐DG for nonlinear HDG; 10) parallel large‐scale HDG for linear and nonlinear MHD simulations.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Time-periodic steady-state solution of fluid-structure interaction and cardiac flow problems through multigrid-reduction-in-time

In this study, a time-periodic MGRIT algorithm is proposed as a means to reduce the time-to-solution of numerical algorithms by exploiting the time periodicity inherent to many applications in science and engineering. The time-periodic MGRIT algorithm is applied to a variety of linear and nonlinear single- and multiphysics problems that are periodic-in-time. It is demonstrated that the proposed parallel-in-time algorithm can obtain the same time-periodic steady-state solution as sequential time-stepping. It is shown that the required number of MGRIT iterations can be estimated a priori and that the new MGRIT variant can significantly and consistently reduce the time-to-solution compared to sequential time-stepping, irrespective of the number of dimensions, linear or nonlinear PDE models, single-physics or coupled problems and the employed computing resources. The numerical experiments demonstrate that the time-periodic MGRIT algorithm enables a greater level of parallelism yielding faster turnaround, and thus, facilitating more complex and more realistic problems to be solved.

97 MATHEMATICS AND COMPUTING↗

Conduct of the International Multigrid Conference

The 1983 International Multigrid Conference was held at Colorado's Copper Mountain Ski Resort, April 5-8. It was organized jointly by the Institute for Computational Studies at Colorado State University, U.S.A., and the Gasellschaft fur Mathematik und Datenverarbeitung Bonn, F.R. Germany, and was sponsored by the Air Force Office of Sponsored Research and National Aeronautics and Space Administration Headquarters. The conference was attended by 80 scientists, divided by institution almost equally into private industry, research laboratories, and academia. Fifteen attendees came from countries other than the U.S.A. In addition to the fruitful discussions, the most significant factor of the conference was of course the lectures. The lecturers include most of the leaders in the field of multigrid research. The program offered a nice integrated blend of theory, numerical studies, basic research, and applications. Some of the new areas of research that have surfaced since the Koln-Porz conference include: the algebraic multigrid approach; multigrid treatment of Euler equations for inviscid fluid flow problems; 3-D problems; and the application of MG methods on vector and parallel computers.

Mccormick, S.↗

Incremental Parallelization of Non-Data-Parallel Programs Using the Charon Message-Passing Library

Message passing is among the most popular techniques for parallelizing scientific programs on distributed-memory architectures. The reasons for its success are wide availability (MPI), efficiency, and full tuning control provided to the programmer. A major drawback, however, is that incremental parallelization, as offered by compiler directives, is not generally possible, because all data structures have to be changed throughout the program simultaneously. Charon remedies this situation through mappings between distributed and non-distributed data. It allows breaking up the parallelization into small steps, guaranteeing correctness at every stage. Several tools are available to help convert legacy codes into high-performance message-passing programs. They usually target data-parallel applications, whose loops carrying most of the work can be distributed among all processors without much dependency analysis. Others do a full dependency analysis and then convert the code virtually automatically. Even more toolkits are available that aid construction from scratch of message passing programs. None, however, allows piecemeal translation of codes with complex data dependencies (i.e. non-data-parallel programs) into message passing codes. The Charon library (available in both C and Fortran) provides incremental parallelization capabilities by linking legacy code arrays with distributed arrays. During the conversion process, non-distributed and distributed arrays exist side by side, and simple mapping functions allow the programmer to switch between the two in any location in the program. Charon also provides wrapper functions that leave the structure of the legacy code intact, but that allow execution on truly distributed data. Finally, the library provides a rich set of communication functions that support virtually all patterns of remote data demands in realistic structured grid scientific programs, including transposition, nearest-neighbor communication, pipelining, gather/scatter, and redistribution. At the end of the conversion process most intermediate Charon function calls will have been removed, the non-distributed arrays will have been deleted, and virtually the only remaining Charon functions calls are the high-level, highly optimized communications. Distribution of the data is under complete control of the programmer, although a wide range of useful distributions is easily available through predefined functions. A crucial aspect of the library is that it does not allocate space for distributed arrays, but accepts programmer-specified memory. This has two major consequences. First, codes parallelized using Charon do not suffer from encapsulation; user data is always directly accessible. This provides high efficiency, and also retains the possibility of using message passing directly for highly irregular communications. Second, non-distributed arrays can be interpreted as (trivial) distributions in the Charon sense, which allows them to be mapped to truly distributed arrays, and vice versa. This is the mechanism that enables incremental parallelization. In this paper we provide a brief introduction of the library and then focus on the actual steps in the parallelization process, using some representative examples from, among others, the NAS Parallel Benchmarks. We show how a complicated two-dimensional pipeline-the prototypical non-data-parallel algorithm- can be constructed with ease. To demonstrate the flexibility of the library, we give examples of the stepwise, efficient parallel implementation of nonlocal boundary conditions common in aircraft simulations, as well as the construction of the sequence of grids required for multigrid.

VanderWijngaart, Rob F.↗

Development of a Navier-Stokes algorithm for parallel-processing supercomputers

An explicit flow solver, applicable to the hierarchy of model equations ranging from Euler to full Navier-Stokes, is combined with several techniques designed to reduce computational expense. The computational domain consists of local grid refinements embedded in a global coarse mesh, where the locations of these refinements are defined by the physics of the flow. Flow characteristics are also used to determine which set of model equations is appropriate for solution in each region, thereby reducing not only the number of grid points at which the solution must be obtained, but also the computational effort required to get that solution. Acceleration to steady-state is achieved by applying multigrid on each of the subgrids, regardless of the particular model equations being solved. Since each of these components is explicit, advantage can readily be taken of the vector- and parallel-processing capabilities of machines such as the Cray X-MP and Cray-2.

Swisshelm, Julie M.↗

Development of an aerodynamics algorithm for parallel-processing supercomputers

An explicit flow solver, applicable to the hierarchy of model equations ranging from Euler to full Navier-Stokes, is combined with several techniques designed to reduce computational expense. The computational domain consists of local grid refinements embedded in a global coarse mesh, where the locations of these refinements are defined by the physics of the flow. Flow characteristics are also used to determine which set of model equations is appropriate for solution in each region, thereby reducing not only the number of grid points at which the solution must be obtained, but also the computational effort required to get that solution. Acceleration to steady-state is achieved by applying multigrid on each of the subgrids, regardless of the particular model equations being solved. Since each of these components is explicit, advantage can readily be taken of the vector- and parallel-processing capabilities of machines such as the Cray X-MP and Cray-2.

Swisshelm, Julie M.↗

Multilevel acceleration of scattering-source iterations with application to electron transport

Acceleration/preconditioning strategies available in the SCEPTRE radiation transport code are described. A flexible transport synthetic acceleration (TSA) algorithm that uses a low-order discrete-ordinates (S N ) or spherical-harmonics (P N ) solve to accelerate convergence of a high-order S N source-iteration (SI) solve is described. Convergence of the low-order solves can be further accelerated by applying off-the-shelf incomplete-factorization or algebraic-multigrid methods. Also available is an algorithm that uses a generalized minimum residual (GMRES) iterative method rather than SI for convergence, using a parallel sweep-based solver to build up a Krylov subspace. TSA has been applied as a preconditioner to accelerate the convergence of the GMRES iterations. The methods are applied to several problems involving electron transport and problems with artificial cross sections with large scattering ratios. These methods were compared and evaluated by considering material discontinuities and scattering anisotropy. Observed accelerations obtained are highly problem dependent, but speedup factors around 10 have been observed in typical applications.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Multitasking a three-dimensional Navier-Stokes algorithm on the Cray-2

A three-dimensional computational aerodynamics algorithm has been multitasked for efficient parallel execution on the Cray-2. It provides a means for examining the multitasking performance of a complete CFD application code. An embedded zonal multigrid scheme is used to solve the Reynolds-averaged Navier-Stokes equations for an internal flow model problem. The explicit nature of each component of the method allows a spatial partitioning of the computational domain to achieve a well-balanced task load for MIMD computers with vector-processing capability. Experiments have been conducted with both two- and three-dimensional multitasked cases. The best speedup attained by an individual task group was 3.54 on four processors of the Cray-2, while the entire solver yielded a speedup of 2.67 on four processors for the three-dimensional case. The multiprocessing efficiency of various types of computational tasks is examined, performance on two Cray-2s with different memory access speeds is compared, and extrapolation to larger problems is discussed.

Swisshelm, Julie M.↗

A Simple, Scalable Large Deformation Solid Mechanics Implementation in the MOOSE Framework

This article describes a large deformation solid mechanics solver implemented as part of the freely available and open source MOOSE finite element simulation framework. The article documents the choices made in developing the solid mechanics framework and describes novel formulations for the gradient operator and constitutive modeling framework made to simplify implementations of different coordinate systems, stabilized gradient operators, and different constitutive model inputs and outputs. In the process, the article describes a new formulation that casts objective integration of the Cauchy stress as a linear transformation of the small stress rate. Finally, the article presents key implementation details and examines the parallel efficiency of the solid mechanics solver implemented in MOOSE. The implementation retains a good weak scaling efficiency beyond 1,000 parallel processes. The article includes a discussion of the factors limiting the parallel efficiency of implicit, large deformation solid mechanics codes on current high-performance computers, with the main current limitation being the scalability of the algebraic multigrid methods used to solve the linearized equilibrium equations.

Applied computing → Computer-aided design↗

AIR Algebraic Multigrid for a Space-Time Hybridizable Discontinuous Galerkin Discretization of Advection(-Diffusion)

This article investigates the efficiency, robustness, and scalability of approximate ideal restriction (AIR) algebraic multigrid as a preconditioner in the all-at-once solution of a space-time hybridizable discontinuous Galerkin discretization of advection-dominated flows. The motivation for this study is that the time-dependent advection-diffusion equation can be seen as a “steady” advection-diffusion problem in $(d+1)$-dimensions and AIR has been shown to be a robust solver for steady advection-dominated problems. Numerical examples demonstrate the effectiveness of AIR as a preconditioner for advection-diffusion problems on fixed and time-dependent domains, using both slab-by-slab and all-at-once space-time discretizations, and in the context of uniform and space-time adaptive mesh refinement. A closer look at the geometric coarsening structure that arises in AIR also explains why AIR can provide robust, scalable, space-time convergence on advective and hyperbolic problems, while most multilevel parallel-in-time schemes struggle with such problems.

97 MATHEMATICS AND COMPUTING↗