Efficient Generating And Processing Of Large-Scale Unstructured Meshes

Unstructured meshes are used in a variety of disciplines to represent simulations and experimental data. Scientists who want to increase accuracy of simulations by increasing resolution must also increase the size of the resulting dataset. However, generating and processing a extremely large unstructured meshes remains a barrier. Researchers have published many parallel Delaunay triangulation (DT) algorithms, often focusing on partitioning the initial mesh domain, so that each rectangular partition can be triangulated in parallel. However, the comproblems for this method is how to merge all triangulated partitions into a single domain-wide mesh or the significant cost for communication the sub-region borders. We devised a novel algorithm --Triangulation of Independent Partitions in Parallel (TIPP) to deal with very large DT problems without requiring inter-processor communication while still guaranteeing the Delaunay criteria. The core of the algorithm is to find a set of independent} partitions such that the circumcircles of triangles in one partition do not enclose any vertex in other partitions. For this reason, this set of independent partitions can be triangulated in parallel without affecting each other. The results of mesh generation is the large unstructured meshes including vertex index and vertex coordinate files which introduce a new challenge \-- locality. Partitioning unstructured meshes to improve locality is a key part of our own approach. Elements that were widely scattered in the original dataset are grouped together, speeding data access. For further improve unstructured mesh partitioning, we also described our new approach. Direct Load which mitigates the challenges of unstructured meshes by maximizing the proportion of useful data retrieved during each read from disk, which in turn reduces the total number of read operations, boosting performance

Simulation of pore-scale flow using finite element-methods

I present a new finite element (FE) simulation method to simulate pore-scale flow. Within the pore-space, I solve a simplified form of the incompressible Navier-Stoke’s equation, yielding the velocity field in a two-step solution approach. First, Poisson’s equation is solved with homogeneous boundary conditions, and then the pore pressure is computed and the velocity field obtained for no slip conditions at the grain boundaries. From the computed velocity field I estimate the effective permeability of porous media samples characterized by thin section micrographs, micro-CT scans and synthetically generated grain packings. This two-step process is much simpler than solving the full Navier Stokes equation and therefore provides the opportunity to study pore geometries with hundreds of thousands of pores in a computationally more cost effective manner than solving the full Navier-Stoke’s equation. My numerical model is verified with an analytical solution and validated on samples whose permeabilities and porosities had been measured in laboratory experiments (Akanji and Matthai, 2010). Comparisons were also made with Stokes solver, published experimental, approximate and exact permeability data. Starting with a numerically constructed synthetic grain packings, I also investigated the extent to which the details of pore micro-structure affect the hydraulic permeability (Garcia et al., 2009). I then estimate the hydraulic anisotropy of unconsolidated granular packings. With the future aim to simulate multiphase flow within the pore-space, I also compute the radii and derive capillary pressure from the Young-Laplace equation (Akanji and Matthai,2010

Image-space decomposition algorithms for sort-first parallel volume rendering of unstructured grids

Twelve adaptive image-space decomposition algorithms are presented for sort-first parallel direct volume rendering (DVR) of unstructured grids on distributed-memory architectures. The algorithms are presented under a novel taxonomy based on the dimension of the screen decomposition, the dimension of the workload arrays used in the decomposition, and the scheme used for workload-array creation and querying the workload of a region. For the 2D decomposition schemes using 2D workload arrays, a novel scheme is proposed to query the exact number of screen-space bounding boxes of the primitives in a screen region in constant time. A probe-based chains-on-chains partitioning algorithm is exploited for load balancing in optimal 1D decomposition and iterative 2D rectilinear decomposition (RD). A new probe-based optimal 2D jagged decomposition (OJD) is proposed which is much faster than the dynamic-programming based OJD scheme proposed in the literature. The summed-area table is successfully exploited to query the workload of a rectangular region in constant time in both OJD and RD schemes for the subdivision of general 2D workload arrays. Two orthogonal recursive bisection (ORB) variants are adapted to relax the straight-line division restriction in conventional ORB through using the medians-of-medians approach on regular mesh and quadtree superimposed on the screen. Two approaches based on the Hilbert space-filling curve and graph-partitioning are also proposed. An efficient primitive classification scheme is proposed for redistribution in 1D, and 2D rectilinear and jagged decompositions. The performance comparison of the decomposition algorithms is modeled by establishing appropriate quality measures for load-balancing, amount of primitive replication and parallel execution time. The experimental results on a Parsytec CC system using a set of benchmark volumetric datasets verify the validity of the proposed performance models. The performance evaluation of the decomposition algorithms is also carried out through the sort-first parallelization of an efficient DVR algorithm

Finite difference grid generation on serial and parallel machines

Thesis (M.S.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 1995.Includes bibliographical references (leaves 67-68).by Naved A. Khan.M.S

Numerical simulation of fracture pattern development and implications for fuid flow

Simulations are instrumental to understanding flow through discrete fracture geometric representations that capture the large-scale permeability structure of fractured porous media. The contribution of this thesis is threefold: an efficient finite-element finite-volume discretisation of the advection/diffusion flow equations, a geomechanical fracture propagation algorithm to create fractured rock analogues, and a study of the effect of growth on hydraulic conductivity. We describe an iterative geomechanics-based finite-element model to simulate quasi-static crack propagation in a linear elastic matrix from an initial set of random flaws. The cornerstones are a failure and propagation criterion as well as a geometric kernel for dynamic shape housekeeping and automatic remeshing. Two-dimensional patterns exhibit connectivity, spacing, and density distributions reproducing en echelon crack linkage, tip hooking, and polygonal shrinkage forms. Differential stresses at the boundaries yield fracture curving. A stress field study shows that curvature can be suppressed by layer interaction effects. Our method is appropriate to model layered media where interaction with neighbouring layers does not dominate deformation. Geomechanically generated fracture patterns are the input to single-phase flow simulations through fractures and matrix. Thus, results are applicable to fractured porous media in addition to crystalline rocks. Stress state and deformation history control emergent local fracture apertures. Results depend on the number of initial flaws, their initial random distribution, and the permeability of the matrix. Straightpath fracture pattern simplifications yield a lower effective permeability in comparison to their curved counterparts. Fixed apertures overestimate the conductivity of the rock by up to six orders of magnitude. Local sample percolation effects are representative of the entire model flow behaviour for geomechanical apertures. Effective permeability in fracture dataset subregions are higher than the overall conductivity of the system. The presented methodology captures emerging patterns due to evolving geometric and flow properties essential to the realistic simulation of subsurface processes

In-situ visualization using Damaris: the Code Saturne use case

PRACE White PaperInternational audienceAs the exascale era approaches, maintaining scalable performance in data management tasks (storage, visualization, analysis, etc.) remains a key challenge in sustaining high performance for the application execution. To address this challenge, the Damaris middleware leverages dedicated computational resources in multicore nodes to offload data management tasks, including I/O, data compression, scheduling of data movements, in-situ analysis, and visualization. In this study we evaluate the benefits of Damaris to improve the efficiency of in-situ visualization for Code_Saturne, a fluid dynamics modeling environment. The experiments show Damaris to adequately hide the I/O processing of various Paraview processing pipelines in Code_Saturne. In all cases the Damaris enabled version of Code_Saturne was found to be more efficient than the identical non-Damaris capable version when running the same Paraview pipeline

Image-space decomposition algorithms for sort-first parallel volume rendering of unstructured grids

Ankara : Department of Computer Engineering and Information Science and the Institute of Engineering and Science of Bilkent University, 1997.Thesis (Master's) -- Bilkent University, 1997.Includes bibliographical references leaves 96-100.Kutluca, HüseyinM.S