Simple and efficient GPU parallelization of existing H-Matrix accelerated BEM code

In this paper, we demonstrate how GPU-accelerated BEM routines can be used in a simple black-box fashion to accelerate fast boundary element formulations based on Hierarchical Matrices (H-Matrices) with ACA (Adaptive Cross Approximation). In particular, we focus on the expensive evaluation of the discrete weak form of boundary operators associated with the Laplace and the Helmholtz equation in three space dimensions. The method is based on offloading the CPU assembly of elements during the ACA assembly onto a GPU device and to use threading strategies across ACA blocks to create sufficient workload for the GPU. The proposed GPU strategy is designed such that it can be implemented in existing code with minimal changes to the surrounding application structure. This is in particular interesting for existing legacy code that is not from the ground-up designed with GPU computing in mind. Our benchmark study gives realistic impressions of the benefits of GPU-accelerated BEM simulations by using state-of-the-art multi-threaded computations on modern high-performance CPUs as a reference, rather than drawing synthetic comparisons with single-threaded codes. Speed-up plots illustrate that performance gains up to a factor of 5.5 could be realized with GPU computing under these conditions. This refers to a boundary element model with about 4 million unknowns, whose H-Matrix weak form associated with a real-valued (Laplace) boundary operator is set up in only 100 minutes harnessing the two GPUs instead of 9 hours when using the 20 CPU cores at disposal only. The benchmark study is followed by a particularly demanding real-life application, where we compute the scattered high-frequency sound field of a submarine to demonstrate the increase in overall application performance from moving to a GPU-based ACA assembly

High-productivity, high-performance workflow for virus-scale electrostatic simulations with Bempp-Exafmm

Biomolecular electrostatics is key in protein function and the chemical processes affecting it.Implicit-solvent models expressed by the Poisson-Boltzmann (PB) equation can provide insights with less computational power than full atomistic models, making large-system studies -- at the scale of viruses, for example -- accessible to more researchers. This paper presents a high-productivity and high-performance computational workflow combining Exafmm, a fast multipole method (FMM) library, and Bempp, a Galerkin boundary element method (BEM) package. It integrates an easy-to-use Python interface with well-optimized computational kernels that are written in compiled languages. Researchers can run PB simulations interactively via Jupyter notebooks, enabling faster prototyping and analyzing. We provide results that showcase the capability of the software, confirm correctness, and evaluate its performance with problem sizes between 8,000 and 2 million boundary elements. A study comparing two variants of the boundary integral formulation in regards to algebraic conditioning showcases the power of this interactive computing platform to give useful answers with just a few lines of code. As a form of solution verification, mesh refinement studies with a spherical geometry as well as with a real biological structure (5PTI) confirm convergence at the expected $1/N$ rate, for $N$ boundary elements. Performance results include timings, breakdowns, and computational complexity. Exafmm offers evaluation speeds of just a few seconds for tens of millions of points, and $\mathcal{O}(N)$ scaling. This allowed computing the solvation free energy of a Zika virus, represented by 1.6 million atoms and 10 million boundary elements, at 80-min runtime on a single compute node (dual 20-core Intel Xeon Gold 6148). All results in the paper are presented with utmost care for reproducibility.Comment: 14 pages, 6 figure

A Study of Speed of the Boundary Element Method as applied to the Realtime Computational Simulation of Biological Organs

In this work, possibility of simulating biological organs in realtime using the Boundary Element Method (BEM) is investigated. Biological organs are assumed to follow linear elastostatic material behavior, and constant boundary element is the element type used. First, a Graphics Processing Unit (GPU) is used to speed up the BEM computations to achieve the realtime performance. Next, instead of the GPU, a computer cluster is used. Results indicate that BEM is fast enough to provide for realtime graphics if biological organs are assumed to follow linear elastostatic material behavior. Although the present work does not conduct any simulation using nonlinear material models, results from using the linear elastostatic material model imply that it would be difficult to obtain realtime performance if highly nonlinear material models that properly characterize biological organs are used. Although the use of BEM for the simulation of biological organs is not new, the results presented in the present study are not found elsewhere in the literature.Comment: preprint, draft, 2 tables, 47 references, 7 files, Codes that can solve three dimensional linear elastostatic problems using constant boundary elements (of triangular shape) while ignoring body forces are provided as supplementary files; codes are distributed under the MIT License in three versions: i) MATLAB version ii) Fortran 90 version (sequential code) iii) Fortran 90 version (parallel code

Spectral/hp element methods: recent developments, applications, and perspectives

The spectral/hp element method combines the geometric flexibility of the classical h-type finite element technique with the desirable numerical properties of spectral methods, employing high-degree piecewise polynomial basis functions on coarse finite element-type meshes. The spatial approximation is based upon orthogonal polynomials, such as Legendre or Chebychev polynomials, modified to accommodate C0-continuous expansions. Computationally and theoretically, by increasing the polynomial order p, high-precision solutions and fast convergence can be obtained and, in particular, under certain regularity assumptions an exponential reduction in approximation error between numerical and exact solutions can be achieved. This method has now been applied in many simulation studies of both fundamental and practical engineering flows. This paper briefly describes the formulation of the spectral/hp element method and provides an overview of its application to computational fluid dynamics. In particular, it focuses on the use the spectral/hp element method in transitional flows and ocean engineering. Finally, some of the major challenges to be overcome in order to use the spectral/hp element method in more complex science and engineering applications are discussed