The Peano software---parallel, automaton-based, dynamically adaptive grid traversals

We discuss the design decisions, design alternatives, and rationale behind the third generation of Peano, a framework for dynamically adaptive Cartesian meshes derived from spacetrees. Peano ties the mesh traversal to the mesh storage and supports only one element-wise traversal order resulting from space-filling curves. The user is not free to choose a traversal order herself. The traversal can exploit regular grid subregions and shared memory as well as distributed memory systems with almost no modifications to a serial application code. We formalize the software design by means of two interacting automata—one automaton for the multiscale grid traversal and one for the application-specific algorithmic steps. This yields a callback-based programming paradigm. We further sketch the supported application types and the two data storage schemes realized before we detail high-performance computing aspects and lessons learned. Special emphasis is put on observations regarding the used programming idioms and algorithmic concepts. This transforms our report from a “one way to implement things” code description into a generic discussion and summary of some alternatives, rationale, and design decisions to be made for any tree-based adaptive mesh refinement software

Parallel Multiscale Contact Dynamics for Rigid Non-spherical Bodies

The simulation of large numbers of rigid bodies of non-analytical shapes or vastly varying sizes which collide with each other is computationally challenging. The fundamental problem is the identification of all contact points between all particles at every time step. In the Discrete Element Method (DEM), this is particularly difficult for particles of arbitrary geometry that exhibit sharp features (e.g. rock granulates). While most codes avoid non-spherical or non-analytical shapes due to the computational complexity, we introduce an iterative-based contact detection method for triangulated geometries. The new method is an improvement over a naive brute force approach which checks all possible geometric constellations of contact and thus exhibits a lot of execution branching. Our iterative approach has limited branching and high floating point operations per processed byte. It thus is suitable for modern Single Instruction Multiple Data (SIMD) CPU hardware. As only the naive brute force approach is robust and always yields a correct solution, we propose a hybrid solution that combines the best of the two worlds to produce fast and robust contacts. In terms of the DEM workflow, we furthermore propose a multilevel tree-based data structure strategy that holds all particles in the domain on multiple scales in grids. Grids reduce the total computational complexity of the simulation. The data structure is combined with the DEM phases to form a single touch tree-based traversal that identifies both contact points between particle pairs and introduces concurrency to the system during particle comparisons in one multiscale grid sweep. Finally, a reluctant adaptivity variant is introduced which enables us to realise an improved time stepping scheme with larger time steps than standard adaptivity while we still minimise the grid administration overhead. Four different parallelisation strategies that exploit multicore architectures are discussed for the triad of methodological ingredients. Each parallelisation scheme exhibits unique behaviour depending on the grid and particle geometry at hand. The fusion of them into a task-based parallelisation workflow yields promising speedups. Our work shows that new computer architecture can push the boundary of DEM computability but this is only possible if the right data structures and algorithms are chosen

Document Collection Visualization and Clustering Using An Atom Metaphor for Display and Interaction

Visual Data Mining have proven to be of high value in exploratory data analysis and data mining because it provides an intuitive feedback on data analysis and support decision-making activities. Several visualization techniques have been developed for cluster discovery such as Grand Tour, HD-Eye, Star Coordinates, etc. They are very useful tool which are visualized in 2D or 3D; however, they have not simple for users who are not trained. This thesis proposes a new approach to build a 3D clustering visualization system for document clustering by using k-mean algorithm. A cluster will be represented by a neutron (centroid) and electrons (documents) which will keep a distance with neutron by force. Our approach employs quantified domain knowledge and explorative observation as prediction to map high dimensional data onto 3D space for revealing the relationship among documents. User can perform an intuitive visual assessment of the consistency of the cluster structure

Using Markov Models to Mine Temporal and Spatial Data

Référence du projet ANR BIODIVAGRIM : ANR 07 BDIV 02Markov models represent a powerful way to approach the problem of mining time and spatial signals whose variability is not yet fully understood. In this chapter, we will present a general methodology to mine different kinds of temporal and spatial signals having contrasting properties: continuous or discrete with few or many modalities. This methodology is based on a high order Markov modelling as implemented in a free software: carottAge (Gnu GPL)Les modèles de Markov sont des modèles puissants pour analyser des signaux temporels et spatiaux dont la variabilité n'est pas entièrement comprise. Dans ce chapitre, nous présentons notre méthodologie pour fouiller différentes sortes de signaux ayant des propriétés différentes: signaux continus ou discrets, simples ou composites. Cette méthodologie s'appuie sur des modèles de Markov cachés du second-ordre tels qu'implantés dans la boîte à outils CarottAge (licence Gnu-GPL)