A GPU-Accelerated Fast Multipole Method for GROMACS:Performance and Accuracy

Eddy current nondestructive evaluation (NDE) of airframe structures involves the detection of electromagnetic field irregularities due to non-conducting inhomogeneities in an electrically conducting material. Usually, the eddy current NDE problem can be formulated by the boundary integral equations (BIE) and discretized into matrix equations by the method of moments (MoM) or the boundary element method (BEM). The fast multipole method (FMM) is a well-established and effective method for accelerating numerical solutions of the matrix equations. Accelerated by the FMM, the BIE method can now solve large-scale electromagnetic wave propagation and diffusion problems. The traditional BIE method requires O(N) operations to compute the system of equations and another O(N) operations to solve the system using direct solvers, with N being the number of unknowns; in contrast, the BIE method accelerated by the two-level FMM can potentially reduce the operations and memory requirement to O(N). Moreover, several approaches have been proposed for the field calculation in the presence of flaws in three dimensional NDE; however, seldom work has been done in applying efficient methods to seek rapid solution in eddy current NDE simulation. As elaborated in the dissertation, we introduce a fast multipole BIE method for two-dimensional diffusive scalar problem and an efficient BIE method for three-dimensional eddy current NDE. Firstly, we work with the two-dimensional Helmholtz equation with a complex wave number for non-trivial boundary geometry. We describe the FMM acceleration procedure of the BIE method and its features briefly, explaining that the FMM is not only efficient in meshing complicated geometries, accurate for solving singular fields or

A Cuda Fast Multipole Method with Highly Efficient M2L Far Field Evaluation

Though computational molecular dynamics is an effective tool for nano-scale phenomenon analysis, computational costs associated with its computer simulation are extremely high. There are two major computational steps associated with computer simulation of dynamics of molecular structures. They are calculation of interatomic forces and formation and solution of the equations of motion. Currently, these two computational steps are treated separately in most commonly-used methods. For example, Fast Multipole Method (FMM) and Cell Multipole Method (CMM) have been used for calculation of interatomic forces, and Cartesian Coordinate Method (CCM) and Internal Coordinate Molecular Dynamics Method (ICMD) have been created for the formation and solution of equations of motion of an atomistic molecular system. In this paper, a new procedure is presented through a proper integration between multibody molecular algorithms (MMA) and fast multipole methods to improve computational efficiency for computer simulation of the dynamical behaviors of multibody molecular structures in polymers and biopolymers. For the computational costs associated with interatomic forces, a fast multipole method is used to calculate the interatomic forces due to the potentials. For the computational costs associated with formation and solution of equations of motion, a multibody molecular algorithm developed by the author in his previous work will be utilized to integrate with fast multipole methods. The algorithm significantly improves computational efficiency when comparing with its counterpart procedures. The fast multipole method begins by scaling all atoms into a box with coordinate ranges to ensure numerical stability of subsequent operations. The parent box is then divided into half in the direction of each Cartesian axis and each child box is then subdivided to form a computational family tree. The flow of calculations is carried out along the tree structure with five passes. The fast multipole method has been improved and modified to achieve better effectiveness and higher efficiency since it was created. The multibody molecular algorithm starts with numbering subsets, forming bond graph, and developing three computing passes along the tree structure of an atomistic molecular system. Computing data flows in the fast multipole method and the multibody molecular algorithm will properly line up with the parent-child recursive relationship along the configuration of the tree structure due to linear recursive natures of both fast multipole method and multibody molecular algorithm. Then the time spent on the recursive simulation passes in the fast multipole method for computing forces may overlap with the time spent on the three recursive computational passes in the multibody molecular algorithm for forming and solving equations of motion.

Abstract: In this paper, a half space adaptive fast multipole boundary facemethod (FMBFM) is presented for solving the three-dimensional half space ex-terior acoustic problems. In the presented method, the Burton-Miller equationbased on the conventional boundary integral equation (CBIE) and its hyper-singularboundary integral equation (HBIE) is used to deal with the fictitious eigenfrequen-cies problem. The half space Green’s function is employed, thus the tree structurein the fast multipole method can be used only for the real domain. The higher orderelements and an adaptive tree structure are used to improve the efficiency of theFMBFM. This half space adaptive FMBFM for half space acoustic problems is anextension of the adaptive FMBFM for full space acoustic problems developed bythe authors. Numerical examples for half space acoustic problems in this paperdemonstrate the efficiency and validity of this method.Keywords: fast multipole boundary face method, Burton-Miller equation, acous-tic problems, half space, modified hyper-singular boundary integral equation1 IntroductionAcoustic problems in half space are a major subject in engineering. Many researchworks have been done on this aspect (Seybert et al., 1988; Secgin et al., 2010; Caoet al., 2010). The half space Green’s function (Seybert et al., 1988) can be appliedby adding the source solution at the image point to the original full-space Green’sfunction for dealing with half space problems. Sound source localization and iden-tification of a refrigerator were accomplished by using the half space boundaryelement method (BEM) (Secgin et al., 2010). Using the half space Green’s func-tion, the discretization of the rigid infinite plane is removed and only the boundaries

Standard numerical models in acoustics rely on the isentropic Helmholtz equation. Its derivation assumes adiabatic and reversible, i.e., dissipation-free, wave propagation. Sound waves in fluids are, however, subject to viscous and thermal losses. These losses originate from viscous friction and heat conduction, leading to the formation of acoustic boundary layers. Considering these effects becomes significant in setups with acoustic cavities of similar dimension as the boundary layers. Recently, boundary element methods (BEM) accounting for the viscothermal dissipation have been proposed. These methods limit the discretization to the surface of the fluid domain and require significantly fewer degrees of freedom than comparable finite element models. However, the BEM coefficient matrices are fully populated, resulting in high computational costs and storage requirements. This study develops a new BEM formulation for acoustics in viscothermal fluids that uses the fast multipole method - a low-rank approximation technique based on a hierarchical subdivision of the computational domain - to alleviate this shortcoming. It is shown that the fast viscothermal BEM improves the algorithmic complexity over the conventional formulation, reducing both the memory requirements and solution time. The results indicate good scalability of the method making it feasible for larger applications such as acoustic metamaterials.

Fast multipole singular boundary method for Stokes flow problems

In dislocation dynamics (DD) simulations, the most computationally intensive step is the evaluation of the elastic interaction forces among dislocation ensembles. Because the pair-wise interaction between dislocations is long-range, this force calculation step can be significantly accelerated by the fast multipole method (FMM). We implemented and compared four different methods in isotropic and anisotropic elastic media: one based on the Taylor series expansion (Taylor FMM), one based on the spherical harmonics expansion (Spherical FMM), one kernel-independent method based on the Chebyshev interpolation (Chebyshev FMM), and a new kernel-independent method that we call the Lagrange FMM. The Taylor FMM is an existing method, used in ParaDiS, one of the most popular DD simulation softwares. The Spherical FMM employs a more compact multipole representation than the Taylor FMM does and is thus more efficient. However, both the Taylor FMM and the Spherical FMM are difficult to derive in anisotropic elastic media because the interaction force is complex and has no closed analytical formula. The Chebyshev FMM requires only being able to evaluate the interaction between dislocations and thus can be applied easily in anisotropic elastic media. But it has a relatively large memory footprint, which limits its usage. The Lagrange FMM was designed to be a memory-efficient black-box method. Various numerical experiments are presented to demonstrate the convergence and the scalability of the four methods.

This paper presents flexible inner-outer Krylov subspace methods, which are implemented using the fast multipole method (FMM) for solving scattering problems with mixed dielectric and conducting object. The flexible Krylov subspace methods refer to a class of methods that accept variable preconditioning. To obtain the maximum efficiency of the inner-outer methods, it is desirable to compute the inner iterations with the least possible effort. Hence, generally, inaccurate matrix-vector multiplication (MVM) is performed in the inner solver within a short computation time. This is realized by using a particular feature of the multipole techniques. The accuracy and computational cost of the FMM can be controlled by appropriately selecting the truncation number, which indicates the number of multipoles used to express far-field interactions. On the basis of the abovementioned fact, we construct a less-accurate but much cheaper version of the FMM by intentionally setting the truncation number to a sufficiently low value, and then use it for the computation of inaccurate MVM in the inner solver. However, there exists no definite rule for determining the suitable level of accuracy for the FMM within the inner solver. The main focus of this study is to clarify the relationship between the overall efficiency of the flexible inner-outer Krylov solver and the accuracy of the FMM within the inner solver. Numerical experiments reveal that there exits an optimal accuracy level for the FMM within the inner solver, and that a moderately accurate FMM operator serves as the optimal preconditioner.

A numerical solution for the diffraction of linear waves around a vertical cylinder is presented in this paper using the fast multipole boundary element method (FMBEM). The fast multipole method (FMM) is employed to accelerate the traditional boundary element method. The accuracy and efficiency of the FMBEM for 2D Helmholtz equation is demonstrated, and it’s proved that this approach is suitable for solving large-scaled problems. In addition, numerical results of water dynamics coefficients, which are related to the diffraction problems of linear waves around a cylinder, are supplied in this paper.

The fast multipole method (FMM) is useful for solving electromagnetic scattering problems through integral equations. Some asymptotic laws are given for the truncation of the series involved in the FMM. Those laws were rigorously proved in Carayol (2002). For the first time, the accuracy of the widely used empirical formulas was studied mathematically. Our results also give some elements to understand the difference of FMM error due to the configuration of points in FMM boxes (connected to the term u/spl I.cap//spl middot/ v/spl I.cap/). We also derived in Carayol some consequences on the number of quadrature points needed for the numerical integrations in the FMM.

ICSM: An order [formula omitted] method for calculating electrostatic interactions added to TINKER

An adaptive expansion technique in the fast multipole method for 3D acoustics problems at low frequencies

In this work, a fast algorithm is proposed to evaluate the radiation properties of antennas near to or attached on a large-scale three-dimensional (3D) PEC object with arbitrary shape using the fast multipole method (FMM) and MRM. Similar to the conventional MRM, the PEC object under consideration is first divided into multiple regions depending on the position of the antenna in the new model. Then FMM is employed to evaluate the current distribution in the rigorous region. Therefore, the rigorous region is referred as the FMM region in the new model. Furthermore, the mutual coupling among multiple regions has also been considered efficiently using FMM. Numerical results are given to show the validity and efficiency of the proposed algorithm.

The static fast multipole method (FMM) has revolutionized the computation of pairwise interaction in N-body systems. This technique has been applied to diverse fields ranging from astrophysics to biochemistry to electrical engineering. The development of static FMM has progressed along two fronts; (i) expansions that are based on tesseral harmonics and (ii) Taylor series expansions. Indeed, the history of an FMM scheme based on the latter can be traced back to the same time period as the former. It was proven that while for a one-level implementation the computational complexity of the former scheme scales as O(p <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> N) the latter scales as O(p <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> N), where p is the number of harmonics used and N is the number of source/observer points. The interest in revisiting this scheme comes from the following observations: (i) Taylor's expansion involves representing the fields in terms of Cartesian tensors; (ii) there is an intimate connection between Cartesian tensors and the spherical harmonics. Indeed, it is well known that the following statements hold true: (i) the components of a traceless tensor of rank n serve as constant coefficients in a spherical harmonic of degree n, and (ii) there is a class of traceless tensors of rank n whose components are n-degree spherical harmonics functions of x, y, z. These connections imply that there should be an intimate connection between the two seemingly disparate schemes, and one should be able to obtain a similar cost structure for both methods. This connection is explored further in this paper. The next section briefly introduces the notation that is used in the rest of this paper. Next is the derivation of the steps necessary to implement the multilevel level FMM. Due to the paucity of space, several theorems (both this paper's and others) are stated without proofs

An efficient molecular dynamics (MD) algorithm is presented in this paper for biomolecular systems, which incorporates a novel variation on the fast multipole method (FMM) coupled to the reversible reference system propagator algorithm (r-RESPA). A top-down FMM is proposed which calculates multipoles recursively from the top of the box tree instead of from the bottom in Greengard’s original FMM, in an effort to be more efficient for noncubic or nonuniform systems. In addition, the use of noncubic box subdivisions of biomolecular systems is used and discussed. Reversible RESPA based on a Trotter factorization of the Liouville propagator in generating numerical integration schemes is coupled to the top-down FMM and applied to a MD study of proteins in vacuo, and is shown to be able to use a much larger time-step than the standard velocity Verlet method for a comparable level of accuracy. Furthermore, by using the FMM it becomes possible to perform MD simulations for very large biomolecules, since memory and CPU time requirements are now nearly of order of O(N) instead of O(N2). For a protein with 9513 atoms (the photosynthetic reaction center), the efficient MD algorithm leads to 20-fold reduction in CPU time for the Coulomb interaction and approximately 15-fold reduction in total CPU time over the standard velocity Verlet algorithm with a direct evaluation of Coulomb forces.