Lessons learned at 208K: Towards debugging millions of cores

Petascale systems will present several new challenges to performance and correctness tools. Such machines may contain millions of cores, requiring that tools use scalable data structures and analysis algorithms to collect and to process application data. In addition, at such scales, each tool itself will become a large parallel application – already, debugging the full BlueGene/L (BG/L) installation at the Lawrence Livermore National Laboratory requires employing 1664 tool daemons. To scale to such counts and beyond, tools must employ a scalable communication infrastructure and manage their own tool processes efficiently. Some system resources, such as the file system, may also become a tool bottleneck. In this paper, we present challenges to petascale tool development, using the Stack Trace Analysis Tool (STAT) as a case study. STAT is a lightweight tool that gathers and merges stack traces from a parallel application to identify process equivalence classes. We use results gathered at thousands of tasks on an Infiniband cluster and results up to 208K processes on BG/L to identify current scalability issues as well as challenges that will be faced at the petas-cale. We then present solutions to these challenges that have been implemented and show the resulting performance improvements. We also discuss future plans to meet the debugging demands of petascale machines.

Enhanced state history tree (eSHT): a stateful data structure for analysis of highly parallel system traces

Behaviors of distributed systems with many cores and/or many threads are difficult to understand. This is why dynamic analysis tools such as tracers are useful to collect run-time data and help programmers debug and optimize complex programs. However, manual trace analysis on very large traces with billions of events can be a difficult problem which automated trace visualizers and analyzers aim to solve. Trace analysis and visualization software needs fast access to data which it cannot achieve by searching through the entire trace for every query. A number of solutions have adopted stateful analysis which rearranges events into a more query friendly structures after a single pass through the trace. In this paper, we look into current implementations and model the behavior of previous work, the State History Tree (SHT), on traces with many thread creation and deletion. This allows us to identify which properties of the SHT are responsible for inefficient disk usage and high memory consumption. We then propose a more efficient data structure, the enhanced State History Tree (eSHT), to store and query computed states, in order to limit disk usage and reduce the query time for any state. Next, we compare the use of SHT and eSHT on traces with many attributes. We finally verify the scalability of our new data structure according to trace size. As shown by our results, the proposed solution makes near optimal use of disk space, reduces the algorithm's memory usage logarithmically for previously problematic cases, and speeds up queries on traces with many attributes by an order of magnitude. The proposed solution builds upon our previous work, enabling it to easily scale up to traces containing a million threads

R-SHT: A state history tree with R-Tree properties for analysis and visualization of highly parallel system traces

Understanding the behaviour of distributed computer systems with many threads and resources is a challenging task. Dynamic analysis tools such as tracers have been developed to assist programmers in debugging and optimizing the performance of such systems. However, complex systems can generate huge traces, with billions of events, which are hard to analyze manually. Trace visualization and analysis programs aim to solve this problem. Such software needs fast access to data, which a linear search through the trace cannot provide. Several programs have resorted to stateful analysis to rearrange data into more query friendly structures. In previous work, we suggested modifications to the State History Tree (SHT) data structure to correct its disk and memory usage. While the improved structure, eSHT, made near optimal disk usage and had reduced memory usage, we found that query performance, while twice as fast, exhibited scaling limitations. In this paper, we proposed a new structure using R-Tree techniques to improve query performance. We explain the hybrid scheme and algorithms used to optimize the structure to model the expected behaviour. Finally, we benchmark the data structure on highly parallel traces and on a demanding trace visualization use case. Our results show that the hybrid R-SHT structure retains the eSHT’s optimal disk usage properties while providing several orders of magnitude speed up to queries on highly parallel traces

Enhanced clustering analysis pipeline for performance analysis of parallel applications

Clustering analysis is widely used to stratify data in the same cluster when they are similar according to the specific metrics. We can use the cluster analysis to group the CPU burst of a parallel application, and the regions on each process in-between communication calls or calls to the parallel runtime. The resulting clusters obtained are the different computational trends or phases that appear in the application. These clusters are useful to understand the behavior of the computation part of the application and focus the analyses on those that present performance issues. Although density-based clustering algorithms are a powerful and efficient tool to summarize this type of information, their traditional user-guided clustering methodology has many shortcomings and deficiencies in dealing with the complexity of data, the diversity of data structures, high-dimensionality of data, and the dramatic increase in the amount of data. Consequently, the majority of DBSCAN-like algorithms have weaknesses to handle high-dimensionality and/or Multi-density data, and they are sensitive to their hyper-parameter configuration. Furthermore, extracting insight from the obtained clusters is an intuitive and manual task. To mitigate these weaknesses, we have proposed a new unified approach to replace the user-guided clustering with an automated clustering analysis pipeline, called Enhanced Cluster Identification and Interpretation (ECII) pipeline. To build the pipeline, we propose novel techniques including Robust Independent Feature Selection, Feature Space Curvature Map, Organization Component Analysis, and hyper-parameters tuning to feature selection, density homogenization, cluster interpretation, and model selection which are the main components of our machine learning pipeline. This thesis contributes four new techniques to the Machine Learning field with a particular use case in Performance Analytics field. The first contribution is a novel unsupervised approach for feature selection on noisy data, called Robust Independent Feature Selection (RIFS). Specifically, we choose a feature subset that contains most of the underlying information, using the same criteria as the Independent component analysis. Simultaneously, the noise is separated as an independent component. The second contribution of the thesis is a parametric multilinear transformation method to homogenize cluster densities while preserving the topological structure of the dataset, called Feature Space Curvature Map (FSCM). We present a new Gravitational Self-organizing Map to model the feature space curvature by plugging the concepts of gravity and fabric of space into the Self-organizing Map algorithm to mathematically describe the density structure of the data. To homogenize the cluster density, we introduce a novel mapping mechanism to project the data from the non-Euclidean curved space to a new Euclidean flat space. The third contribution is a novel topological-based method to study potentially complex high-dimensional categorized data by quantifying their shapes and extracting fine-grain insights from them to interpret the clustering result. We introduce our Organization Component Analysis (OCA) method for the automatic arbitrary cluster-shape study without an assumption about the data distribution. Finally, to tune the DBSCAN hyper-parameters, we propose a new tuning mechanism by combining techniques from machine learning and optimization domains, and we embed it in the ECII pipeline. Using this cluster analysis pipeline with the CPU burst data of a parallel application, we provide the developer/analyst with a high-quality SPMD computation structure detection with the added value that reflects the fine grain of the computation regions.El análisis de conglomerados se usa ampliamente para estratificar datos en el mismo conglomerado cuando son similares según las métricas específicas. Nosotros puede usar el análisis de clúster para agrupar la ráfaga de CPU de una aplicación paralela y las regiones en cada proceso intermedio llamadas de comunicación o llamadas al tiempo de ejecución paralelo. Los clusters resultantes obtenidos son las diferentes tendencias computacionales o fases que aparecen en la solicitud. Estos clusters son útiles para entender el comportamiento de la parte de computación del aplicación y centrar los análisis en aquellos que presenten problemas de rendimiento. Aunque los algoritmos de agrupamiento basados en la densidad son una herramienta poderosa y eficiente para resumir este tipo de información, su La metodología tradicional de agrupación en clústeres guiada por el usuario tiene muchas deficiencias y deficiencias al tratar con la complejidad de los datos, la diversidad de estructuras de datos, la alta dimensionalidad de los datos y el aumento dramático en la cantidad de datos. En consecuencia, el La mayoría de los algoritmos similares a DBSCAN tienen debilidades para manejar datos de alta dimensionalidad y/o densidad múltiple, y son sensibles a su configuración de hiperparámetros. Además, extraer información de los clústeres obtenidos es una forma intuitiva y tarea manual Para mitigar estas debilidades, hemos propuesto un nuevo enfoque unificado para reemplazar el agrupamiento guiado por el usuario con un canalización de análisis de agrupamiento automatizado, llamada canalización de identificación e interpretación de clúster mejorada (ECII). para construir el tubería, proponemos técnicas novedosas que incluyen la selección robusta de características independientes, el mapa de curvatura del espacio de características, Análisis de componentes de la organización y ajuste de hiperparámetros para la selección de características, homogeneización de densidad, agrupación interpretación y selección de modelos, que son los componentes principales de nuestra canalización de aprendizaje automático. Esta tesis aporta cuatro nuevas técnicas al campo de Machine Learning con un caso de uso particular en el campo de Performance Analytics. La primera contribución es un enfoque novedoso no supervisado para la selección de características en datos ruidosos, llamado Robust Independent Feature. Selección (RIFS).Específicamente, elegimos un subconjunto de funciones que contiene la mayor parte de la información subyacente, utilizando el mismo criterios como el análisis de componentes independientes. Simultáneamente, el ruido se separa como un componente independiente. La segunda contribución de la tesis es un método de transformación multilineal paramétrica para homogeneizar densidades de clústeres mientras preservando la estructura topológica del conjunto de datos, llamado Mapa de Curvatura del Espacio de Características (FSCM). Presentamos un nuevo Gravitacional Mapa autoorganizado para modelar la curvatura del espacio característico conectando los conceptos de gravedad y estructura del espacio en el Algoritmo de mapa autoorganizado para describir matemáticamente la estructura de densidad de los datos. Para homogeneizar la densidad del racimo, introducimos un mecanismo de mapeo novedoso para proyectar los datos del espacio curvo no euclidiano a un nuevo plano euclidiano espacio. La tercera contribución es un nuevo método basado en topología para estudiar datos categorizados de alta dimensión potencialmente complejos mediante cuantificando sus formas y extrayendo información detallada de ellas para interpretar el resultado de la agrupación. presentamos nuestro Método de análisis de componentes de organización (OCA) para el estudio automático de forma arbitraria de conglomerados sin una suposición sobre el distribución de datos.Postprint (published version

Visualising software in cyberspace

The problems of maintaining software systems are well documented. The increasing size and complexity of modern software serves only to worsen matters. Software maintainers are typically confronted with very large and very complex software systems, of which they may have little or no prior knowledge. At this stage they will normally have some maintenance task to perform, though possibly little indication of where or how to start. They need to investigate and understand the software to some extent in order to begin maintenance. This understanding process is termed program comprehension. There are various theories on program comprehension, many of which put emphasis on the construction of a mental model of the software within the mind of the maintainor. These same theories hypothesise a number of techniques employed by the maintainer for the creation and revision of this mental model. Software visualisation attempts to provide tool support for generating, supplementing and verifying the maintainer’s mental model. The majority of software visualisations to date have concentrated on producing two dimensional representations and animations of various aspects of a software system. Very little work has been performed previously regarding the issues involved in visualising software within a virtual reality environment. This research represents a significant first step into this exciting field and offers insight into the problems posed by this new media. This thesis provides an identification of the possibilities afforded byU3D graphics for software visualisation and program comprehension. It begins by defining seven key areas of 3D software visualisation, followed by the definition of two terms, visualisation and representation. These two terms provide a conceptual division between a visualisation and the elements of which it is comprised. This division enables improved discussion of the properties of a 3D visualisation and particularly the idenfification of properties that are desirable for a successful visualisation. A number of such desirable properties are suggested for both visualisations and representations, providing support for the design and evaluation of a 3D software visualisation system. Also presented are a number of prototype visualisations, each providing a different approach to the visualisation of a software system. The prototypes help demonstrate the practicalities and feasibility of 3D software visualisation. Evaluation of these prototypes is performed using a variety of techniques, the results of which emphasise the fact that there is substantial potential for the application of 3D graphics and virtual reality to software visualisation

Advanced Memory Data Structures for Scalable Event Trace Analysis

The thesis presents a contribution to the analysis and visualization of computational performance based on event traces with a particular focus on parallel programs and High Performance Computing (HPC). Event traces contain detailed information about specified incidents (events) during run-time of programs and allow minute investigation of dynamic program behavior, various performance metrics, and possible causes of performance flaws. Due to long running and highly parallel programs and very fine detail resolutions, event traces can accumulate huge amounts of data which become a challenge for interactive as well as automatic analysis and visualization tools. The thesis proposes a method of exploiting redundancy in the event traces in order to reduce the memory requirements and the computational complexity of event trace analysis. The sources of redundancy are repeated segments of the original program, either through iterative or recursive algorithms or through SPMD-style parallel programs, which produce equal or similar repeated event sequences. The data reduction technique is based on the novel Complete Call Graph (CCG) data structure which allows domain specific data compression for event traces in a combination of lossless and lossy methods. All deviations due to lossy data compression can be controlled by constant bounds. The compression of the CCG data structure is incorporated in the construction process, such that at no point substantial uncompressed parts have to be stored. Experiments with real-world example traces reveal the potential for very high data compression. The results range from factors of 3 to 15 for small scale compression with minimum deviation of the data to factors > 100 for large scale compression with moderate deviation. Based on the CCG data structure, new algorithms for the most common evaluation and analysis methods for event traces are presented, which require no explicit decompression. By avoiding repeated evaluation of formerly redundant event sequences, the computational effort of the new algorithms can be reduced in the same extent as memory consumption. The thesis includes a comprehensive discussion of the state-of-the-art and related work, a detailed presentation of the design of the CCG data structure, an elaborate description of algorithms for construction, compression, and analysis of CCGs, and an extensive experimental validation of all components.Diese Dissertation stellt einen neuartigen Ansatz für die Analyse und Visualisierung der Berechnungs-Performance vor, der auf dem Ereignis-Tracing basiert und insbesondere auf parallele Programme und das Hochleistungsrechnen (High Performance Computing, HPC) zugeschnitten ist. Ereignis-Traces (Ereignis-Spuren) enthalten detaillierte Informationen über spezifizierte Ereignisse während der Laufzeit eines Programms und erlauben eine sehr genaue Untersuchung des dynamischen Verhaltens, verschiedener Performance-Metriken und potentieller Performance-Probleme. Aufgrund lang laufender und hoch paralleler Anwendungen und dem hohen Detailgrad kann das Ereignis-Tracing sehr große Datenmengen produzieren. Diese stellen ihrerseits eine Herausforderung für interaktive und automatische Analyse- und Visualisierungswerkzeuge dar. Die vorliegende Arbeit präsentiert eine Methode, die Redundanzen in den Ereignis-Traces ausnutzt, um sowohl die Speicheranforderungen als auch die Laufzeitkomplexität der Trace-Analyse zu reduzieren. Die Ursachen für Redundanzen sind wiederholt ausgeführte Programmabschnitte, entweder durch iterative oder rekursive Algorithmen oder durch SPMD-Parallelisierung, die gleiche oder ähnliche Ereignis-Sequenzen erzeugen. Die Datenreduktion basiert auf der neuartigen Datenstruktur der "Vollständigen Aufruf-Graphen" (Complete Call Graph, CCG) und erlaubt eine Kombination von verlustfreier und verlustbehafteter Datenkompression. Dabei können konstante Grenzen für alle Abweichungen durch verlustbehaftete Kompression vorgegeben werden. Die Datenkompression ist in den Aufbau der Datenstruktur integriert, so dass keine umfangreichen unkomprimierten Teile vor der Kompression im Hauptspeicher gehalten werden müssen. Das enorme Kompressionsvermögen des neuen Ansatzes wird anhand einer Reihe von Beispielen aus realen Anwendungsszenarien nachgewiesen. Die dabei erzielten Resultate reichen von Kompressionsfaktoren von 3 bis 5 mit nur minimalen Abweichungen aufgrund der verlustbehafteten Kompression bis zu Faktoren > 100 für hochgradige Kompression. Basierend auf der CCG_Datenstruktur werden außerdem neue Auswertungs- und Analyseverfahren für Ereignis-Traces vorgestellt, die ohne explizite Dekompression auskommen. Damit kann die Laufzeitkomplexität der Analyse im selben Maß gesenkt werden wie der Hauptspeicherbedarf, indem komprimierte Ereignis-Sequenzen nicht mehrmals analysiert werden. Die vorliegende Dissertation enthält eine ausführliche Vorstellung des Stands der Technik und verwandter Arbeiten in diesem Bereich, eine detaillierte Herleitung der neu eingeführten Daten-strukturen, der Konstruktions-, Kompressions- und Analysealgorithmen sowie eine umfangreiche experimentelle Auswertung und Validierung aller Bestandteile

Linked Open Data - Creating Knowledge Out of Interlinked Data: Results of the LOD2 Project

Database Management; Artificial Intelligence (incl. Robotics); Information Systems and Communication Servic

Topology Control Multi-Objective Optimisation in Wireless Sensor Networks: Connectivity-Based Range Assignment and Node Deployment

The distinguishing characteristic that sets topology control apart from other methods, whose motivation is to achieve effects of energy minimisation and an increased network capacity, is its network-wide perspective. In other words, local choices made at the node-level always have the goal in mind of achieving a certain global, network-wide property, while not excluding the possibility for consideration of more localised factors. As such, our approach is marked by being a centralised computation of the available location-based data and its reduction to a set of non-homogeneous transmitting range assignments, which elicit a certain network-wide property constituted as a whole, namely, strong connectedness and/or biconnectedness. As a means to effect, we propose a variety of GA which by design is multi-morphic, where dependent upon model parameters that can be dynamically set by the user, the algorithm, acting accordingly upon either single or multiple objective functions in response. In either case, leveraging the unique faculty of GAs for finding multiple optimal solutions in a single pass. Wherefore it is up to the designer to select the singular solution which best meets requirements. By means of simulation, we endeavour to establish its relative performance against an optimisation typifying a standard topology control technique in the literature in terms of the proportion of time the network exhibited the property of strong connectedness. As to which, an analysis of the results indicates that such is highly sensitive to factors of: the effective maximum transmitting range, node density, and mobility scenario under observation. We derive an estimate of the optimal constitution thereof taking into account the specific conditions within the domain of application in that of a WSN, thereby concluding that only GA optimising for the biconnected components in a network achieves the stated objective of a sustained connected status throughout the duration.fi=Opinnäytetyö kokotekstinä PDF-muodossa.|en=Thesis fulltext in PDF format.|sv=Lärdomsprov tillgängligt som fulltext i PDF-format