Streamline Integration using MPI-Hybrid Parallelism on a Large Multi-Core Architecture

Streamline computation in a very large vector field data set represents a significant challenge due to the non-local and datadependentnature of streamline integration. In this paper, we conduct a study of the performance characteristics of hybrid parallel programmingand execution as applied to streamline integration on a large, multicore platform. With multi-core processors now prevalent in clustersand supercomputers, there is a need to understand the impact of these hybrid systems in order to make the best implementation choice.We use two MPI-based distribution approaches based on established parallelization paradigms, parallelize-over-seeds and parallelize-overblocks,and present a novel MPI-hybrid algorithm for each approach to compute streamlines. Our findings indicate that the work sharing betweencores in the proposed MPI-hybrid parallel implementation results in much improved performance and consumes less communication andI/O bandwidth than a traditional, non-hybrid distributed implementation

HARE: Final Report

This report documents the results of work done over a 6 year period under the FAST-OS programs. The first effort was called Right-Weight Kernels, (RWK) and was concerned with improving measurements of OS noise so it could be treated quantitatively; and evaluating the use of two operating systems, Linux and Plan 9, on HPC systems and determining how these operating systems needed to be extended or changed for HPC, while still retaining their general-purpose nature. The second program, HARE, explored the creation of alternative runtime models, building on RWK. All of the HARE work was done on Plan 9. The HARE researchers were mindful of the very good Linux and LWK work being done at other labs and saw no need to recreate it. Even given this limited funding, the two efforts had outsized impact: _ Helped Cray decide to use Linux, instead of a custom kernel, and provided the tools needed to make Linux perform well _ Created a successor operating system to Plan 9, NIX, which has been taken in by Bell Labs for further development _ Created a standard system measurement tool, Fixed Time Quantum or FTQ, which is widely used for measuring operating systems impact on applications _ Spurred the use of the 9p protocol in several organizations, including IBM _ Built software in use at many companies, including IBM, Cray, and Google _ Spurred the creation of alternative runtimes for use on HPC systems _ Demonstrated that, with proper modifications, a general purpose operating systems can provide communications up to 3 times as effective as user-level libraries Open source was a key part of this work. The code developed for this project is in wide use and available at many places. The core Blue Gene code is available at https://bitbucket.org/ericvh/hare. We describe details of these impacts in the following sections. The rest of this report is organized as follows: First, we describe commercial impact; next, we describe the FTQ benchmark and its impact in more detail; operating systems and runtime research follows; we discuss infrastructure software; and close with a description of the new NIX operating system, future work, and conclusions

Recent Developments in the General Atomic and Molecular Electronic Structure System

A discussion of many of the recently implemented features of GAMESS (General Atomic and Molecular Electronic Structure System) and LibCChem (the C++ CPU/GPU library associated with GAMESS) is presented. These features include fragmentation methods such as the fragment molecular orbital, effective fragment potential and effective fragment molecular orbital methods, hybrid MPI/OpenMP approaches to Hartree-Fock, and resolution of the identity second order perturbation theory. Many new coupled cluster theory methods have been implemented in GAMESS, as have multiple levels of density functional/tight binding theory. The role of accelerators, especially graphical processing units, is discussed in the context of the new features of LibCChem, as it is the associated problem of power consumption as the power of computers increases dramatically. The process by which a complex program suite such as GAMESS is maintained and developed is considered. Future developments are briefly summarized

Conception et réalisation d'un solveur pour les problèmes de dynamique des fluides pour les architectures many-core

Numerical simulation is nowadays an essential part of engineering analysis, be it to design anew plane, or to detect underground oil reservoirs. Numerical simulations have indeed become an important complement to theoretical and experimental investigation, allowing one to reduce the cost of engineering design processes. In order to achieve a high level of precision, one need to increase the resolution of his computational domain. So to keep getting results in reasonable time, one shall nd a way to speed-up computations. To do this, we use high performance computing, HPC, to exploit the complex architecture of modern supercomputers. Under these two constraints, and some other like the genericity of finite elements, or the mesh dimension, we developed a new platform AeroSol. In this thesis, we present the mathematical background, and the two types of schemes that are implemented in the platform, the continuous finite elements method, and the discontinuous one. Then, we present the design choices made in the platform,then, we study a sub-problem, the assembly operation, which can be found in linear algebra multi-frontal methods.La simulation numérique fait partie intégrante du processus d'analyse. Que l'on veuille concevoir le profil d'un véhicule, ou chercher à prévoir le résultat d'un forage pétrolier, la simulation numérique est devenue un outil complémentaire à la théorie et aux expérimentations. Cet outildoit produire des résultats précis en un minimum de temps. Pour cela, nous avons à disposition des méthodes numériques précises, et des machines de calcul aux performances importantes. Cet outil doit être générique sur les maillages, l'ordre de la solution, les méthodes numériques, et doitmaintenir ses performances sur les machines de calculs modernes avec une hiérarchie complexes d'unité de calculs. Nous présentons dans cette thèse le background mathématiques de deux classes de schémas numériques, les méthodes aux éléments finis continus et discontinus. Puis nous présentons les enjeux de la conception d'une plateforme en prenant en compte l'ensemble de ces contraintes. Ensuite nous nous intéressons au sous-problème de l'assemblage au dessus d'un support d'exécution. L'opération d'assemblage se retrouve en algèbre linéaire dans les méthodes multi-frontales ou dans les applications de simulations assemblant un système linéaire. Puis, nous concluons en dressant un bilan sur la plateforme AeroSol et donnons des pistes d'évolution possibles

General Purpose Flow Visualization at the Exascale

Exascale computing, i.e., supercomputers that can perform 1018 math operations per second, provide significant opportunity for improving the computational sciences. That said, these machines can be difficult to use efficiently, due to their massive parallelism, due to the use of accelerators, and due to the diversity of accelerators used. All areas of the computational science stack need to be reconsidered to address these problems. With this dissertation, we consider flow visualization, which is critical for analyzing vector field data from simulations. We specifically consider flow visualization techniques that use particle advection, i.e., tracing particle trajectories, which presents performance and implementation challenges. The dissertation makes four primary contributions. First, it synthesizes previous work on particle advection performance and introduces a high-level analytical cost model. Second, it proposes an approach for performance portability across accelerators. Third, it studies expected speedups based on using accelerators, including the importance of factors such as duration, particle count, data set, and others. Finally, it proposes an exascale-capable particle advection system that addresses diversity in many dimensions, including accelerator type, parallelism approach, analysis use case, underlying vector field, and more

Das unstetige Galerkinverfahren für Strömungen mit freier Oberfläche und im Grundwasserbereich in geophysikalischen Anwendungen

Free surface flows and subsurface flows appear in a broad range of geophysical applications and in many environmental settings situations arise which even require the coupling of free surface and subsurface flows. Many of these application scenarios are characterized by large domain sizes and long simulation times. Hence, they need considerable amounts of computational work to achieve accurate solutions and the use of efficient algorithms and high performance computing resources to obtain results within a reasonable time frame is mandatory. Discontinuous Galerkin methods are a class of numerical methods for solving differential equations that share characteristics with methods from the finite volume and finite element frameworks. They feature high approximation orders, offer a large degree of flexibility, and are well-suited for parallel computing. This thesis consists of eight articles and an extended summary that describe the application of discontinuous Galerkin methods to mathematical models including free surface and subsurface flow scenarios with a strong focus on computational aspects. It covers discretization and implementation aspects, the parallelization of the method, and discrete stability analysis of the coupled model.Für viele geophysikalische Anwendungen spielen Strömungen mit freier Oberfläche und im Grundwasserbereich oder sogar die Kopplung dieser beiden eine zentrale Rolle. Oftmals charakteristisch für diese Anwendungsszenarien sind große Rechengebiete und lange Simulationszeiten. Folglich ist das Berechnen akkurater Lösungen mit beträchtlichem Rechenaufwand verbunden und der Einsatz effizienter Lösungsverfahren sowie von Techniken des Hochleistungsrechnens obligatorisch, um Ergebnisse innerhalb eines annehmbaren Zeitrahmens zu erhalten. Unstetige Galerkinverfahren stellen eine Gruppe numerischer Verfahren zum Lösen von Differentialgleichungen dar, und kombinieren Eigenschaften von Methoden der Finiten Volumen- und Finiten Elementeverfahren. Sie ermöglichen hohe Approximationsordnungen, bieten einen hohen Grad an Flexibilität und sind für paralleles Rechnen gut geeignet. Diese Dissertation besteht aus acht Artikeln und einer erweiterten Zusammenfassung, in diesen die Anwendung unstetiger Galerkinverfahren auf mathematische Modelle inklusive solcher für Strömungen mit freier Oberfläche und im Grundwasserbereich beschrieben wird. Die behandelten Themen umfassen Diskretisierungs- und Implementierungsaspekte, die Parallelisierung der Methode sowie eine diskrete Stabilitätsanalyse des gekoppelten Modells