New Algebraic Formulation of Density Functional Calculation

This article addresses a fundamental problem faced by the ab initio community: the lack of an effective formalism for the rapid exploration and exchange of new methods. To rectify this, we introduce a novel, basis-set independent, matrix-based formulation of generalized density functional theories which reduces the development, implementation, and dissemination of new ab initio techniques to the derivation and transcription of a few lines of algebra. This new framework enables us to concisely demystify the inner workings of fully functional, highly efficient modern ab initio codes and to give complete instructions for the construction of such for calculations employing arbitrary basis sets. Within this framework, we also discuss in full detail a variety of leading-edge ab initio techniques, minimization algorithms, and highly efficient computational kernels for use with scalar as well as shared and distributed-memory supercomputer architectures

Parallel hierarchical global illumination

Solving the global illumination problem is equivalent to determining the intensity of every wavelength of light in all directions at every point in a given scene. The complexity of the problem has led researchers to use approximation methods for solving the problem on serial computers. Rather than using an approximation method, such as backward ray tracing or radiosity, we have chosen to solve the Rendering Equation by direct simulation of light transport from the light sources. This paper presents an algorithm that solves the Rendering Equation to any desired accuracy, and can be run in parallel on distributed memory or shared memory computer systems with excellent scaling properties. It appears superior in both speed and physical correctness to recent published methods involving bidirectional ray tracing or hybrid treatments of diffuse and specular surfaces. Like progressive radiosity methods, it dynamically refines the geometry decomposition where required, but does so without the excessive storage requirements for ray histories. The algorithm, called Photon, produces a scene which converges to the global illumination solution. This amounts to a huge task for a 1997-vintage serial computer, but using the power of a parallel supercomputer significantly reduces the time required to generate a solution. Currently, Photon can be run on most parallel environments from a shared memory multiprocessor to a parallel supercomputer, as well as on clusters of heterogeneous workstations

An open-source implementation for full-wave 2D scattering by million-wavelength-size objects

In this contribution, we demonstrate that recent improvements in "fast methods" allow for fully error-controlled full-wave simulations of two-dimensional objects with sizes over a million wavelengths using relatively simple computing environments. We review how a fully scalable parallel version of the Multilevel Fast Multipole Algorithm (MLFMA) is obtained to accelerate a two-dimensional boundary integral equation for the scattering by multiple large dielectric and/or perfectly conducting objects. Several complex and large-scale examples demonstrate the capabilities of the algorithm. This implementation is available as open source under GPL license (http://www.openfmm.net)

A Multi-Code Analysis Toolkit for Astrophysical Simulation Data

The analysis of complex multiphysics astrophysical simulations presents a unique and rapidly growing set of challenges: reproducibility, parallelization, and vast increases in data size and complexity chief among them. In order to meet these challenges, and in order to open up new avenues for collaboration between users of multiple simulation platforms, we present yt (available at http://yt.enzotools.org/), an open source, community-developed astrophysical analysis and visualization toolkit. Analysis and visualization with yt are oriented around physically relevant quantities rather than quantities native to astrophysical simulation codes. While originally designed for handling Enzo's structure adaptive mesh refinement (AMR) data, yt has been extended to work with several different simulation methods and simulation codes including Orion, RAMSES, and FLASH. We report on its methods for reading, handling, and visualizing data, including projections, multivariate volume rendering, multi-dimensional histograms, halo finding, light cone generation and topologically-connected isocontour identification. Furthermore, we discuss the underlying algorithms yt uses for processing and visualizing data, and its mechanisms for parallelization of analysis tasks.Comment: 18 pages, 6 figures, emulateapj format. Resubmitted to Astrophysical Journal Supplement Series with revisions from referee. yt can be found at http://yt.enzotools.org

Computational Methods in Science and Engineering : Proceedings of the Workshop SimLabs@KIT, November 29 - 30, 2010, Karlsruhe, Germany

In this proceedings volume we provide a compilation of article contributions equally covering applications from different research fields and ranging from capacity up to capability computing. Besides classical computing aspects such as parallelization, the focus of these proceedings is on multi-scale approaches and methods for tackling algorithm and data complexity. Also practical aspects regarding the usage of the HPC infrastructure and available tools and software at the SCC are presented