Parametric micro-level performance models for parallel computing and parallel implementation of hydrostatic MM5

This dissertation presents Parametric micro-level performance models and Parallel implementation of the hydrostatic version of MM5;Parametric micro-level (PM) performance models are introduced to address the important issue of how to realistically model parallel performance. These models can be used to predict execution times and identify performance bottlenecks. The accurate prediction and analysis of execution times is achieved by incorporating precise details of interprocessor communication, memory operations, auxiliary instructions, and effects of communication and computation schedules. The parameters provide the flexibility to study various algorithmic and architectural issues. The development and verification process, parameters and the scope of applicability of these models are discussed. A coherent view of performance is obtained from the execution profiles generated by PM models. The models are targeted at a large class numerical algorithms commonly implemented on both SIMD and MIMD machines. Specific models are presented for matrix multiplication, LU decomposition, and FFT on a 2-D processor array with distributed memory. A case study includes comparison of parallel machines and parallel algorithms. In a comparison of parallel machines, PM models are used to analyze execution times so as to relate the performance to architectural attributes of a machine. In a comparison of parallel algorithms, PM models are used to study performance of two LU decomposition algorithms: non-blocked and blocked. Two algorithms are compared to identify the tradeoffs between them. This analysis is useful to determine an optimum block size for the blocked algorithm. The case study is done on MasPar MP-1 and MP-2 machines;The dissertation also describes the parallel implementation of the hydrostatic version of MM5 (the fifth generation of Mesoscale Model), which has been widely used for climate studies. The model was parallelized in machine-independent manner using the Runtime System Library (RSL), a runtime library for handling message-passing and index transformation. The dissertation discusses validation of the parallel implementation of MM5 using field data and presents performance results. The parallel model was tested on the IBM SP1, a distributed memory parallel computer

Teadusarvutuse algoritmide taandamine hajusarvutuse raamistikele

Teadusarvutuses kasutatakse arvuteid ja algoritme selleks, et lahendada probleeme erinevates reaalteadustes nagu geneetika, bioloogia ja keemia. Tihti on eesmärgiks selliste loodusnähtuste modelleerimine ja simuleerimine, mida päris keskkonnas oleks väga raske uurida. Näiteks on võimalik luua päikesetormi või meteoriiditabamuse mudel ning arvutisimulatsioonide abil hinnata katastroofi mõju keskkonnale. Mida keerulisemad ja täpsemad on sellised simulatsioonid, seda rohkem arvutusvõimsust on vaja. Tihti kasutatakse selleks suurt hulka arvuteid, mis kõik samaaegselt töötavad ühe probleemi kallal. Selliseid arvutusi nimetatakse paralleel- või hajusarvutusteks. Hajusarvutuse programmide loomine on aga keeruline ning nõuab palju rohkem aega ja ressursse, kuna vaja on sünkroniseerida erinevates arvutites samaaegselt tehtavat tööd. On loodud mitmeid tarkvararaamistikke, mis lihtsustavad seda tööd automatiseerides osa hajusprogrammeerimisest. Selle teadustöö eesmärk oli uurida selliste hajusarvutusraamistike sobivust keerulisemate teadusarvutuse algoritmide jaoks. Tulemused näitasid, et olemasolevad raamistikud on üksteisest väga erinevad ning neist ükski ei ole sobiv kõigi erinevat tüüpi algoritmide jaoks. Mõni raamistik on sobiv ainult lihtsamate algoritmide jaoks; mõni ei sobi olukorras, kus andmed ei mahu arvutite mällu. Algoritmi jaoks kõige sobivama hajusarvutisraamistiku valimine võib olla väga keeruline ülesanne, kuna see nõuab olemasolevate raamistike uurimist ja rakendamist. Sellele probleemile lahendust otsides otsustati luua dünaamiline algoritmide modelleerimise rakendus (DAMR), mis oskab simuleerida algoritmi implementatsioone erinevates hajusarvutusraamistikes. DAMR aitab hinnata milline hajusraamistik on kõige sobivam ette antud algoritmi jaoks, ilma algoritmi reaalselt ühegi hajusraamistiku peale implementeerimata. Selle uurimustöö peamine panus on hajusarvutusraamistike kasutuselevõtu lihtsamaks tegemine teadlastele, kes ei ole varem nende kasutamisega kokku puutunud. See peaks märkimisväärselt aega ja ressursse kokku hoidma, kuna ei pea ükshaaval kõiki olemasolevaid hajusraamistikke tundma õppima ja rakendama.Scientific computing uses computers and algorithms to solve problems in various sciences such as genetics, biology and chemistry. Often the goal is to model and simulate different natural phenomena which would otherwise be very difficult to study in real environments. For example, it is possible to create a model of a solar storm or a meteor hit and run computer simulations to assess the impact of the disaster on the environment. The more sophisticated and accurate the simulations are the more computing power is required. It is often necessary to use a large number of computers, all working simultaneously on a single problem. These kind of computations are called parallel or distributed computing. However, creating distributed computing programs is complicated and requires a lot more time and resources, because it is necessary to synchronize different computers working at the same time. A number of software frameworks have been created to simplify this process by automating part of a distributed programming. The goal of this research was to assess the suitability of such distributed computing frameworks for complex scientific computing algorithms. The results showed that existing frameworks are very different from each other and none of them are suitable for all different types of algorithms. Some frameworks are only suitable for simple algorithms; others are not suitable when data does not fit into the computer memory. Choosing the most appropriate distributed computing framework for an algorithm can be a very complex task, because it requires studying and applying the existing frameworks. While searching for a solution to this problem, it was decided to create a Dynamic Algorithms Modelling Application (DAMA), which is able to simulate the implementation of the algorithm in different distributed computing frameworks. DAMA helps to estimate which distributed framework is the most appropriate for a given algorithm, without actually implementing it in any of the available frameworks. This main contribution of this study is simplifying the adoption of distributed computing frameworks for researchers who are not yet familiar with using them. It should save significant time and resources as it is not necessary to study each of the available distributed computing frameworks in detail

Partial aggregation for collective communication in distributed memory machines

High Performance Computing (HPC) systems interconnect a large number of Processing Elements (PEs) in high-bandwidth networks to simulate complex scientific problems. The increasing scale of HPC systems poses great challenges on algorithm designers. As the average distance between PEs increases, data movement across hierarchical memory subsystems introduces high latency. Minimizing latency is particularly challenging in collective communications, where many PEs may interact in complex communication patterns. Although collective communications can be optimized for network-level parallelism, occasional synchronization delays due to dependencies in the communication pattern degrade application performance. To reduce the performance impact of communication and synchronization costs, parallel algorithms are designed with sophisticated latency hiding techniques. The principle is to interleave computation with asynchronous communication, which increases the overall occupancy of compute cores. However, collective communication primitives abstract parallelism which limits the integration of latency hiding techniques. Approaches to work around these limitations either modify the algorithmic structure of application codes, or replace collective primitives with verbose low-level communication calls. While these approaches give fine-grained control for latency hiding, implementing collective communication algorithms is challenging and requires expertise knowledge about HPC network topologies. A collective communication pattern is commonly described as a Directed Acyclic Graph (DAG) where a set of PEs, represented as vertices, resolve data dependencies through communication along the edges. Our approach improves latency hiding in collective communication through partial aggregation. Based on mathematical rules of binary operations and homomorphism, we expose data parallelism in a respective DAG to overlap computation with communication. The proposed concepts are implemented and evaluated with a subset of collective primitives in the Message Passing Interface (MPI), an established communication standard in scientific computing. An experimental analysis with communication-bound microbenchmarks shows considerable performance benefits for the evaluated collective primitives. A detailed case study with a large-scale distributed sort algorithm demonstrates, how partial aggregation significantly improves performance in data-intensive scenarios. Besides better latency hiding capabilities with collective communication primitives, our approach enables further optimizations of their implementations within MPI libraries. The vast amount of asynchronous programming models, which are actively studied in the HPC community, benefit from partial aggregation in collective communication patterns. Future work can utilize partial aggregation to improve the interaction of MPI collectives with acclerator architectures, and to design more efficient communication algorithms

Efficient I/O for Computational Grid Applications

High-performance computing increasingly occurs on computational grids composed of heterogeneous and geographically distributed systems of computers, networks, and storage devices that collectively act as a single virtual computer. A key challenge in this environment is to provide efficient access to data distributed across remote data servers. This dissertation explores some of the issues associated with I/O for wide-area distributed computing and describes an I/O system, called Armada, with the following features: a framework to allow application and dataset providers to flexibly compose graphs of processing modules that describe the distribution, application interfaces, and processing required of the dataset before or after computation; an algorithm to restructure application graphs to increase parallelism and to improve network performance in a wide-area network; and a hierarchical graph-partitioning scheme that deploys components of the application graph in a way that is both beneficial to the application and sensitive to the administrative policies of the different administrative domains. Experiments show that applications using Armada perform well in both low- and high-bandwidth environments, and that our approach does an exceptional job of hiding the network latency inherent in grid computing

Realtime ray tracing and interactive global illumination

One of the most sought-for goals in computer graphics is to generate "realism in real time". i.e. the generation of realistically looking images at realtime frame rates. Today, virtually all approaches towards realtime rendering use graphics hardware, which is based almost exclusively on triangle rasterization. Unfortunately, though this technology has seen tremendous progress over the last few years, for many applications it is currently reaching its limits in both model complexity, supported features, and achievable realism. An alternative to triangle rasterizations is the ray tracing algorithm, which is well-known for its higher flexibility, its generally higher achievable realism, and its superior scalability in both model size and compute power. However, ray tracing is also computationally demanding and thus so far is used almost exclusively for high-quality offline rendering tasks. This dissertation focuses on the question why ray tracing is likely to soon play a larger role for interactive applications, and how this scenario can be reached. To this end, we discuss the RTRT/OpenRT realtime ray tracing system, a software based ray tracing system that achieves interactive to realtime frame rates on todays commodity CPUs. In particular, we discuss the overall system design, the efficient implementation of the core ray tracing algorithms, techniques for handling dynamic scenes, an efficient parallelization framework, and an OpenGL-like low-level API. Taken together, these techniques form a complete realtime rendering engine that supports massively complex scenes, highley realistic and physically correct shading, and even physically based lighting simulation at interactive rates. In the last part of this thesis we then discuss the implications and potential of realtime ray tracing on global illumination, and how the availability of this new technology can be leveraged to finally achieve interactive global illumination - the physically correct simulation of light transport at interactive rates.Eines der wichtigsten Ziele der Computer-Graphik ist die Generierung von "Realismus in Echtzeit\u27; — die Erzeugung von realistisch wirkenden, computer- generierten Bildern in Echtzeit. Heutige Echtzeit-Graphikanwendungen werden derzeit zum überwiegenden Teil mit schneller Graphik-Hardware realisiert, welche zum aktuellen Stand der Technik fast ausschliesslich auf dem Dreiecksrasterisierungsalgorithmus basiert. Obwohl diese Rasterisierungstechnologie in den letzten Jahren zunehmend beeindruckende Fortschritte gemacht hat, stößt sie heutzutage zusehends an ihre Grenzen, speziell im Hinblick auf Modellkomplexität, unterstützte Beleuchtungseffekte, und erreichbaren Realismus. Eine Alternative zur Dreiecksrasterisierung ist das "Ray-Tracing\u27; (Stahl-Rückverfolgung), welches weithin bekannt ist für seine höhere Flexibilität, seinen im Großen und Ganzen höheren erreichbaren Realismus, und seine bessere Skalierbarkeit sowohl in Szenengröße als auch in Rechner-Kapazitäten. Allerdings ist Ray-Tracing ebenso bekannt für seinen hohen Rechenbedarf, und wird daher heutzutage fast ausschließlich für die hochqualitative, nichtinteraktive Bildsynthese benutzt. Diese Dissertation behandelt die Gründe warum Ray-Tracing in näherer Zukunft voraussichtlich eine größere Rolle für interaktive Graphikanwendungen spielen wird, und untersucht, wie dieses Szenario des Echtzeit Ray-Tracing erreicht werden kann. Hierfür stellen wir das RTRT/OpenRT Echtzeit Ray-Tracing System vor, ein software-basiertes Ray-Tracing System, welches es erlaubt, interaktive Performanz auf heutigen Standard-PC-Prozessoren zu erreichen. Speziell diskutieren wir das grundlegende System-Design, die effiziente Implementierung der Kern-Algorithmen, Techniken zur Unterstützung von dynamischen Szenen, ein effizientes Parallelisierungs-Framework, und eine OpenGL-ähnliche Anwendungsschnittstelle. In ihrer Gesamtheit formen diese Techniken ein komplettes Echtzeit-Rendering-System, welches es erlaubt, extrem komplexe Szenen, hochgradig realistische und physikalisch korrekte Effekte, und sogar physikalisch-basierte Beleuchtungssimulation interaktiv zu berechnen. Im letzten Teil der Dissertation behandeln wir dann die Implikationen und das Potential, welches Echtzeit Ray-Tracing für die Globale Beleuchtungssimulation bietet, und wie die Verfügbarkeit dieser neuen Technologie benutzt werden kann, um letztendlich auch Globale Belechtung — die physikalisch korrekte Simulation des Lichttransports — interaktiv zu berechnen

The Investigation of Efficiency of Physical Phenomena Modelling Using Differential Equations on Distributed Systems

This work is dedicated to development of mathematical modelling software. In this dissertation numerical methods and algorithms are investigated in software making context. While applying a numerical method it is important to take into account the limited computer resources, the architecture of these resources and how do methods affect software robustness. Three main aspects of this investigation are that software implementation must be efficient, robust and be able to utilize specific hardware resources. The hardware specificity in this work is related to distributed computations of different types: single CPU with multiple cores, multiple CPUs with multiple cores and highly parallel multithreaded GPU device. The investigation is done in three directions: GPU usage for 3D FDTD calculations, FVM method usage to implement efficient calculations of a very specific heat transferring problem, and development of special techniques for software for specific bacteria self organization problem when the results are sensitive to numerical methods, initial data and even computer round-off errors. All these directions are dedicated to create correct technological components that make a software implementation robust and efficient. The time prediction model for 3D FDTD calculations is proposed, which lets to evaluate the efficiency of different GPUs. A reasonable speedup with GPU comparing to CPU is obtained. For FVM implementation the OpenFOAM open source software is selected as a basis for implementation of calculations and a few algorithms and their modifications to solve efficiency issues are proposed. The FVM parallel solver is implemented and analyzed, it is adapted to heterogeneous cluster Vilkas. To create robust software for simulation of bacteria self organization mathematically robust methods are applied and results are analyzed, the algorithm is modified for parallel computations

Software for Exascale Computing - SPPEXA 2016-2019

This open access book summarizes the research done and results obtained in the second funding phase of the Priority Program 1648 "Software for Exascale Computing" (SPPEXA) of the German Research Foundation (DFG) presented at the SPPEXA Symposium in Dresden during October 21-23, 2019. In that respect, it both represents a continuation of Vol. 113 in Springer’s series Lecture Notes in Computational Science and Engineering, the corresponding report of SPPEXA’s first funding phase, and provides an overview of SPPEXA’s contributions towards exascale computing in today's sumpercomputer technology. The individual chapters address one or more of the research directions (1) computational algorithms, (2) system software, (3) application software, (4) data management and exploration, (5) programming, and (6) software tools. The book has an interdisciplinary appeal: scholars from computational sub-fields in computer science, mathematics, physics, or engineering will find it of particular interest

Intelligent Energy-Savings and Process Improvement Strategies in Energy-Intensive Industries

S tím, jak se neustále vyvíjejí nové technologie pro energeticky náročná průmyslová odvětví, stávající zařízení postupně zaostávají v efektivitě a produktivitě. Tvrdá konkurence na trhu a legislativa v oblasti životního prostředí nutí tato tradiční zařízení k ukončení provozu a k odstavení. Zlepšování procesu a projekty modernizace jsou zásadní v udržování provozních výkonů těchto zařízení. Současné přístupy pro zlepšování procesů jsou hlavně: integrace procesů, optimalizace procesů a intenzifikace procesů. Obecně se v těchto oblastech využívá matematické optimalizace, zkušeností řešitele a provozní heuristiky. Tyto přístupy slouží jako základ pro zlepšování procesů. Avšak, jejich výkon lze dále zlepšit pomocí moderní výpočtové inteligence. Účelem této práce je tudíž aplikace pokročilých technik umělé inteligence a strojového učení za účelem zlepšování procesů v energeticky náročných průmyslových procesech. V této práci je využit přístup, který řeší tento problém simulací průmyslových systémů a přispívá následujícím: (i)Aplikace techniky strojového učení, která zahrnuje jednorázové učení a neuro-evoluci pro modelování a optimalizaci jednotlivých jednotek na základě dat. (ii) Aplikace redukce dimenze (např. Analýza hlavních komponent, autoendkodér) pro vícekriteriální optimalizaci procesu s více jednotkami. (iii) Návrh nového nástroje pro analýzu problematických částí systému za účelem jejich odstranění (bottleneck tree analysis – BOTA). Bylo také navrženo rozšíření nástroje, které umožňuje řešit vícerozměrné problémy pomocí přístupu založeného na datech. (iv) Prokázání účinnosti simulací Monte-Carlo, neuronové sítě a rozhodovacích stromů pro rozhodování při integraci nové technologie procesu do stávajících procesů. (v) Porovnání techniky HTM (Hierarchical Temporal Memory) a duální optimalizace s několika prediktivními nástroji pro podporu managementu provozu v reálném čase. (vi) Implementace umělé neuronové sítě v rámci rozhraní pro konvenční procesní graf (P-graf). (vii) Zdůraznění budoucnosti umělé inteligence a procesního inženýrství v biosystémech prostřednictvím komerčně založeného paradigmatu multi-omics.Zlepšení průmyslových procesů, Model založený na datech, Optimalizace procesu, Strojové učení, Průmyslové systémy, Energeticky náročná průmyslová odvětví, Umělá inteligence.