The Parallelism Motifs of Genomic Data Analysis

Genomic data sets are growing dramatically as the cost of sequencing continues to decline and small sequencing devices become available. Enormous community databases store and share this data with the research community, but some of these genomic data analysis problems require large scale computational platforms to meet both the memory and computational requirements. These applications differ from scientific simulations that dominate the workload on high end parallel systems today and place different requirements on programming support, software libraries, and parallel architectural design. For example, they involve irregular communication patterns such as asynchronous updates to shared data structures. We consider several problems in high performance genomics analysis, including alignment, profiling, clustering, and assembly for both single genomes and metagenomes. We identify some of the common computational patterns or motifs that help inform parallelization strategies and compare our motifs to some of the established lists, arguing that at least two key patterns, sorting and hashing, are missing

Recent Advances in Fully Dynamic Graph Algorithms

In recent years, significant advances have been made in the design and analysis of fully dynamic algorithms. However, these theoretical results have received very little attention from the practical perspective. Few of the algorithms are implemented and tested on real datasets, and their practical potential is far from understood. Here, we present a quick reference guide to recent engineering and theory results in the area of fully dynamic graph algorithms

An extensive study on iterative solver resilience : characterization, detection and prediction

Soft errors caused by transient bit flips have the potential to significantly impactan applicalion's behavior. This has motivated the design of an array of techniques to detect, isolate, and correct soft errors using microarchitectural, architectural, compilation­based, or application-level techniques to minimize their impact on the executing application. The first step toward the design of good error detection/correction techniques involves an understanding of an application's vulnerability to soft errors. This work focuses on silent data e orruption's effects on iterative solvers and efforts to mitigate those effects. In this thesis, we first present the first comprehensive characterizalion of !he impact of soft errors on !he convergen ce characteris tics of six iterative methods using application-level fault injection. We analyze the impact of soft errors In terms of the type of error (single-vs multi-bit), the distribution and location of bits affected, the data structure and statement impacted, and varialion with time. We create a public access database with more than 1.5 million fault injection results. We then analyze the performance of soft error detection mechanisms and present the comparalive results. Molivated by our observations, we evaluate a machine-learning based detector that takes as features that are the runtime features observed by the individual detectors to arrive al their conclusions. Our evalualion demonstrates improved results over individual detectors. We then propase amachine learning based method to predict a program's error behavior to make fault injection studies more efficient. We demonstrate this method on asse ssing the performance of soft error detectors. We show that our method maintains 84% accuracy on average with up to 53% less cost. We also show, once a model is trained further fault injection tests would cost 10% of the expected full fault injection runs.“Soft errors” causados por cambios de estado transitorios en bits, tienen el potencial de impactar significativamente el comportamiento de una aplicación. Esto, ha motivado el diseño de una variedad de técnicas para detectar, aislar y corregir soft errors aplicadas a micro-arquitecturas, arquitecturas, tiempo de compilación y a nivel de aplicación para minimizar su impacto en la ejecución de una aplicación. El primer paso para diseñar una buna técnica de detección/corrección de errores, implica el conocimiento de las vulnerabilidades de la aplicación ante posibles soft errors. Este trabajo se centra en los efectos de la corrupción silenciosa de datos en soluciones iterativas, así como en los esfuerzos para mitigar esos efectos. En esta tesis, primeramente, presentamos la primera caracterización extensiva del impacto de soft errors sobre las características convergentes de seis métodos iterativos usando inyección de fallos a nivel de aplicación. Analizamos el impacto de los soft errors en términos del tipo de error (único vs múltiples-bits), de la distribución y posición de los bits afectados, las estructuras de datos, instrucciones afectadas y de las variaciones en el tiempo. Creamos una base de datos pública con más de 1.5 millones de resultados de inyección de fallos. Después, analizamos el desempeño de mecanismos de detección de soft errors actuales y presentamos los resultados de su comparación. Motivados por las observaciones de los resultados presentados, evaluamos un detector de soft errors basado en técnicas de machine learning que toma como entrada las características observadas en el tiempo de ejecución individual de los detectores anteriores al llegar a su conclusión. La evaluación de los resultados obtenidos muestra una mejora por sobre los detectores individualmente. Basados en estos resultados propusimos un método basado en machine learning para predecir el comportamiento de los errores en un programa con el fin de hacer el estudio de inyección de errores mas eficiente. Presentamos este método para evaluar el rendimiento de los detectores de soft errors. Demostramos que nuestro método mantiene una precisión del 84% en promedio con hasta un 53% de mejora en el tiempo de ejecución. También mostramos que una vez que un modelo ha sido entrenado, las pruebas de inyección de errores siguientes costarían 10% del tiempo esperado de ejecución.Postprint (published version

APRIL: Approximating Polygons as Raster Interval Lists

The spatial intersection join an important spatial query operation, due to its popularity and high complexity. The spatial join pipeline takes as input two collections of spatial objects (e.g., polygons). In the filter step, pairs of object MBRs that intersect are identified and passed to the refinement step for verification of the join predicate on the exact object geometries. The bottleneck of spatial join evaluation is in the refinement step. We introduce APRIL, a powerful intermediate step in the pipeline, which is based on raster interval approximations of object geometries. Our technique applies a sequence of interval joins on 'intervalized' object approximations to determine whether the objects intersect or not. Compared to previous work, APRIL approximations are simpler, occupy much less space, and achieve similar pruning effectiveness at a much higher speed. Besides intersection joins between polygons, APRIL can directly be applied and has high effectiveness for polygonal range queries, within joins, and polygon-linestring joins. By applying a lightweight compression technique, APRIL approximations may occupy even less space than object MBRs. Furthermore, APRIL can be customized to apply on partitioned data and on polygons of varying sizes, rasterized at different granularities. Our last contribution is a novel algorithm that computes the APRIL approximation of a polygon without having to rasterize it in full, which is orders of magnitude faster than the computation of other raster approximations. Experiments on real data demonstrate the effectiveness and efficiency of APRIL; compared to the state-of-the-art intermediate filter, APRIL occupies 2x-8x less space, is 3.5x-8.5x more time-efficient, and reduces the end-to-end join cost up to 3 times.Comment: 12 page

A systematic review on cloud storage mechanisms concerning e-healthcare systems

As the expenses of medical care administrations rise and medical services experts are becoming rare, it is up to medical services organizations and institutes to consider the implementation of medical Health Information Technology (HIT) innovation frameworks. HIT permits health associations to smooth out their considerable cycles and offer types of assistance in a more productive and financially savvy way. With the rise of Cloud Storage Computing (CSC), an enormous number of associations and undertakings have moved their healthcare data sources to distributed storage. As the information can be mentioned whenever universally, the accessibility of information becomes an urgent need. Nonetheless, outages in cloud storage essentially influence the accessibility level. Like the other basic variables of cloud storage (e.g., reliability quality, performance, security, and protection), availability also directly impacts the data in cloud storage for e-Healthcare systems. In this paper, we systematically review cloud storage mechanisms concerning the healthcare environment. Additionally, in this paper, the state-of-the-art cloud storage mechanisms are critically reviewed for e-Healthcare systems based on their characteristics. In short, this paper summarizes existing literature based on cloud storage and its impact on healthcare, and it likewise helps researchers, medical specialists, and organizations with a solid foundation for future studies in the healthcare environment.Qatar University [IRCC-2020-009]

Parallel Working-Set Search Structures

In this paper we present two versions of a parallel working-set map on p processors that supports searches, insertions and deletions. In both versions, the total work of all operations when the map has size at least p is bounded by the working-set bound, i.e., the cost of an item depends on how recently it was accessed (for some linearization): accessing an item in the map with recency r takes O(1+log r) work. In the simpler version each map operation has O((log p)^2+log n) span (where n is the maximum size of the map). In the pipelined version each map operation on an item with recency r has O((log p)^2+log r) span. (Operations in parallel may have overlapping span; span is additive only for operations in sequence.) Both data structures are designed to be used by a dynamic multithreading parallel program that at each step executes a unit-time instruction or makes a data structure call. To achieve the stated bounds, the pipelined data structure requires a weak-priority scheduler, which supports a limited form of 2-level prioritization. At the end we explain how the results translate to practical implementations using work-stealing schedulers. To the best of our knowledge, this is the first parallel implementation of a self-adjusting search structure where the cost of an operation adapts to the access sequence. A corollary of the working-set bound is that it achieves work static optimality: the total work is bounded by the access costs in an optimal static search tree.Comment: Authors' version of a paper accepted to SPAA 201

A reference model for integrated energy and power management of HPC systems

Optimizing a computer for highest performance dictates the efficient use of its limited resources. Computers as a whole are rather complex. Therefore, it is not sufficient to consider optimizing hardware and software components independently. Instead, a holistic view to manage the interactions of all components is essential to achieve system-wide efficiency. For High Performance Computing (HPC) systems, today, the major limiting resources are energy and power. The hardware mechanisms to measure and control energy and power are exposed to software. The software systems using these mechanisms range from firmware, operating system, system software to tools and applications. Efforts to improve energy and power efficiency of HPC systems and the infrastructure of HPC centers achieve perpetual advances. In isolation, these efforts are unable to cope with the rising energy and power demands of large scale systems. A systematic way to integrate multiple optimization strategies, which build on complementary, interacting hardware and software systems is missing. This work provides a reference model for integrated energy and power management of HPC systems: the Open Integrated Energy and Power (OIEP) reference model. The goal is to enable the implementation, setup, and maintenance of modular system-wide energy and power management solutions. The proposed model goes beyond current practices, which focus on individual HPC centers or implementations, in that it allows to universally describe any hierarchical energy and power management systems with a multitude of requirements. The model builds solid foundations to be understandable and verifiable, to guarantee stable interaction of hardware and software components, for a known and trusted chain of command. This work identifies the main building blocks of the OIEP reference model, describes their abstract setup, and shows concrete instances thereof. A principal aspect is how the individual components are connected, interface in a hierarchical manner and thus can optimize for the global policy, pursued as a computing center's operating strategy. In addition to the reference model itself, a method for applying the reference model is presented. This method is used to show the practicality of the reference model and its application. For future research in energy and power management of HPC systems, the OIEP reference model forms a cornerstone to realize --- plan, develop and integrate --- innovative energy and power management solutions. For HPC systems themselves, it supports to transparently manage current systems with their inherent complexity, it allows to integrate novel solutions into existing setups, and it enables to design new systems from scratch. In fact, the OIEP reference model represents a basis for holistic efficient optimization.Computer auf höchstmögliche Rechenleistung zu optimieren bedingt Effizienzmaximierung aller limitierenden Ressourcen. Computer sind komplexe Systeme. Deshalb ist es nicht ausreichend, Hardware und Software isoliert zu betrachten. Stattdessen ist eine Gesamtsicht des Systems notwendig, um die Interaktionen aller Einzelkomponenten zu organisieren und systemweite Optimierungen zu ermöglichen. Für Höchstleistungsrechner (HLR) ist die limitierende Ressource heute ihre Leistungsaufnahme und der resultierende Gesamtenergieverbrauch. In aktuellen HLR-Systemen sind Energie- und Leistungsaufnahme programmatisch auslesbar als auch direkt und indirekt steuerbar. Diese Mechanismen werden in diversen Softwarekomponenten von Firmware, Betriebssystem, Systemsoftware bis hin zu Werkzeugen und Anwendungen genutzt und stetig weiterentwickelt. Durch die Komplexität der interagierenden Systeme ist eine systematische Optimierung des Gesamtsystems nur schwer durchführbar, als auch nachvollziehbar. Ein methodisches Vorgehen zur Integration verschiedener Optimierungsansätze, die auf komplementäre, interagierende Hardware- und Softwaresysteme aufbauen, fehlt. Diese Arbeit beschreibt ein Referenzmodell für integriertes Energie- und Leistungsmanagement von HLR-Systemen, das „Open Integrated Energy and Power (OIEP)“ Referenzmodell. Das Ziel ist ein Referenzmodell, dass die Entwicklung von modularen, systemweiten energie- und leistungsoptimierenden Sofware-Verbunden ermöglicht und diese als allgemeines hierarchisches Managementsystem beschreibt. Dies hebt das Modell von bisherigen Ansätzen ab, welche sich auf Einzellösungen, spezifischen Software oder die Bedürfnisse einzelner Rechenzentren beschränken. Dazu beschreibt es Grundlagen für ein planbares und verifizierbares Gesamtsystem und erlaubt nachvollziehbares und sicheres Delegieren von Energie- und Leistungsmanagement an Untersysteme unter Aufrechterhaltung der Befehlskette. Die Arbeit liefert die Grundlagen des Referenzmodells. Hierbei werden die Einzelkomponenten der Software-Verbunde identifiziert, deren abstrakter Aufbau sowie konkrete Instanziierungen gezeigt. Spezielles Augenmerk liegt auf dem hierarchischen Aufbau und der resultierenden Interaktionen der Komponenten. Die allgemeine Beschreibung des Referenzmodells erlaubt den Entwurf von Systemarchitekturen, welche letztendlich die Effizienzmaximierung der Ressource Energie mit den gegebenen Mechanismen ganzheitlich umsetzen können. Hierfür wird ein Verfahren zur methodischen Anwendung des Referenzmodells beschrieben, welches die Modellierung beliebiger Energie- und Leistungsverwaltungssystemen ermöglicht. Für Forschung im Bereich des Energie- und Leistungsmanagement für HLR bildet das OIEP Referenzmodell Eckstein, um Planung, Entwicklung und Integration von innovativen Lösungen umzusetzen. Für die HLR-Systeme selbst unterstützt es nachvollziehbare Verwaltung der komplexen Systeme und bietet die Möglichkeit, neue Beschaffungen und Entwicklungen erfolgreich zu integrieren. Das OIEP Referenzmodell bietet somit ein Fundament für gesamtheitliche effiziente Systemoptimierung

Exploiting Spatio-Temporal Coherence for Video Object Detection in Robotics

This paper proposes a method to enhance video object detection for indoor environments in robotics. Concretely, it exploits knowledge about the camera motion between frames to propagate previously detected objects to successive frames. The proposal is rooted in the concepts of planar homography to propose regions of interest where to find objects, and recursive Bayesian filtering to integrate observations over time. The proposal is evaluated on six virtual, indoor environments, accounting for the detection of nine object classes over a total of ∼ 7k frames. Results show that our proposal improves the recall and the F1-score by a factor of 1.41 and 1.27, respectively, as well as it achieves a significant reduction of the object categorization entropy (58.8%) when compared to a two-stage video object detection method used as baseline, at the cost of small time overheads (120 ms) and precision loss (0.92).</p

Proceedings of the 2nd Conference on Production Systems and Logistics (CPSL 2021)

Proceedings of the CPSL 202