Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Fast parallel algorithms for short-range molecular dynamics

EvoCOMNET Contributions.- New Research in Nature Inspired Algorithms for Mobility Management in GSM Networks.- Adaptive Local Search for a New Military Frequency Hopping Planning Problem.- SS vs PBIL to Solve a Real-World Frequency Assignment Problem in GSM Networks.- Reconstruction of Networks from Their Betweenness Centrality.- A Self-learning Optimization Technique for Topology Design of Computer Networks.- A Comparative Study of Fuzzy Inference Systems, Neural Networks and Adaptive Neuro Fuzzy Inference Systems for Portscan Detection.- EvoFIN Contributions.- Evolutionary Single-Position Automated Trading.- Genetic Programming in Statistical Arbitrage.- Evolutionary System for Generating Investment Strategies.- Horizontal Generalization Properties of Fuzzy Rule-Based Trading Models.- Particle Swarm Optimization for Tackling Continuous Review Inventory Models.- Option Model Calibration Using a Bacterial Foraging Optimization Algorithm.- A SOM and GP Tool for Reducing the Dimensionality of a Financial Distress Prediction Problem.- Quantum-Inspired Evolutionary Algorithms for Financial Data Analysis.- EvoHOT Contributions.- Analysis of Reconfigurable Logic Blocks for Evolvable Digital Architectures.- Analogue Circuit Control through Gene Expression.- Discovering Several Robot Behaviors through Speciation.- Architecture Performance Prediction Using Evolutionary Artificial Neural Networks.- Evolving a Vision-Driven Robot Controller for Real-World Indoor Navigation.- Evolving an Automatic Defect Classification Tool.- Deterministic Test Pattern Generator Design.- An Evolutionary Methodology for Test Generation for Peripheral Cores Via Dynamic FSM Extraction.- Exploiting MOEA to Automatically Geneate Test Programs for Path-Delay Faults in Microprocessors.- EvoIASP Contributions.- Evolutionary Object Detection by Means of Naive Bayes Models Estimation.- An Evolutionary Framework for Colorimetric Characterization of Scanners.- Artificial Creatures for Object Tracking and Segmentation.- Automatic Recognition of Hand Gestures with Differential Evolution.- Optimizing Computed Tomographic Angiography Image Segmentation Using Fitness Based Partitioning.- A GA-Based Feature Selection Algorithm for Remote Sensing Images.- An Evolutionary Approach for Ontology Driven Image Interpretation.- Hybrid Genetic Algorithm Based on Gene Fragment Competition for Polyphonic Music Transcription.- Classification of Seafloor Habitats Using Genetic Programming.- Selecting Local Region Descriptors with a Genetic Algorithm for Real-World Place Recognition.- Object Detection Using Neural Networks and Genetic Programming.- Direct 3D Metric Reconstruction from Multiple Views Using Differential Evolution.- Discrete Tomography Reconstruction through a New Memetic Algorithm.- A Fuzzy Hybrid Method for Image Decomposition Problem.- Triangulation Using Differential Evolution.- Fast Multi-template Matching Using a Particle Swarm Optimization Algorithm for PCB Inspection.- EvoMUSART Contributions.- A Generative Representation for the Evolution of Jazz Solos.- Automatic Invention of Fitness Functions with Application to Scene Generation.- Manipulating Artificial Ecosystems.- Evolved Diffusion Limited Aggregation Compositions.- Scaffolding for Interactively Evolving Novel Drum Tracks for Existing Songs.- AtomSwarm: A Framework for Swarm Improvisation.- Using DNA to Generate 3D Organic Art Forms.- Towards Music Fitness Evaluation with the Hierarchical SOM.- Evolutionary Pointillist Modules: Evolving Assemblages of 3D Objects.- An Artificial-Chemistry Approach to Generating Polyphonic Musical Phrases.- Implicit Fitness Functions for Evolving a Drawing Robot.- Free Flight in Parameter Space: A Dynamic Mapping Strategy for Expressive Free Impro.- Modelling Video Games' Landscapes by Means of Genetic Terrain Programming - A New Approach for Improving Users' Experience.- Virtual Constructive Swarm Compositions and Inspirations.- New-Generation Methods in an Interpolating EC Synthesizer Interface.- Composing Music with Neural Networks and Probabilistic Finite-State Machines.- TransFormer #13: Exploration and Adaptation of Evolution Expressed in a Dynamic Sculpture.- EvoNUM Contributions.- Multiobjective Tuning of Robust PID Controllers Using Evolutionary Algorithms.- Truncation Selection and Gaussian EDA: Bounds for Sustainable Progress in High-Dimensional Spaces.- Scalable Continuous Multiobjective Optimization with a Neural Network-Based Estimation of Distribution Algorithm.- Cumulative Step Length Adaptation for Evolution Strategies Using Negative Recombination Weights.- Computing Surrogate Constraints for Multidimensional Knapsack Problems Using Evolution Strategies.- A Critical Assessment of Some Variants of Particle Swarm Optimization.- An Evolutionary Game-Theoretical Approach to Particle Swarm Optimisation.- A Hybrid Particle Swarm Optimization Algorithm for Function Optimization.- EvoSTOC Contributions.- Memory Based on Abstraction for Dynamic Fitness Functions.- A Memory Enhanced Evolutionary Algorithm for Dynamic Scheduling Problems.- Compound Particle Swarm Optimization in Dynamic Environments.- An Evolutionary Algorithm for Adaptive Online Services in Dynamic Environment.- EvoTHEORY Contributions.- A Study of Some Implications of the No Free Lunch Theorem.- Negative Slope Coefficient and the Difficulty of Random 3-SAT Instances.- EvoTRANSLOG Contributions.- A Memetic Algorithm for the Team Orienteering Problem.- Decentralized Evolutionary Optimization Approach to the p-Median Problem.- Genetic Computation of Road Network Design and Pricing Stackelberg Games with Multi-class Users.- Constrained Local Search Method for Bus Fleet Scheduling Problem with Multi-depot with Line Change.- Evolutionary System with Precedence Constraints for Ore Harbor Schedule Optimization.

Applications of evolutionary computing: EvoWorkshops 2008: EvoCOMNET, EvoFIN, EvoHOT, EvoIASP, EvoMUSART, EvoNUM, EvoSTOC, and EvoTransLog, Naples, Italy, March 26-28, 2008. Proceedings.

Cloud computing data centers are becoming increasingly popular for the provisioning of computing resources. The cost and operating expenses of data centers have skyrocketed with the increase in computing capacity. Several governmental, industrial, and academic surveys indicate that the energy utilized by computing and communication units within a data center contributes to a considerable slice of the data center operational costs. In this paper, we present a simulation environment for energy-aware cloud computing data centers. Along with the workload distribution, the simulator is designed to capture details of the energy consumed by data center components (servers, switches, and links) as well as packet-level communication patterns in realistic setups. The simulation results obtained for two-tier, three- tier, and three-tier high-speed data center architectures demonstrate the effectiveness of the simulator in utilizing power management schema, such as voltage scaling, frequency scaling, and dynamic shutdown that are applied to the computing and networking components.

/pdf/greencloud-a-packet-level-simulator-of-energy-aware-cloud-526e1edu1n.pdf

GreenCloud: A Packet-Level Simulator of Energy-Aware Cloud Computing Data Centers

Methods and problems of communication in usual networks

The vast majority of the research efforts in project scheduling over the past several years has concentrated on the development of exact and suboptimal procedures for the generation of a baseline schedule assuming complete information and a deterministic environment. During execution, however, projects may be the subject of considerable uncertainty, which may lead to numerous schedule disruptions. Predictive-reactive scheduling refers to the process where a baseline schedule is developed prior to the start of the project and updated if necessary during project execution. It is the objective of this paper to review possible procedures for the generation of proactive (robust) schedules, which are as well as possible protected against schedule disruptions, and for the deployment of reactive scheduling procedures that may be used to revise or re-optimize the baseline schedule when unexpected events occur. We also offer a framework that should allow project management to identify the proper scheduling methodol...

/pdf/robust-and-reactive-project-scheduling-a-review-and-2s1kxh6zoo.pdf

Robust and reactive project scheduling: a review and classification of procedures

A malleable task is a computational unit that may be executed on any arbitrary number of processors, whose execution time depends on the amount of resources allotted to it This paper presents a new approach for scheduling a set of independent malleable tasks which leads to a worst case guarantee of $\frac{3}{2}+\varepsilon$ for the minimization of the parallel execution time for any fixed $\varepsilon > 0$ The main idea of this approach is to focus on the determination of a good allotment and then to solve the resulting problem with a fixed number of processors by a simple scheduling algorithm The first phase is based on a dual approximation technique where the allotment problem is expressed as a knapsack problem for partitioning the set of tasks into two shelves of respective heights $1$ and $\frac{1}{2}$

/pdf/a-frac32-approximation-algorithm-for-scheduling-independent-182hmuvs82.pdf

A $\frac32$-Approximation Algorithm for Scheduling Independent Monotonic Malleable Tasks

The problem of optimal scheduling n independent malleable tasks in a parallel processor system is studied. It is assumed that an execution of any task can be preempted and the number of processors allocated to the same task can change during its execution. We present a rectangle packing algorithm, which converts an optimal solution for the relaxed problem, in which the number of processors allocated to a task is not required to be integer, into an optimal solution for the original problem in O(n) time.

Preemptable malleable task scheduling problem

Communication dans les réseaux de processeurs

Cet article est le fruit de deux annees de reflexions et de partage d'experiences au sein du groupe de travail flexibilite, qui s'est regulierement reuni durant les journees du Groupe de recherche sur l'Ordonnancement Theorique et Applique (GOThA). Les membres du groupe partagent une preoccupation commune, comment reagir aux aleas lors de la resolution d'un probleme d'ordonnancment, ils viennent cependant d'horizons applicatifs tres differents. Un des objectifs du groupe est de proposer un cadre de reference qui soit acceptable par les differents intervenants concernes~: problematique, definitions, mise en oeuvre de la flexibilite.

Flexibilité et Robustesse en Ordonnancement

https://hal.archives-ouvertes.fr/hal-00001546/document

Denis Trystram

Papers

A $\frac32$-Approximation Algorithm for Scheduling Independent Monotonic Malleable Tasks

Preemptable malleable task scheduling problem

Communication dans les réseaux de processeurs

Flexibilité et Robustesse en Ordonnancement

An approximation algorithm for scheduling trees of malleable tasks