High Performance Computing on Vector Systems 2010

This book covers the results of the 11th and 12th Tera?op Workshop and continued a series initiated by NEC and the HLRS in 2004. As part of the Tera?op Workbench, it has become a meeting platform for scientists, application developers, international experts and hardware designers to discuss the current state and future directions of supercomputing with the aim of achieving the highest sustained application perf- mance. The Tera?op Workbench Project is a collaboration between the High Perf- mance Computing Center Stuttgart (HLRS) and NEC Deutschland GmbH (NEC HPCE) to support users to achieve their research goals using High Performance Computing. The ?rst stage of the Tera?op Workbench project (2004–2008) c- centrated on user’s applications and their optimization for the 72-node NEC SX-8 installation at HLRS. During this stage, numerous individual codes, developed and maintained by researchers or commercial organizations, have been analyzed and - timized. Several of the codes have shown the ability to outreach the TFlop/s thre- old of sustained performance. This created the possibility for new science and a deeper understanding of the underlying physics. Preface Contents Operating System and Software for Large Scale Systems Light-Weight Kernel with Portals Introduction Kitten OFED Benchmarks Portals Portals: A Brief Introduction Optimizing Portals for LWK A High-Performance Infiniband NAL Benchmarks MPI ORTE Job Preparation and Startup Job Start on the Light-Weight Kernel Architecture of OOB/Portals Conclusion and Future Work References Towards an Architecture for Management of Very Large Computing Systems Introduction Specific Challenges in HPC Challenges Jitter Scalability Data Correlation Error Handling Scheduler Awareness Tool Integration TIMaCS---The Project Idea and Objectives Issues---Addressed and Not Addressed Architecture Administrational Benefits Security Constraints Mission-Critical Constraints Performance Tuning Dynamic Changes Hardware Management Business-Benefits with Business-Policy Based Management Need for Business-Policy Based Job-Scheduling in HPC Approach Conclusion and Future Outlook References Empirical Optimization of Collective Communications with ADCL Introduction and Motivation The Abstract Data and Communication Library (ADCL) Semantics of the New ADCL Interfaces The Vector-Map Object Extension of the ADCL Interfaces The New Function Sets Performance Evaluation Integration of ADCL Setup Results Summary and Outlook References I/O Strategies I/O Forwarding on NEC SX-9 IOFWD Implementation Design of IOFWD IOFWD Components Implementation Status Performance Results IOFWD Usage System Overview at HLRS Application Workflow Example Application Integration, Compilation, Building and Running First Real Application Experiences Conclusion References High-Speed Data Transmission Technology for the NEC SX-9 Introduction LSI Technology Serial Interface Clocks High-Speed Circuit Technology Transmission Technology Power Noise Countermeasures Summary References Grid and Cloud Computing The Vector Computing Cloud: Toward a Vector Meta-Computing Environment Introduction Basic Concept of the Vector Computing Clouds Prototyping of the Vector Computing Cloud Virtualizing Vector Supercomputers: GRID VM for SX Job Scheduling on the Vector Computing Cloud MPI Environment for Vector Computing Cloud Feasibility Study and Early Performance Evaluations Performance Evaluation of the Job Scheduling Mechanism System Tests Performance of HPL Conclusions References Full-Scale 3D Vibration Simulator of an Entire Nuclear Power Plant on Simple Orchestration Application Framework Introduction Full-Scale 3D Vibration Simulator for an Entire Nuclear Power Plant GDS Application of Full-Scale 3D Vibration Simulator Needs of Pipelined Data-Transfer Scenario Development of Simple Orchestration Application Framework Functionalities Implementation Full-Scale Simulation of High Temperature Test Engineering Reactor Summaries References Development of Simple Orchestration Application Framework and Its Application to Burning Plasma Simulation Introduction Simple Orchestration Application Framework (SOAF) Overview of SOAF Controller Sentinel Configuration File Development of Simple Orchestration Application Framework Burning Plasma Simulation Experiment Summaries References Acoustics and Structural Mechanic On Sound Generated by a Globally Unstable Round Jet Introduction Numerical Setup Round Jet Flow Simulation Aeroacoustic Computation Parallelization of the Acoustic Solver Results Jet Characteristics Acoustic Results Conclusion References Numerical Simulation of Sibilant [s] Using the Real Geometry of a Human Vocal Tract Introduction Signal Processing for Consonants Sound Induced Flow Sibiant [s] in Dental Treatments Computational Analyses for Sibilant [s] Complicated Morphology of Vocal Tracts LES and Aeroacoustics Materials and Methods Result Discussion Validity of Real Morphological Geometry Aeroacoustic Analyses Requirements for High Performance Computing Conclusion References Identification of Anisotropic Elastic Material Properties by Direct Mechanical Simulations: Estimation of Process Chain Resource Requirements Introduction Material and Methods Theoretical Background---Standard Mechanics Approach Process Chain Description Results Single Sub-Domain Domain Count Accumulation over Process Summary & Conclusions References Computational Fluid Dynamics Downscaling Climate Simulations for Use in Hydrological Modeling of Medium-Sized River Catchments Introduction The CCLM Model Performance on the HLRS Systems Results Discussion References DNS of Rising Bubbles Using VOF and Balanced Force Surface Tension Introduction Governing Equations Continuity and Navier-Stokes Equations Interface Tracking by the VOF Method Moving Frame of Reference Surface Tension The Continuum Surface Force (CSF) Model Balanced-Force Algorithm Curvature Estimation Numerical Setup Results: Rise Behavior of Bubbles Reduction of Spurious Currents Terminal Rise Velocity Bubble Shape Conclusion References Large-Eddy Simulation of Double-Row Compound-Angle Film-Cooling: Computational Aspects Introduction Simulation Methods Code and Governing Equations Integration and Flux Evaluation Turbulence Modeling Boundary Treatment Computational Environment and Measuring Procedure Performance Results and Flow Field Visualization Sequential Performance of Individual Code Components Overall Parallel Performance Flow Field Visualization Conclusions References Large Eddy Simulation of Wind Turbulence for Appropriate Urban Environment