Efficient Multigrid Preconditioners for Atmospheric Flow Simulations at High Aspect Ratio

Many problems in fluid modelling require the efficient solution of highly anisotropic elliptic partial differential equations (PDEs) in "flat" domains. For example, in numerical weather- and climate-prediction an elliptic PDE for the pressure correction has to be solved at every time step in a thin spherical shell representing the global atmosphere. This elliptic solve can be one of the computationally most demanding components in semi-implicit semi-Lagrangian time stepping methods which are very popular as they allow for larger model time steps and better overall performance. With increasing model resolution, algorithmically efficient and scalable algorithms are essential to run the code under tight operational time constraints. We discuss the theory and practical application of bespoke geometric multigrid preconditioners for equations of this type. The algorithms deal with the strong anisotropy in the vertical direction by using the tensor-product approach originally analysed by B\"{o}rm and Hiptmair [Numer. Algorithms, 26/3 (2001), pp. 219-234]. We extend the analysis to three dimensions under slightly weakened assumptions, and numerically demonstrate its efficiency for the solution of the elliptic PDE for the global pressure correction in atmospheric forecast models. For this we compare the performance of different multigrid preconditioners on a tensor-product grid with a semi-structured and quasi-uniform horizontal mesh and a one dimensional vertical grid. The code is implemented in the Distributed and Unified Numerics Environment (DUNE), which provides an easy-to-use and scalable environment for algorithms operating on tensor-product grids. Parallel scalability of our solvers on up to 20,480 cores is demonstrated on the HECToR supercomputer.Comment: 22 pages, 6 Figures, 2 Table

Preparing sparse solvers for exascale computing.

Sparse solvers provide essential functionality for a wide variety of scientific applications. Highly parallel sparse solvers are essential for continuing advances in high-fidelity, multi-physics and multi-scale simulations, especially as we target exascale platforms. This paper describes the challenges, strategies and progress of the US Department of Energy Exascale Computing project towards providing sparse solvers for exascale computing platforms. We address the demands of systems with thousands of high-performance node devices where exposing concurrency, hiding latency and creating alternative algorithms become essential. The efforts described here are works in progress, highlighting current success and upcoming challenges. This article is part of a discussion meeting issue 'Numerical algorithms for high-performance computational science'

High Order Cell-Centered Lagrangian-Type Finite Volume Schemes with Time-Accurate Local Time Stepping on Unstructured Triangular Meshes

We present a novel cell-centered direct Arbitrary-Lagrangian-Eulerian (ALE) finite volume scheme on unstructured triangular meshes that is high order accurate in space and time and that also allows for time-accurate local time stepping (LTS). The new scheme uses the following basic ingredients: a high order WENO reconstruction in space on unstructured meshes, an element-local high-order accurate space-time Galerkin predictor that performs the time evolution of the reconstructed polynomials within each element, the computation of numerical ALE fluxes at the moving element interfaces through approximate Riemann solvers, and a one-step finite volume scheme for the time update which is directly based on the integral form of the conservation equations in space-time. The inclusion of the LTS algorithm requires a number of crucial extensions, such as a proper scheduling criterion for the time update of each element and for each node; a virtual projection of the elements contained in the reconstruction stencils of the element that has to perform the WENO reconstruction; and the proper computation of the fluxes through the space-time boundary surfaces that will inevitably contain hanging nodes in time due to the LTS algorithm. We have validated our new unstructured Lagrangian LTS approach over a wide sample of test cases solving the Euler equations of compressible gasdynamics in two space dimensions, including shock tube problems, cylindrical explosion problems, as well as specific tests typically adopted in Lagrangian calculations, such as the Kidder and the Saltzman problem. When compared to the traditional global time stepping (GTS) method, the newly proposed LTS algorithm allows to reduce the number of element updates in a given simulation by a factor that may depend on the complexity of the dynamics, but which can be as large as 4.7.Comment: 31 pages, 13 figure

Matrix-free GPU implementation of a preconditioned conjugate gradient solver for anisotropic elliptic PDEs

Many problems in geophysical and atmospheric modelling require the fast solution of elliptic partial differential equations (PDEs) in "flat" three dimensional geometries. In particular, an anisotropic elliptic PDE for the pressure correction has to be solved at every time step in the dynamical core of many numerical weather prediction models, and equations of a very similar structure arise in global ocean models, subsurface flow simulations and gas and oil reservoir modelling. The elliptic solve is often the bottleneck of the forecast, and an algorithmically optimal method has to be used and implemented efficiently. Graphics Processing Units have been shown to be highly efficient for a wide range of applications in scientific computing, and recently iterative solvers have been parallelised on these architectures. We describe the GPU implementation and optimisation of a Preconditioned Conjugate Gradient (PCG) algorithm for the solution of a three dimensional anisotropic elliptic PDE for the pressure correction in NWP. Our implementation exploits the strong vertical anisotropy of the elliptic operator in the construction of a suitable preconditioner. As the algorithm is memory bound, performance can be improved significantly by reducing the amount of global memory access. We achieve this by using a matrix-free implementation which does not require explicit storage of the matrix and instead recalculates the local stencil. Global memory access can also be reduced by rewriting the algorithm using loop fusion and we show that this further reduces the runtime on the GPU. We demonstrate the performance of our matrix-free GPU code by comparing it to a sequential CPU implementation and to a matrix-explicit GPU code which uses existing libraries. The absolute performance of the algorithm for different problem sizes is quantified in terms of floating point throughput and global memory bandwidth.Comment: 18 pages, 7 figure

Parallel unstructured solvers for linear partial differential equations

This thesis presents the development of a parallel algorithm to solve symmetric systems of linear equations and the computational implementation of a parallel partial differential equations solver for unstructured meshes. The proposed method, called distributive conjugate gradient - DCG, is based on a single-level domain decomposition method and the conjugate gradient method to obtain a highly scalable parallel algorithm. An overview on methods for the discretization of domains and partial differential equations is given. The partition and refinement of meshes is discussed and the formulation of the weighted residual method for two- and three-dimensions presented. Some of the methods to solve systems of linear equations are introduced, highlighting the conjugate gradient method and domain decomposition methods. A parallel unstructured PDE solver is proposed and its actual implementation presented. Emphasis is given to the data partition adopted and the scheme used for communication among adjacent subdomains is explained. A series of experiments in processor scalability is also reported. The derivation and parallelization of DCG are presented and the method validated throughout numerical experiments. The method capabilities and limitations were investigated by the solution of the Poisson equation with various source terms. The experimental results obtained using the parallel solver developed as part of this work show that the algorithm presented is accurate and highly scalable, achieving roughly linear parallel speed-up in many of the cases tested

High order direct Arbitrary-Lagrangian-Eulerian schemes on moving Voronoi meshes with topology changes

We present a new family of very high order accurate direct Arbitrary-Lagrangian-Eulerian (ALE) Finite Volume (FV) and Discontinuous Galerkin (DG) schemes for the solution of nonlinear hyperbolic PDE systems on moving 2D Voronoi meshes that are regenerated at each time step and which explicitly allow topology changes in time. The Voronoi tessellations are obtained from a set of generator points that move with the local fluid velocity. We employ an AREPO-type approach, which rapidly rebuilds a new high quality mesh rearranging the element shapes and neighbors in order to guarantee a robust mesh evolution even for vortex flows and very long simulation times. The old and new Voronoi elements associated to the same generator are connected to construct closed space--time control volumes, whose bottom and top faces may be polygons with a different number of sides. We also incorporate degenerate space--time sliver elements, needed to fill the space--time holes that arise because of topology changes. The final ALE FV-DG scheme is obtained by a redesign of the fully discrete direct ALE schemes of Boscheri and Dumbser, extended here to moving Voronoi meshes and space--time sliver elements. Our new numerical scheme is based on the integration over arbitrary shaped closed space--time control volumes combined with a fully-discrete space--time conservation formulation of the governing PDE system. In this way the discrete solution is conservative and satisfies the GCL by construction. Numerical convergence studies as well as a large set of benchmarks for hydrodynamics and magnetohydrodynamics (MHD) demonstrate the accuracy and robustness of the proposed method. Our numerical results clearly show that the new combination of very high order schemes with regenerated meshes with topology changes lead to substantial improvements compared to direct ALE methods on conforming meshes