Task-based adaptive multiresolution for time-space multi-scale reaction-diffusion systems on multi-core architectures

A new solver featuring time-space adaptation and error control has been recently introduced to tackle the numerical solution of stiff reaction-diffusion systems. Based on operator splitting, finite volume adaptive multiresolution and high order time integrators with specific stability properties for each operator, this strategy yields high computational efficiency for large multidimensional computations on standard architectures such as powerful workstations. However, the data structure of the original implementation, based on trees of pointers, provides limited opportunities for efficiency enhancements, while posing serious challenges in terms of parallel programming and load balancing. The present contribution proposes a new implementation of the whole set of numerical methods including Radau5 and ROCK4, relying on a fully different data structure together with the use of a specific library, TBB, for shared-memory, task-based parallelism with work-stealing. The performance of our implementation is assessed in a series of test-cases of increasing difficulty in two and three dimensions on multi-core and many-core architectures, demonstrating high scalability

Krylov implicit integration factor discontinuous Galerkin methods on sparse grids for high dimensional reaction-diffusion equations

Computational costs of numerically solving multidimensional partial differential equations (PDEs) increase significantly when the spatial dimensions of the PDEs are high, due to large number of spatial grid points. For multidimensional reaction-diffusion equations, stiffness of the system provides additional challenges for achieving efficient numerical simulations. In this paper, we propose a class of Krylov implicit integration factor (IIF) discontinuous Galerkin (DG) methods on sparse grids to solve reaction-diffusion equations on high spatial dimensions. The key ingredient of spatial DG discretization is the multiwavelet bases on nested sparse grids, which can significantly reduce the numbers of degrees of freedom. To deal with the stiffness of the DG spatial operator in discretizing reaction-diffusion equations, we apply the efficient IIF time discretization methods, which are a class of exponential integrators. Krylov subspace approximations are used to evaluate the large size matrix exponentials resulting from IIF schemes for solving PDEs on high spatial dimensions. Stability and error analysis for the semi-discrete scheme are performed. Numerical examples of both scalar equations and systems in two and three spatial dimensions are provided to demonstrate the accuracy and efficiency of the methods. The stiffness of the reaction-diffusion equations is resolved well and large time step size computations are obtained

The Investigation of Efficiency of Physical Phenomena Modelling Using Differential Equations on Distributed Systems

This work is dedicated to development of mathematical modelling software. In this dissertation numerical methods and algorithms are investigated in software making context. While applying a numerical method it is important to take into account the limited computer resources, the architecture of these resources and how do methods affect software robustness. Three main aspects of this investigation are that software implementation must be efficient, robust and be able to utilize specific hardware resources. The hardware specificity in this work is related to distributed computations of different types: single CPU with multiple cores, multiple CPUs with multiple cores and highly parallel multithreaded GPU device. The investigation is done in three directions: GPU usage for 3D FDTD calculations, FVM method usage to implement efficient calculations of a very specific heat transferring problem, and development of special techniques for software for specific bacteria self organization problem when the results are sensitive to numerical methods, initial data and even computer round-off errors. All these directions are dedicated to create correct technological components that make a software implementation robust and efficient. The time prediction model for 3D FDTD calculations is proposed, which lets to evaluate the efficiency of different GPUs. A reasonable speedup with GPU comparing to CPU is obtained. For FVM implementation the OpenFOAM open source software is selected as a basis for implementation of calculations and a few algorithms and their modifications to solve efficiency issues are proposed. The FVM parallel solver is implemented and analyzed, it is adapted to heterogeneous cluster Vilkas. To create robust software for simulation of bacteria self organization mathematically robust methods are applied and results are analyzed, the algorithm is modified for parallel computations

Uniformly convergent additive schemes for 2d singularly perturbed parabolic systems of reaction-diffusion type

In this work, we consider parabolic 2D singularly perturbed systems of reaction-diffusion type on a rectangle, in the simplest case that the diffusion parameter is the same for all equations of the system. The solution is approximated on a Shishkin mesh with two splitting or additive methods in time and standard central differences in space. It is proved that they are first-order in time and almost second-order in space uniformly convergent schemes. The additive schemes decouple the components of the vector solution at each time level of the discretization which makes the computation more efficient. Moreover, a multigrid algorithm is used to solve the resulting linear systems. Numerical results for some test problems are showed, which illustrate the theoretical results and the efficiency of the splitting and multigrid techniques

A uniformly convergent scheme to solve two-dimensional parabolic singularly perturbed systems of reaction-diffusion type with multiple diffusion parameters

In this work, we deal with solving two-dimensional parabolic singularly perturbed systems of reaction-diffusion type where the diffusion parameters at each equation of the system can be small and of different scale. In such case, in general, overlapping boundary layers appear at the boundary of the spatial domain and, because of this, special meshes are required to resolve them. The numerical scheme combines the central difference scheme to discretize in space and the fractional implicit Euler method together with a splitting by components to discretize in time. If the fully discrete scheme is defined on an adequate piecewise uniform Shishkin mesh in space then it is uniformly convergent of first order in time and of almost second order in space. Some numerical results illustrate the theoretical results. © 2020 John Wiley & Sons, Ltd