High-Performance Computational and Information Technologies for Numerical Models and Data Processing

This chapter discusses high-performance computational and information technologies for numerical models and data processing. In the first part of the chapter, the numerical model of the oil displacement problem was considered by injection of chemical reagents to increase oil recovery of reservoir. Moreover the fragmented algorithm was developed for solving this problem and the algorithm for high-performance visualization of calculated data. Analysis and comparison of parallel algorithms based on the fragmented approach and using MPI technologies are also presented. The algorithm for solving given problem on mobile platforms and analysis of computational results is given too. In the second part of the chapter, the problem of unstructured and semi-structured data processing was considered. It was decided to address the task of n-gram extraction which requires a lot of computing with large amount of textual data. In order to deal with such complexity, there was a need to adopt and implement parallelization patterns. The second part of the chapter also describes parallel implementation of the document clustering algorithm that used a heuristic genetic algorithm. Finally, a novel UPC implementation of MapReduce framework for semi-structured data processing was introduced which allows to express data parallel applications using simple sequential code

Koneoppimiskehys petrokemianteollisuuden sovelluksille

Machine learning has many potentially useful applications in process industry, for example in process monitoring and control. Continuously accumulating process data and the recent development in software and hardware that enable more advanced machine learning, are fulfilling the prerequisites of developing and deploying process automation integrated machine learning applications which improve existing functionalities or even implement artificial intelligence. In this master's thesis, a framework is designed and implemented on a proof-of-concept level, to enable easy acquisition of process data to be used with modern machine learning libraries, and to also enable scalable online deployment of the trained models. The literature part of the thesis concentrates on studying the current state and approaches for digital advisory systems for process operators, as a potential application to be developed on the machine learning framework. The literature study shows that the approaches for process operators' decision support tools have shifted from rule-based and knowledge-based methods to machine learning. However, no standard methods can be concluded, and most of the use cases are quite application-specific. In the developed machine learning framework, both commercial software and open source components with permissive licenses are used. Data is acquired over OPC UA and then processed in Python, which is currently almost the de facto standard language in data analytics. Microservice architecture with containerization is used in the online deployment, and in a qualitative evaluation, it proved to be a versatile and functional solution.Koneoppimisella voidaan osoittaa olevan useita hyödyllisiä käyttökohteita prosessiteollisuudessa, esimerkiksi prosessinohjaukseen liittyvissä sovelluksissa. Jatkuvasti kerääntyvä prosessidata ja toisaalta koneoppimiseen soveltuvien ohjelmistojen sekä myös laitteistojen viimeaikainen kehitys johtavat tilanteeseen, jossa prosessiautomaatioon liitettyjen koneoppimissovellusten avulla on mahdollista parantaa nykyisiä toiminnallisuuksia tai jopa toteuttaa tekoälysovelluksia. Tässä diplomityössä suunniteltiin ja toteutettiin prototyypin tasolla koneoppimiskehys, jonka avulla on helppo käyttää prosessidataa yhdessä nykyaikaisten koneoppimiskirjastojen kanssa. Kehys mahdollistaa myös koneopittujen mallien skaalautuvan käyttöönoton. Diplomityön kirjallisuusosa keskittyy prosessioperaattoreille tarkoitettujen digitaalisten avustajajärjestelmien nykytilaan ja toteutustapoihin, avustajajärjestelmän tai sen päätöstukijärjestelmän ollessa yksi mahdollinen koneoppimiskehyksen päälle rakennettava ohjelma. Kirjallisuustutkimuksen mukaan prosessioperaattorin päätöstukijärjestelmien taustalla olevat menetelmät ovat yhä useammin koneoppimiseen perustuvia, aiempien sääntö- ja tietämyskantoihin perustuvien menetelmien sijasta. Selkeitä yhdenmukaisia lähestymistapoja ei kuitenkaan ole helposti pääteltävissä kirjallisuuden perusteella. Lisäksi useimmat tapausesimerkit ovat sovellettavissa vain kyseisissä erikoistapauksissa. Kehitetyssä koneoppimiskehyksessä on käytetty sekä kaupallisia että avoimen lähdekoodin komponentteja. Prosessidata haetaan OPC UA -protokollan avulla, ja sitä on mahdollista käsitellä Python-kielellä, josta on muodostunut lähes de facto -standardi data-analytiikassa. Kehyksen käyttöönottokomponentit perustuvat mikropalveluarkkitehtuuriin ja konttiteknologiaan, jotka osoittautuivat laadullisessa testauksessa monipuoliseksi ja toimivaksi toteutustavaksi

Effizientes Programmiermodell für OpenMP auf einem Cluster-basierten Many-Core-System

Da die Komplexität „System-on-Chip“ (SoC) auch weiterhin zunimmt, wird man die Herausforderungen aufgrund der Konvergenz der Software- und Hardwareentwicklung nicht ignorieren können. Dies gilt auch für den Umgang mit dem hierarchischen Design, in dem die Prozessorkerne in Clustern oder sogenannten „Tiles“ angeordnet werden, um mittels eines schnellen lokalen Speicherzugriffs eine geringe Latenz und eine hohe Bandbreite der lokalen Kommunikation zu gewährleisten. Aus der Sicht eines Programmierers ist es wünschenswert, sich diese Eigenheiten der Hardware zunutze zu machen und sie bei der Ausgestaltung der abstrakten Parallel-Programmierung gewissenhaft und zielführend zu berücksichtigen. Diese Dissertation überwindet viele Engpässe in Bezug auf die Skalierbarkeit Cluster-basierter Many-Core-Systeme und führt das Programmiermodell OpenMP zur Vereinfachung der Anwendungsentwicklung ein. OpenMP abstrahiert von der Sichtweise des Programmierers – und es werden Richtlinien eingeführt, mit denen Schleifen in Programmsequenzen eingeteilt werden, als Basis für die parallele Programmierung. In dieser Arbeit wird das OpenMP-Modell bespielhaft in einem konkreten Cluster-basierten Many-Core-System umgesetzt; dem Intel Single-Chip Cloud Computer (SCC). Es wird eine schlanke und hoch-optimierte Laufzeitschicht für die Ausführung von OpenMP sowie ein Speichermodell vorgestellt. Auf Basis dieser Laufzeitschicht wird der parallele Code automatisch von einem nativen Backend-Compiler (GCC 4.6) erzeugt, der mit der Laufzeitbibliothek verknüpft ist. Im Rahmen der Arbeit wird auf einen effizienten Designansatz für die OpenMP-Programmierung eingegangen, wobei der Intel SCC als Beispiel für Cluster-basierte Systeme zum Einsatz kommt. In nicht-Cache-kohärenten Systemen dient die SCC OpenMP Laufzeitbibliothek primär dazu, die folgenden Herausforderungen zu bewältigen: 1. Die Ausführung von unmodifizierten, bestehenden OpenMP Programmen auf solchen Systemen. 2. Die Portierung des OpenMP-Speichermodells auf den SCC. 3. Die Synchronisation der parallelen Threads, auf die ein beträchtlicher Anteil der Ausführungszeit einer Anwendung entfällt. Eine Reihe weiterer Beispiele, basierend auf verschiedenen gebräuchlichen Kernen und realen Anwendungen, untermauert die Tauglichkeit von OpenMP – und eine Reihe von Experimenten zeigt, wie dieses Modell zu einer deutlichen Beschleunigung (bis zu 48-fach) in verschiedenen parallelen Anwendungen führt.As the complexity of systems-on-chip (SoCs) continues to increase, it is no longer possible to ignore the challenges caused by the convergence of software and hardware development. This involves attempts to deal with the hierarchical design – in which several cores are grouped in clusters or tiles – to ensure low-latency, high-bandwidth local communication by relying on fast local memories. From a programmer’s perspec- tive, it is desirable to make use of these peculiarities of the hardware, which must be clearly and carefully taken into account when designing the support for high-level parallel programming models. This dissertation overcomes many scalability bottlenecks in cluster-based many-core systems and introduces the OpenMP programming model as a means of simplifying application development. OpenMP represents an abstraction of the programmer’s view by providing abundant directives that decompose loops in sequential programs and lead to parallel programs. In this work, the full OpenMP model is implemented on a specific instance of a cluster-based many-core system: the Intel Single-chip Cloud Computer (SCC). In this thesis, a lightweight and highly optimized runtime layer for OpenMP execution and memory model by generating the parallel code that is automatically compiled by native back-end compiler (GCC 4.6) that linked with the runtime library. In this dissertation, I will address an efficient design approach of the OpenMP pro- gramming model for the Intel SCC as an example for cluster-based systems. The SCC OpenMP runtime library is designed to cope with three main challenges in a non-cache coherent system: 1. Executing unmodified legacy OpenMP programs on such system. 2. Landing OpenMP memory model on the SCC. 3. Synchronization in the work of parallel threads accounts for a sizeable fraction of an application’s execution time. Furthermore, the effectiveness of OpenMP is demonstrated on a set of widely used kernels and real-world applications. An extensive set of experiments shows how this model achieves significant parallel speedups up to 48x in several applications

Using MapReduce Streaming for Distributed Life Simulation on the Cloud

Distributed software simulations are indispensable in the study of large-scale life models but often require the use of technically complex lower-level distributed computing frameworks, such as MPI. We propose to overcome the complexity challenge by applying the emerging MapReduce (MR) model to distributed life simulations and by running such simulations on the cloud. Technically, we design optimized MR streaming algorithms for discrete and continuous versions of Conway’s life according to a general MR streaming pattern. We chose life because it is simple enough as a testbed for MR’s applicability to a-life simulations and general enough to make our results applicable to various lattice-based a-life models. We implement and empirically evaluate our algorithms’ performance on Amazon’s Elastic MR cloud. Our experiments demonstrate that a single MR optimization technique called strip partitioning can reduce the execution time of continuous life simulations by 64%. To the best of our knowledge, we are the first to propose and evaluate MR streaming algorithms for lattice-based simulations. Our algorithms can serve as prototypes in the development of novel MR simulation algorithms for large-scale lattice-based a-life models.https://digitalcommons.chapman.edu/scs_books/1014/thumbnail.jp

Focus: A Graph Approach for Data-Mining and Domain-Specific Assembly of Next Generation Sequencing Data

Next Generation Sequencing (NGS) has emerged as a key technology leading to revolutionary breakthroughs in numerous biomedical research areas. These technologies produce millions to billions of short DNA reads that represent a small fraction of the original target DNA sequence. These short reads contain little information individually but are produced at a high coverage of the original sequence such that many reads overlap. Overlap relationships allow for the reads to be linearly ordered and merged by computational programs called assemblers into long stretches of contiguous sequence called contigs that can be used for research applications. Although the assembly of the reads produced by NGS remains a difficult task, it is the process of extracting useful knowledge from these relatively short sequences that has become one of the most exciting and challenging problems in Bioinformatics. The assembly of short reads is an aggregative process where critical information is lost as reads are merged into contigs. In addition, the assembly process is treated as a black box, with generic assembler tools that do not adapt to input data set characteristics. Finally, as NGS data throughput continues to increase, there is an increasing need for smart parallel assembler implementations. In this dissertation, a new assembly approach called Focus is proposed. Unlike previous assemblers, Focus relies on a novel hybrid graph constructed from multiple graphs at different levels of granularity to represent the assembly problem, facilitating information capture and dynamic adjustment to input data set characteristics. This work is composed of four specific aims: 1) The implementation of a robust assembly and analysis tool built on the hybrid graph platform 2) The development and application of graph mining to extract biologically relevant features in NGS data sets 3) The integration of domain specific knowledge to improve the assembly and analysis process. 4) The construction of smart parallel computing approaches, including the application of energy-aware computing for NGS assembly and knowledge integration to improve algorithm performance. In conclusion, this dissertation presents a complete parallel assembler called Focus that is capable of extracting biologically relevant features directly from its hybrid assembly graph

Laboratory Directed Research and Development FY2010 Annual Report

A premier applied-science laboratory, Lawrence Livermore National Laboratory (LLNL) has at its core a primary national security mission - to ensure the safety, security, and reliability of the nation's nuclear weapons stockpile without nuclear testing, and to prevent and counter the spread and use of weapons of mass destruction: nuclear, chemical, and biological. The Laboratory uses the scientific and engineering expertise and facilities developed for its primary mission to pursue advanced technologies to meet other important national security needs - homeland defense, military operations, and missile defense, for example - that evolve in response to emerging threats. For broader national needs, LLNL executes programs in energy security, climate change and long-term energy needs, environmental assessment and management, bioscience and technology to improve human health, and for breakthroughs in fundamental science and technology. With this multidisciplinary expertise, the Laboratory serves as a science and technology resource to the U.S. government and as a partner with industry and academia. This annual report discusses the following topics: (1) Advanced Sensors and Instrumentation; (2) Biological Sciences; (3) Chemistry; (4) Earth and Space Sciences; (5) Energy Supply and Use; (6) Engineering and Manufacturing Processes; (7) Materials Science and Technology; Mathematics and Computing Science; (8) Nuclear Science and Engineering; and (9) Physics