A bibliography on parallel and vector numerical algorithms

This is a bibliography of numerical methods. It also includes a number of other references on machine architecture, programming language, and other topics of interest to scientific computing. Certain conference proceedings and anthologies which have been published in book form are listed also

ELSI: A Unified Software Interface for Kohn-Sham Electronic Structure Solvers

Solving the electronic structure from a generalized or standard eigenproblem is often the bottleneck in large scale calculations based on Kohn-Sham density-functional theory. This problem must be addressed by essentially all current electronic structure codes, based on similar matrix expressions, and by high-performance computation. We here present a unified software interface, ELSI, to access different strategies that address the Kohn-Sham eigenvalue problem. Currently supported algorithms include the dense generalized eigensolver library ELPA, the orbital minimization method implemented in libOMM, and the pole expansion and selected inversion (PEXSI) approach with lower computational complexity for semilocal density functionals. The ELSI interface aims to simplify the implementation and optimal use of the different strategies, by offering (a) a unified software framework designed for the electronic structure solvers in Kohn-Sham density-functional theory; (b) reasonable default parameters for a chosen solver; (c) automatic conversion between input and internal working matrix formats, and in the future (d) recommendation of the optimal solver depending on the specific problem. Comparative benchmarks are shown for system sizes up to 11,520 atoms (172,800 basis functions) on distributed memory supercomputing architectures.Comment: 55 pages, 14 figures, 2 table

Solution of partial differential equations on vector and parallel computers

The present status of numerical methods for partial differential equations on vector and parallel computers was reviewed. The relevant aspects of these computers are discussed and a brief review of their development is included, with particular attention paid to those characteristics that influence algorithm selection. Both direct and iterative methods are given for elliptic equations as well as explicit and implicit methods for initial boundary value problems. The intent is to point out attractive methods as well as areas where this class of computer architecture cannot be fully utilized because of either hardware restrictions or the lack of adequate algorithms. Application areas utilizing these computers are briefly discussed

Simulating water-entry/exit problems using Eulerian-Lagrangian and fully-Eulerian fictitious domain methods within the open-source IBAMR library

In this paper we employ two implementations of the fictitious domain (FD) method to simulate water-entry and water-exit problems and demonstrate their ability to simulate practical marine engineering problems. In FD methods, the fluid momentum equation is extended within the solid domain using an additional body force that constrains the structure velocity to be that of a rigid body. Using this formulation, a single set of equations is solved over the entire computational domain. The constraint force is calculated in two distinct ways: one using an Eulerian-Lagrangian framework of the immersed boundary (IB) method and another using a fully-Eulerian approach of the Brinkman penalization (BP) method. Both FSI strategies use the same multiphase flow algorithm that solves the discrete incompressible Navier-Stokes system in conservative form. A consistent transport scheme is employed to advect mass and momentum in the domain, which ensures numerical stability of high density ratio multiphase flows involved in practical marine engineering applications. Example cases of a free falling wedge (straight and inclined) and cylinder are simulated, and the numerical results are compared against benchmark cases in literature.Comment: The current paper builds on arXiv:1901.07892 and re-explains some parts of it for the reader's convenienc

A 3D radiative transfer framework: XI. multi-level NLTE

Multi-level non-local thermodynamic equilibrium (NLTE) radiation transfer calculations have become standard throughout the stellar atmospheres community and are applied to all types of stars as well as dynamical systems such as novae and supernovae. Even today spherically symmetric 1D calculations with full physics are computationally intensive. We show that full NLTE calculations can be done with fully 3 dimensional (3D) radiative transfer. With modern computational techniques and current massive parallel computational resources, full detailed solution of the multi-level NLTE problem coupled to the solution of the radiative transfer scattering problem can be solved without sacrificing the micro physics description. We extend the use of a rate operator developed to solve the coupled NLTE problem in spherically symmetric 1D systems. In order to spread memory among processors we have implemented the NLTE/3D module with a hierarchical domain decomposition method that distributes the NLTE levels, radiative rates, and rate operator data over a group of processes so that each process only holds the data for a fraction of the voxels. Each process in a group holds all the relevant data to participate in the solution of the 3DRT problem so that the 3DRT solution is parallelized within a domain decomposition group. We solve a spherically symmetric system in 3D spherical coordinates in order to directly compare our well-tested 1D code to the 3D case. We compare three levels of tests: a) a simple H+He test calculation, b) H+He+CNO+Mg, c) H+He+Fe. The last test is computationally large and shows that realistic astrophysical problems are solvable now, but they do require significant computational resources. With presently available computational resources it is possible to solve the full 3D multi-level problem with the same detailed micro-physics as included in 1D modeling.Comment: 20 pages, 14 figures, A&A, in pres

Chaste: a test-driven approach to software development for biological modelling

Chaste (‘Cancer, heart and soft-tissue environment’) is a software library and a set of test suites for computational simulations in the domain of biology. Current functionality has arisen from modelling in the fields of cancer, cardiac physiology and soft-tissue mechanics. It is released under the LGPL 2.1 licence.\ud \ud Chaste has been developed using agile programming methods. The project began in 2005 when it was reasoned that the modelling of a variety of physiological phenomena required both a generic mathematical modelling framework, and a generic computational/simulation framework. The Chaste project evolved from the Integrative Biology (IB) e-Science Project, an inter-institutional project aimed at developing a suitable IT infrastructure to support physiome-level computational modelling, with a primary focus on cardiac and cancer modelling

Research and Education in Computational Science and Engineering

Over the past two decades the field of computational science and engineering (CSE) has penetrated both basic and applied research in academia, industry, and laboratories to advance discovery, optimize systems, support decision-makers, and educate the scientific and engineering workforce. Informed by centuries of theory and experiment, CSE performs computational experiments to answer questions that neither theory nor experiment alone is equipped to answer. CSE provides scientists and engineers of all persuasions with algorithmic inventions and software systems that transcend disciplines and scales. Carried on a wave of digital technology, CSE brings the power of parallelism to bear on troves of data. Mathematics-based advanced computing has become a prevalent means of discovery and innovation in essentially all areas of science, engineering, technology, and society; and the CSE community is at the core of this transformation. However, a combination of disruptive developments---including the architectural complexity of extreme-scale computing, the data revolution that engulfs the planet, and the specialization required to follow the applications to new frontiers---is redefining the scope and reach of the CSE endeavor. This report describes the rapid expansion of CSE and the challenges to sustaining its bold advances. The report also presents strategies and directions for CSE research and education for the next decade.Comment: Major revision, to appear in SIAM Revie