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Matthew G. Knepley

Publications and source records attributed to Matthew G. Knepley.

At least 37 records · Page 2Linked to original sources

An Algorithm for Computing Lipschitz Inner Functions in Kolmogorov's Superposition Theorem

Kolmogorov famously proved that multivariate continuous functions can be represented as a superposition of a small number of univariate continuous functions, $$ f(x_1,\dots,x_n) = \sum_{q=0}^{2n+1} χ^q \left( \sum_{p=1}^n ψ^{pq}(x_p) \right).$$ Fridman \cite{fridman} posed the best smoothness bound for the functions $ψ^{pq}$, that such functions can be constructed to be Lipschitz continuous with constant 1. Previous algorithms to describe these inner functions have only been Hölder continuous, such as those proposed by Köppen and Braun and Griebel. This is problematic, as pointed out by Griebel, in that non-smooth functions have very high storage/evaluation complexity, and this makes Kolmogorov's representation (KR) impractical using the standard definition of the inner functions. To date, no one has presented a method to compute a Lipschitz continuous inner function. In this paper, we revisit Kolmogorov's theorem along with Fridman's result. We examine a simple Lipschitz function which appear to satisfy the necessary criteria for Kolmogorov's representation, but fails in the limit. We then present a full solution to the problem, including an algorithm that computes such a Lipschitz function.

math.NA↗

Efficient Evaluation of Ellipsoidal Harmonics for Potential Modeling

Ellipsoidal harmonics are a useful generalization of spherical harmonics but present additional numerical challenges. One such challenge is in computing ellipsoidal normalization constants which require approximating a singular integral. In this paper, we present results for approximating normalization constants using a well-known decomposition and applying tanh-sinh quadrature to the resulting integrals. Tanh-sinh has been shown to be an effective quadrature scheme for a certain subset of singular integrands. To support our numerical results, we prove that the decomposed integrands lie in the space of functions where tanh-sinh is optimal and compare our results to a variety of similar change-of-variable quadratures.

math.NA↗

Scalable smoothing strategies for a geometric multigrid method for the immersed boundary equations

The immersed boundary (IB) method is a widely used approach to simulating fluid-structure interaction (FSI). Although explicit versions of the IB method can suffer from severe time step size restrictions, these methods remain popular because of their simplicity and generality. In prior work (Guy et al., Adv Comput Math, 2015), some of us developed a geometric multigrid preconditioner for a stable semi-implicit IB method under Stokes flow conditions; however, this solver methodology used a Vanka-type smoother that presented limited opportunities for parallelization. This work extends this Stokes-IB solver methodology by developing smoothing techniques that are suitable for parallel implementation. Specifically, we demonstrate that an additive version of the Vanka smoother can yield an effective multigrid preconditioner for the Stokes-IB equations, and we introduce an efficient Schur complement-based smoother that is also shown to be effective for the Stokes-IB equations. We investigate the performance of these solvers for a broad range of material stiffnesses, both for Stokes flows and flows at nonzero Reynolds numbers, and for thick and thin structural models. We show here that linear solver performance degrades with increasing Reynolds number and material stiffness, especially for thin interface cases. Nonetheless, the proposed approaches promise to yield effective solution algorithms, especially at lower Reynolds numbers and at modest-to-high elastic stiffnesses.

math.NA↗

Predicting Solvation Free Energies and Thermodynamics in Polar Solvents and Mixtures Using a Solvation-Layer Interface Condition

We demonstrate that with two small modifications, the popular dielectric continuum model is capable of predicting, with high accuracy, ion solvation thermodynamics in numerous polar solvents, and ion solvation free energies in water--co-solvent mixtures. The first modification involves perturbing the macroscopic dielectric-flux interface condition at the solute--solvent interface with a nonlinear function of the local electric field, giving what we have called a solvation-layer interface condition (SLIC). The second modification is a simple treatment of the microscopic interface potential (static potential). We show that the resulting model exhibits high accuracy without the need for fitting solute atom radii in a state-dependent fashion. Compared to experimental results in nine water--co-solvent mixtures, SLIC predicts transfer free energies to within 2.5 kJ/mol. The co-solvents include both protic and aprotic species, as well as biologically relevant denaturants such as urea and dimethylformamide. Furthermore, our results indicate that the interface potential is essential to reproduce entropies and heat capacities. The present work, together with previous studies of SLIC illustrating its accuracy for biomolecules in water, indicates it as a promising dielectric continuum model for accurate predictions of molecular solvation in a wide range of conditions.

physics.chem-ph↗

Anisotropic mesh adaptation in Firedrake with PETSc DMPlex

Despite decades of research in this area, mesh adaptation capabilities are still rarely found in numerical simulation software. We postulate that the primary reason for this is lack of usability. Integrating mesh adaptation into existing software is difficult as non-trivial operators, such as error metrics and interpolation operators, are required, and integrating available adaptive remeshers is not straightforward. Our approach presented here is to first integrate Pragmatic, an anisotropic mesh adaptation library, into DMPlex, a PETSc object that manages unstructured meshes and their interactions with PETSc's solvers and I/O routines. As PETSc is already widely used, this will make anisotropic mesh adaptation available to a much larger community. As a demonstration of this we describe the integration of anisotropic mesh adaptation into Firedrake, an automated Finite Element based system for the portable solution of partial differential equations which already uses PETSc solvers and I/O via DMPlex. We present a proof of concept of this integration with a three-dimensional advection test case.

math.NA↗

Finite Element Integration with Quadrature on the GPU

We present a novel, quadrature-based finite element integration method for low-order elements on GPUs, using a pattern we call \textit{thread transposition} to avoid reductions while vectorizing aggressively. On the NVIDIA GTX580, which has a nominal single precision peak flop rate of 1.5 TF/s and a memory bandwidth of 192 GB/s, we achieve close to 300 GF/s for element integration on first-order discretization of the Laplacian operator with variable coefficients in two dimensions, and over 400 GF/s in three dimensions. From our performance model we find that this corresponds to 90\% of our measured achievable bandwidth peak of 310 GF/s. Further experimental results also match the predicted performance when used with double precision (120 GF/s in two dimensions, 150 GF/s in three dimensions). Results obtained for the linear elasticity equations (220 GF/s and 70 GF/s in two dimensions, 180 GF/s and 60 GF/s in three dimensions) also demonstrate the applicability of our method to vector-valued partial differential equations.

cs.MS↗

Generalizing The Mean Spherical Approximation as a Multiscale, Nonlinear Boundary Condition at the Solute--Solvent Interface

In this paper we extend the familiar continuum electrostatic model with a perturbation to the usual macroscopic boundary condition. The perturbation is based on the mean spherical approximation (MSA), to derive a multiscale hydration-shell boundary condition (HSBC). We show that the HSBC/MSA model reproduces MSA predictions for Born ions in a variety of polar solvents, including both protic and aprotic solvents. Importantly, the HSBC/MSA model predicts not only solvation free energies accurately but also solvation entropies, which standard continuum electrostatic models fail to predict. The HSBC/MSA model depends only on the normal electric field at the dielectric boundary, similar to our recent development of an HSBC model for charge-sign hydration asymmetry, and the reformulation of the MSA as a boundary condition enables its straightforward application to complex molecules such as proteins.

math.NA↗

Composing Scalable Nonlinear Algebraic Solvers

Most efficient linear solvers use composable algorithmic components, with the most common model being the combination of a Krylov accelerator and one or more preconditioners. A similar set of concepts may be used for nonlinear algebraic systems, where nonlinear composition of different nonlinear solvers may significantly improve the time to solution. We describe the basic concepts of nonlinear composition and preconditioning and present a number of solvers applicable to nonlinear partial differential equations. We have developed a software framework in order to easily explore the possible combinations of solvers. We show that the performance gains from using composed solvers can be substantial compared with gains from standard Newton-Krylov methods.

math.NA↗

Extreme-scale Multigrid Components within PETSc

Elliptic partial differential equations (PDEs) frequently arise in continuum descriptions of physical processes relevant to science and engineering. Multilevel preconditioners represent a family of scalable techniques for solving discrete PDEs of this type and thus are the method of choice for high-resolution simulations. The scalability and time-to-solution of massively parallel multilevel preconditioners can be adversely effected by using a coarse-level solver with sub-optimal algorithmic complexity. To maintain scalability, agglomeration techniques applied to the coarse level have been shown to be necessary. In this work, we present a new software component introduced within the Portable Extensible Toolkit for Scientific computation (PETSc) which permits agglomeration. We provide an overview of the design and implementation of this functionality, together with several use cases highlighting the benefits of agglomeration. Lastly, we demonstrate via numerical experiments employing geometric multigrid with structured meshes, the flexibility and performance gains possible using our MPI-rank agglomeration implementation.

cs.MS↗

A Stochastic Performance Model for Pipelined Krylov Methods

Pipelined Krylov methods seek to ameliorate the latency due to inner products necessary for projection by overlapping it with the computation associated with sparse matrix-vector multiplication. We clarify a folk theorem that this can only result in a speedup of $2\times$ over the naive implementation. Examining many repeated runs, we show that stochastic noise also contributes to the latency, and we model this using an analytical probability distribution. Our analysis shows that speedups greater than $2\times$ are possible with these algorithms.

cs.DC↗

Work/Precision Tradeoffs in Continuum Models of Biomolecular Electrostatics

The structure and function of biological molecules are strongly influenced by the water and dissolved ions that surround them. This aqueous solution (solvent) exerts significant electrostatic forces in response to the biomolecule's ubiquitous atomic charges and polar chemical groups. In this work, we investigate a simple approach to numerical calculation of this model using boundary-integral equation (BIE) methods and boundary-element methods (BEM). Traditional BEM discretizes the protein--solvent boundary into a set of boundary elements, or panels, and the approximate solution is defined as a weighted combination of basis functions with compact support. The resulting BEM matrix then requires integrating singular or near singular functions, which can be slow and challenging to compute. Here we investigate the accuracy and convergence of a simpler representation, namely modeling the unknown surface charge distribution as a set of discrete point charges on the surface. We find that at low resolution, point-based BEM is more accurate than panel-based methods, due to the fact that the protein surface is sampled directly, and can be of significant value for numerous important calculations that require only moderate accuracy, such as the preliminary stages of rational drug design and protein engineering.

math.NA↗

Multiscale models and approximation algorithms for protein electrostatics

Electrostatic forces play many important roles in molecular biology, but are hard to model due to the complicated interactions between biomolecules and the surrounding solvent, a fluid composed of water and dissolved ions. Continuum model have been surprisingly successful for simple biological questions, but fail for important problems such as understanding the effects of protein mutations. In this paper we highlight the advantages of boundary-integral methods for these problems, and our use of boundary integrals to design and test more accurate theories. Examples include a multiscale model based on nonlocal continuum theory, and a nonlinear boundary condition that captures atomic-scale effects at biomolecular surfaces.

math.NA↗

Support for Non-conformal Meshes in PETSc's DMPlex Interface

PETSc's DMPlex interface for unstructured meshes has been extended to support non-conformal meshes. The topological construct that DMPlex implements---the CW-complex---is by definition conformal, so representing non- conformal meshes in a way that hides complexity requires careful attention to the interface between DMPlex and numerical methods such as the finite element method. Our approach---which combines a tree structure for subset- superset relationships and a "reference tree" describing the types of non-conformal interfaces---allows finite element code written for conformal meshes to extend automatically: in particular, all "hanging-node" constraint calculations are handled behind the scenes. We give example code demonstrating the use of this extension, and use it to convert forests of quadtrees and forests of octrees from the p4est library to DMPlex meshes.

cs.MS↗

Efficient mesh management in Firedrake using PETSc-DMPlex

The use of composable abstractions allows the application of new and established algorithms to a wide range of problems while automatically inheriting the benefits of well-known performance optimisations. This work highlights the composition of the PETSc DMPlex domain topology abstraction with the Firedrake automated finite element system to create a PDE solving environment that combines expressiveness, flexibility and high performance. We describe how Firedrake utilises DMPlex to provide the indirection maps required for finite element assembly, while supporting various mesh input formats and runtime domain decomposition. In particular, we describe how DMPlex and its accompanying data structures allow the generic creation of user-defined discretisations, while utilising data layout optimisations that improve cache coherency and ensure overlapped communication during assembly computation.

cs.MS↗

Unstructured Overlapping Mesh Distribution in Parallel

We present a simple mathematical framework and API for parallel mesh and data distribution, load balancing, and overlap generation. It relies on viewing the mesh as a Hasse diagram, abstracting away information such as cell shape, dimension, and coordinates. The high level of abstraction makes our interface both concise and powerful, as the same algorithm applies to any representable mesh, such as hybrid meshes, meshes embedded in higher dimension, and overlapped meshes in parallel. We present evidence, both theoretical and experimental, that the algorithms are scalable and efficient. A working implementation can be found in the latest release of the PETSc libraries.

cs.MS↗

Flexible, Scalable Mesh and Data Management using PETSc DMPlex

Designing a scientific software stack to meet the needs of the next-generation of mesh-based simulation demands, not only scalable and efficient mesh and data management on a wide range of platforms, but also an abstraction layer that makes it useful for a wide range of application codes. Common utility tasks, such as file I/O, mesh distribution, and work partitioning, should be delegated to external libraries in order to promote code re-use, extensibility and software interoperability. In this paper we demonstrate the use of PETSc's DMPlex data management API to perform mesh input and domain partitioning in Fluidity, a large scale CFD application. We demonstrate that raising the level of abstraction adds new functionality to the application code, such as support for additional mesh file formats and mesh re- ordering, while improving simulation startup cost through more efficient mesh distribution. Moreover, the separation of concerns accomplished through this interface shifts critical performance and interoperability issues, such as scalable I/O and file format support, to a widely used and supported open source community library, improving the sustainability, performance, and functionality of Fluidity.

cs.MS↗

Modeling Charge-Sign Asymmetric Solvation Free Energies With Nonlinear Boundary Conditions

We show that charge-sign-dependent asymmetric hydration can be modeled accurately using linear Poisson theory but replacing the standard electric-displacement boundary condition with a simple nonlinear boundary condition. Using a single multiplicative scaling factor to determine atomic radii from molecular dynamics Lennard-Jones parameters, the new model accurately reproduces MD free-energy calculations of hydration asymmetries for (i) monatomic ions, (ii) titratable amino acids in both their protonated and unprotonated states, and (iii) the Mobley "bracelet" and "rod" test problems [J. Phys. Chem. B, v. 112:2408, 2008]. Remarkably, the model also justifies the use of linear response expressions for charging free energies. Our boundary-element method implementation demonstrates the ease with which other continuum-electrostatic solvers can be extended to include asymmetry.

physics.chem-ph↗

Run-time extensibility and librarization of simulation software

Build-time configuration and environment assumptions are hampering progress and usability in scientific software. That which would be utterly unacceptable in non-scientific software somehow passes for the norm in scientific packages. The community needs reusable software packages that are easy use and flexible enough to accommodate next-generation simulation and analysis demands.

cs.SE↗