A Variational Level Set Approach for Surface Area Minimization of Triply Periodic Surfaces

In this paper, we study triply periodic surfaces with minimal surface area under a constraint in the volume fraction of the regions (phases) that the surface separates. Using a variational level set method formulation, we present a theoretical characterization of and a numerical algorithm for computing these surfaces. We use our theoretical and computational formulation to study the optimality of the Schwartz P, Schwartz D, and Schoen G surfaces when the volume fractions of the two phases are equal and explore the properties of optimal structures when the volume fractions of the two phases not equal. Due to the computational cost of the fully, three-dimensional shape optimization problem, we implement our numerical simulations using a parallel level set method software package.Comment: 28 pages, 16 figures, 3 table

OPENMENDEL: A Cooperative Programming Project for Statistical Genetics

Statistical methods for genomewide association studies (GWAS) continue to improve. However, the increasing volume and variety of genetic and genomic data make computational speed and ease of data manipulation mandatory in future software. In our view, a collaborative effort of statistical geneticists is required to develop open source software targeted to genetic epidemiology. Our attempt to meet this need is called the OPENMENDELproject (https://openmendel.github.io). It aims to (1) enable interactive and reproducible analyses with informative intermediate results, (2) scale to big data analytics, (3) embrace parallel and distributed computing, (4) adapt to rapid hardware evolution, (5) allow cloud computing, (6) allow integration of varied genetic data types, and (7) foster easy communication between clinicians, geneticists, statisticians, and computer scientists. This article reviews and makes recommendations to the genetic epidemiology community in the context of the OPENMENDEL project.Comment: 16 pages, 2 figures, 2 table

Parallel graphics and visualization

Computer Graphics and Visualization are two fields that continue to evolve at a fast pace, always addressing new application areas and achieving better and faster results. The volume of data processed by such applications keeps getting larger and the illumination and light transport models used to generate pictorial representations of this data keep getting more sophisticated. Richer illumination and light transport models allow the generation of richer images that convey more information about the phenomenons or virtual worlds represented by the data and are more realistic and engaging to the user. The combination of large data sets, rich illumination models and large, sophisticated displays results in huge workloads that cannot be processed sequentially and still maintain acceptable response times. Parallel processing is thus an obvious approach to such problems, creating the field of Parallel Graphics and Visualization. The Eurographics Symposium on Parallel Graphics and Visualization (EGPGV) gathers together researchers from all over the world to foster research focused on theoretical and applied issues critical to parallel and distributed computing and its application to all aspects of computer graphics, virtual reality, scientific and engineering visualization. This special issue is a collection of five papers selected from those presented at the 7th EGPGV, which took place in Lugano, Switzerland, in May, 2007. The research presented in this symposium has evolved over the years, often reflecting the evolution of the underlying systems’ architectures. While papers presented in the first few events focused on Single Instruction Multiple Data and Massively Parallel Multi-Processing systems, in recent years the focus was mainly on Symmetric Multiprocessing machines and PC clusters, often also including the utilization of multiple Graphics Processing Units. The 2007 event witnessed the first papers addressing multicore processors, thus following the general trend of computer systems’ architecture. The paper by Wald, Ize and Parker discusses acceleration structures for interactive ray tracing of dynamic scenes. They propose the utilization of Bounding Volume Hierarchies (BVH), which for deformable scenes can be rapidly updated by adjusting the bounding primitives while maintaining the hierarchy. To avoid a significant performance penalty due to a large mismatch between the scene geometry and the tree topology the BVH is rebuilt asynchronously and concurrently with rendering. According to the authors, in the near future interactive ray tracers are expected to run on highly parallel multicore architectures. Thus, all results reported were obtained on an 8 processor dual core system, totalling 16 cores. Gribble, Brownlee and Parker propose two algorithms targeting highly parallel multicore architectures enabling interactive navigation and exploration of large particle data sets with global illumination effects. Rendering samples are lazily evaluated using Monte Carlo path tracing, while visualization occurs asynchronously by using Dynamic Luminance Textures that cache the renderer results. The combined utilization of particle based simulation methods and global illumination enables the effective communication of subtle changes in the three-dimensional structure of the data. All results were also obtained on a 16 cores architecture. The paper by Thomaszweski, Pabst and Blochinger analyzes parallel techniques for physically based simulation, in particular, the time integration and collision handling phases. The former is addressed using the conjugate gradient algorithm and static problem decomposition, while the latter exhibits a dynamic structure, thus requiring fully dynamic task decomposition. Their results were obtained using three different quad-core systems. Hong and Shen derive an efficient parallel algorithm for symmetry computation in volume data represented by regular grids. Sequential detection of symmetric features in volumetric data sets has a prohibitive cost, thus requiring efficient parallel algorithms and powerful parallel systems. The authors obtained the reported results on a PC cluster with Infiniband and 64 nodes, each being a dual processor, single core Opteron. Bettio, Gobbetti, Marton and Pintore describe a scalable multiresolution rendering system targeting massive triangle meshes and driving different sized light field displays. The larger light field display ð1:6 0:9m2Þ is based on a special arrangement of projectors and a holographic screen. It allows multiple freely moving viewers to see the scene from their respective points of view and enjoy continuous horizontal parallax without any specialized viewing devices. To drive this 35 Mbeams display they use a scalable parallel renderer, resorting to out of core and level of detail techniques, and running on a 15 nodes PC cluster

Parallel load balancing strategy for Volume-of-Fluid methods on 3-D unstructured meshes

© 2016. This version is made available under the CC-BY-NC-ND 4.0 license http://creativecommons.org/licenses/by-nc-nd/4.0/l Volume-of-Fluid (VOF) is one of the methods of choice to reproduce the interface motion in the simulation of multi-fluid flows. One of its main strengths is its accuracy in capturing sharp interface geometries, although requiring for it a number of geometric calculations. Under these circumstances, achieving parallel performance on current supercomputers is a must. The main obstacle for the parallelization is that the computing costs are concentrated only in the discrete elements that lie on the interface between fluids. Consequently, if the interface is not homogeneously distributed throughout the domain, standard domain decomposition (DD) strategies lead to imbalanced workload distributions. In this paper, we present a new parallelization strategy for general unstructured VOF solvers, based on a dynamic load balancing process complementary to the underlying DD. Its parallel efficiency has been analyzed and compared to the DD one using up to 1024 CPU-cores on an Intel SandyBridge based supercomputer. The results obtained on the solution of several artificially generated test cases show a speedup of up to similar to 12x with respect to the standard DD, depending on the interface size, the initial distribution and the number of parallel processes engaged. Moreover, the new parallelization strategy presented is of general purpose, therefore, it could be used to parallelize any VOF solver without requiring changes on the coupled flow solver. Finally, note that although designed for the VOF method, our approach could be easily adapted to other interface-capturing methods, such as the Level-Set, which may present similar workload imbalances. (C) 2014 Elsevier Inc. Allrights reserved.Peer ReviewedPostprint (author's final draft