Aceleración de algoritmos de procesamiento de imágenes para el análisis de partículas individuales con microscopia electrónica

Tesis Doctoral inédita cotutelada por la Masaryk University (República Checa) y la Universidad Autónoma de Madrid, Escuela Politécnica Superior, Departamento de Ingeniería Informática. Fecha de Lectura: 24-10-2022Cryogenic Electron Microscopy (Cryo-EM) is a vital field in current structural biology. Unlike X-ray crystallography and Nuclear Magnetic Resonance, it can be used to analyze membrane proteins and other samples with overlapping spectral peaks. However, one of the significant limitations of Cryo-EM is the computational complexity. Modern electron microscopes can produce terabytes of data per single session, from which hundreds of thousands of particles must be extracted and processed to obtain a near-atomic resolution of the original sample. Many existing software solutions use high-Performance Computing (HPC) techniques to bring these computations to the realm of practical usability. The common approach to acceleration is parallelization of the processing, but in praxis, we face many complications, such as problem decomposition, data distribution, load scheduling, balancing, and synchronization. Utilization of various accelerators further complicates the situation, as heterogeneous hardware brings additional caveats, for example, limited portability, under-utilization due to synchronization, and sub-optimal code performance due to missing specialization. This dissertation, structured as a compendium of articles, aims to improve the algorithms used in Cryo-EM, esp. the SPA (Single Particle Analysis). We focus on the single-node performance optimizations, using the techniques either available or developed in the HPC field, such as heterogeneous computing or autotuning, which potentially needs the formulation of novel algorithms. The secondary goal of the dissertation is to identify the limitations of state-of-the-art HPC techniques. Since the Cryo-EM pipeline consists of multiple distinct steps targetting different types of data, there is no single bottleneck to be solved. As such, the presented articles show a holistic approach to performance optimization. First, we give details on the GPU acceleration of the specific programs. The achieved speedup is due to the higher performance of the GPU, adjustments of the original algorithm to it, and application of the novel algorithms. More specifically, we provide implementation details of programs for movie alignment, 2D classification, and 3D reconstruction that have been sped up by order of magnitude compared to their original multi-CPU implementation or sufficiently the be used on-the-fly. In addition to these three programs, multiple other programs from an actively used, open-source software package XMIPP have been accelerated and improved. Second, we discuss our contribution to HPC in the form of autotuning. Autotuning is the ability of software to adapt to a changing environment, i.e., input or executing hardware. Towards that goal, we present cuFFTAdvisor, a tool that proposes and, through autotuning, finds the best configuration of the cuFFT library for given constraints of input size and plan settings. We also introduce a benchmark set of ten autotunable kernels for important computational problems implemented in OpenCL or CUDA, together with the introduction of complex dynamic autotuning to the KTT tool. Third, we propose an image processing framework Umpalumpa, which combines a task-based runtime system, data-centric architecture, and dynamic autotuning. The proposed framework allows for writing complex workflows which automatically use available HW resources and adjust to different HW and data but at the same time are easy to maintainThe project that gave rise to these results received the support of a fellowship from the “la Caixa” Foundation (ID 100010434). The fellowship code is LCF/BQ/DI18/11660021. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 71367

Vers la Compression à Tous les Niveaux de la Hiérarchie de la Mémoire

Hardware compression techniques are typically simplifications of software compression methods. They must, however, comply with area, power and latency constraints. This study unveils the challenges of adopting compression in memory design. The goal of this analysis is not to summarize proposals, but to put in evidence the solutions they employ to handle those challenges. An in-depth description of the main characteristics of multiple methods is provided, as well as criteria that can be used as a basis for the assessment of such schemes.Typically, these schemes are not very efficient, and those that do compress well decompress slowly. This work explores their granularity to redefine their perspectives and improve their efficiency, through a concept called Region-Chunk compression. Its goal is to achieve low (good) compression ratio and fast decompression latency. The key observation is that by further sub-dividing the chunks of data being compressed one can reduce data duplication. This concept can be applied to several previously proposed compressors, resulting in a reduction of their average compressed size. In particular, a single-cycle-decompression compressor is boosted to reach a compressibility level competitive to state-of-the-art proposals.Finally, to increase the probability of successfully co-allocating compressed lines, Pairwise Space Sharing (PSS) is proposed. PSS can be applied orthogonally to compaction methods at no extra latency penalty, and with a cost-effective metadata overhead. The proposed system (Region-Chunk+PSS) further enhances the normalized average cache capacity by 2.7% (geometric mean), while featuring short decompression latency.Les techniques de compression matérielle sont généralement des simplifications des méthodes de compression logicielle. Elles doivent, toutefois, se conformer aux contraintes de surface, de puissance et de latence. Cette étude dévoile les défis de l’adoption de la compression dans la conception de la mémoire. Le but de l’analyse n’est pas de résumer les propositions, mais de mettre en évidence les solutions qu’ils emploient pour relever ces défis. Une description détaillée des principales caractéristiques de plusieurs méthodes est fournie, ainsi que des critères qui peuvent être utilisés comme base pour l’évaluation de ces systèmes.Généralement, ces schémas ne sont pas très efficaces, et les schémas qui compressent bien décompressent lentement. Ce travail explore leur granularité pour redéfinir leurs perspectives et améliorer leur efficacité, à travers un concept appelé compression Region-Chunk. Son objectif est d’obtenir un haut (bon) taux de compression et une latence de décompression rapide. L’observation clé est qu’en subdivisant davantage les blocs de données compressés, on peut réduire la duplication des données. Ce concept peut être appliqué à plusieurs compresseurs précédemment proposés, entraînant une réduction de leur taille moyenne compressée. En particulier, un compresseur à décompression à cycle unique est boosté pour atteindre un niveau de compressibilité compétitif par rapport aux propositions de pointe.Enfin, pour augmenter la probabilité de co-allouer avec succès des lignes compressées, Pairwise Space Sharing (PSS) est proposé. PSS peutêtre appliqué orthogonalement aux méthodes de compactage sans pénalité de latence supplémentaire, et avec une surcharge de métadonnées rentable. Le système proposé (Region-Chunk + PSS) améliore encore la capacité normalisé moyenne du cache de 2,7% (moyenne géométrique), tout en offrant une courte latence de décompression

Fundamental Approaches to Software Engineering

This open access book constitutes the proceedings of the 25th International Conference on Fundamental Approaches to Software Engineering, FASE 2022, which was held during April 4-5, 2022, in Munich, Germany, as part of the European Joint Conferences on Theory and Practice of Software, ETAPS 2022. The 17 regular papers presented in this volume were carefully reviewed and selected from 64 submissions. The proceedings also contain 3 contributions from the Test-Comp Competition. The papers deal with the foundations on which software engineering is built, including topics like software engineering as an engineering discipline, requirements engineering, software architectures, software quality, model-driven development, software processes, software evolution, AI-based software engineering, and the specification, design, and implementation of particular classes of systems, such as (self-)adaptive, collaborative, AI, embedded, distributed, mobile, pervasive, cyber-physical, or service-oriented applications

Development and certification of mixed-criticality embedded systems based on probabilistic timing analysis

An increasing variety of emerging systems relentlessly replaces or augments the functionality of mechanical subsystems with embedded electronics. For quantity, complexity, and use, the safety of such subsystems is an increasingly important matter. Accordingly, those systems are subject to safety certification to demonstrate system's safety by rigorous development processes and hardware/software constraints. The massive augment in embedded processors' complexity renders the arduous certification task significantly harder to achieve. The focus of this thesis is to address the certification challenges in multicore architectures: despite their potential to integrate several applications on a single platform, their inherent complexity imperils their timing predictability and certification. Recently, the Measurement-Based Probabilistic Timing Analysis (MBPTA) technique emerged as an alternative to deal with hardware/software complexity. The innovation that MBPTA brings about is, however, a major step from current certification procedures and standards. The particular contributions of this Thesis include: (i) the definition of certification arguments for mixed-criticality integration upon multicore processors. In particular we propose a set of safety mechanisms and procedures as required to comply with functional safety standards. For timing predictability, (ii) we present a quantitative approach to assess the likelihood of execution-time exceedance events with respect to the risk reduction requirements on safety standards. To this end, we build upon the MBPTA approach and we present the design of a safety-related source of randomization (SoR), that plays a key role in the platform-level randomization needed by MBPTA. And (iii) we evaluate current certification guidance with respect to emerging high performance design trends like caches. Overall, this Thesis pushes the certification limits in the use of multicore and MBPTA technology in Critical Real-Time Embedded Systems (CRTES) and paves the way towards their adoption in industry.Una creciente variedad de sistemas emergentes reemplazan o aumentan la funcionalidad de subsistemas mecánicos con componentes electrónicos embebidos. El aumento en la cantidad y complejidad de dichos subsistemas electrónicos así como su cometido, hacen de su seguridad una cuestión de creciente importancia. Tanto es así que la comercialización de estos sistemas críticos está sujeta a rigurosos procesos de certificación donde se garantiza la seguridad del sistema mediante estrictas restricciones en el proceso de desarrollo y diseño de su hardware y software. Esta tesis trata de abordar los nuevos retos y dificultades dadas por la introducción de procesadores multi-núcleo en dichos sistemas críticos: aunque su mayor rendimiento despierta el interés de la industria para integrar múltiples aplicaciones en una sola plataforma, suponen una mayor complejidad. Su arquitectura desafía su análisis temporal mediante los métodos tradicionales y, asimismo, su certificación es cada vez más compleja y costosa. Con el fin de lidiar con estas limitaciones, recientemente se ha desarrollado una novedosa técnica de análisis temporal probabilístico basado en medidas (MBPTA). La innovación de esta técnica, sin embargo, supone un gran cambio cultural respecto a los estándares y procedimientos tradicionales de certificación. En esta línea, las contribuciones de esta tesis están agrupadas en tres ejes principales: (i) definición de argumentos de seguridad para la certificación de aplicaciones de criticidad-mixta sobre plataformas multi-núcleo. Se definen, en particular, mecanismos de seguridad, técnicas de diagnóstico y reacción de faltas acorde con el estándar IEC 61508 sobre una arquitectura multi-núcleo de referencia. Respecto al análisis temporal, (ii) presentamos la cuantificación de la probabilidad de exceder un límite temporal y su relación con los requisitos de reducción de riesgos derivados de los estándares de seguridad funcional. Con este fin, nos basamos en la técnica MBPTA y presentamos el diseño de una fuente de números aleatorios segura; un componente clave para conseguir las propiedades aleatorias requeridas por MBPTA a nivel de plataforma. Por último, (iii) extrapolamos las guías actuales para la certificación de arquitecturas multi-núcleo a una solución comercial de 8 núcleos y las evaluamos con respecto a las tendencias emergentes de diseño de alto rendimiento (caches). Con estas contribuciones, esta tesis trata de abordar los retos que el uso de procesadores multi-núcleo y MBPTA implican en el proceso de certificación de sistemas críticos de tiempo real y facilita, de esta forma, su adopción por la industria.Postprint (published version

Fundamental Approaches to Software Engineering

This open access book constitutes the proceedings of the 25th International Conference on Fundamental Approaches to Software Engineering, FASE 2022, which was held during April 4-5, 2022, in Munich, Germany, as part of the European Joint Conferences on Theory and Practice of Software, ETAPS 2022. The 17 regular papers presented in this volume were carefully reviewed and selected from 64 submissions. The proceedings also contain 3 contributions from the Test-Comp Competition. The papers deal with the foundations on which software engineering is built, including topics like software engineering as an engineering discipline, requirements engineering, software architectures, software quality, model-driven development, software processes, software evolution, AI-based software engineering, and the specification, design, and implementation of particular classes of systems, such as (self-)adaptive, collaborative, AI, embedded, distributed, mobile, pervasive, cyber-physical, or service-oriented applications

Optimization of survey procedures and application of integrated digital tools for seismic risk mitigation of cultural heritage: The Emilia-Romagna damaged theatres.

Starting from current procedures, standards and tools for seismic damage survey, the research presents an integrated workflow for seismic damage documentation and survey applied to historic theatres in the Emilia-Romagna region damaged by the 2012 earthquake. The 2012 earthquake highlighted the fragility of the cultural heritage and underscored the lack of proactive conservation and management of historic assets. The research starts by analysing Agenzia Regionale per la Ricostruzione della Regione Emilia-Romagna- ARRER’s requests, which had found criticalities in applying the current Mic (Ministero della Cultura) procedures for the damage survey of complex types: the A-DC form for churches and the B-DP form for buildings. Using the two types of forms highlighted the lack of ad hoc tools for complex architectural styles such as castles, cemeteries and theatres, resulting in the loss of quantitative and qualitative information necessary for knowledge, conservation and thus management of the reconstruction process. As a result of these considerations, national and international standards of integrated documentation, existing digital databases for cataloguing and classification of cultural property, and seismic risk management were studied to develop a workflow of integrated procedures for seismic damage survey on the specific assigned case study: Regional Historic Theaters affected by the 2012 earthquake. The research used the holistic and interdisciplinary approach of integrated documentation to develop the integrated procedural workflow to enhance and optimise seismic damage detection operations in the case study. In providing a workflow of integrated procedures for the prevention and mitigation of hazards related to potential states of emergency, both natural and anthropic, the research follows an “extensive” methodological approach to test the survey outside the Emilia crater. The methodological framework led to the critical-comparative analysis, divided into two levels: the first involved studying critical issues in the B-DP form, mainly used in the 2012 theatre survey. The second level covered the techniques - laser scanning, digital photogrammetry - and integrated survey methodologies applied during the in-depth investigations for repair and restoration work. The critical-comparative analysis and morpho-typological study led to the development of an integrated procedural flow to survey damage in historic theatres. It is aimed at systematising and optimising the stages of damage documentation. The workflow consists of three information levels: L1. Screening level for the visual survey; L2 survey level defines the 3D acquisition steps for the geometric-dimensional study by theatres. The BIM L3 Plus level guides implementing the level of knowledge of parametric HBIM models for documentation, management and monitoring of historic theatres

Tools and Algorithms for the Construction and Analysis of Systems

This open access two-volume set constitutes the proceedings of the 27th International Conference on Tools and Algorithms for the Construction and Analysis of Systems, TACAS 2021, which was held during March 27 – April 1, 2021, as part of the European Joint Conferences on Theory and Practice of Software, ETAPS 2021. The conference was planned to take place in Luxembourg and changed to an online format due to the COVID-19 pandemic. The total of 41 full papers presented in the proceedings was carefully reviewed and selected from 141 submissions. The volume also contains 7 tool papers; 6 Tool Demo papers, 9 SV-Comp Competition Papers. The papers are organized in topical sections as follows: Part I: Game Theory; SMT Verification; Probabilities; Timed Systems; Neural Networks; Analysis of Network Communication. Part II: Verification Techniques (not SMT); Case Studies; Proof Generation/Validation; Tool Papers; Tool Demo Papers; SV-Comp Tool Competition Papers

Computational Intelligence and Human- Computer Interaction: Modern Methods and Applications

The present book contains all of the articles that were accepted and published in the Special Issue of MDPI’s journal Mathematics titled "Computational Intelligence and Human–Computer Interaction: Modern Methods and Applications". This Special Issue covered a wide range of topics connected to the theory and application of different computational intelligence techniques to the domain of human–computer interaction, such as automatic speech recognition, speech processing and analysis, virtual reality, emotion-aware applications, digital storytelling, natural language processing, smart cars and devices, and online learning. We hope that this book will be interesting and useful for those working in various areas of artificial intelligence, human–computer interaction, and software engineering as well as for those who are interested in how these domains are connected in real-life situations

Software doping – Theory and detection

Software is doped if it contains a hidden functionality that is intentionally included by the manufacturer and is not in the interest of the user or society. This thesis complements this informal definition by a set of formal cleanness definitions that characterise the absence of software doping. These definitions reflect common expectations on clean software behaviour and are applicable to many types of software, from printers to cars to discriminatory AI systems. We use these definitions to propose white-box and black-box analysis techniques to detect software doping. In particular, we present a provably correct, model-based testing algorithm that is intertwined with a probabilistic-falsification-based test input selection technique. We identify and explain how to overcome the challenges that are specific to real-world software doping tests and analyses. The most prominent example of software doping in recent years is the Diesel Emissions Scandal. We demonstrate the strength of our cleanness definitions and analysis techniques by applying them to emission cleaning systems of diesel cars. All our car related research is unified in a Car Data Platform. The mobile app LolaDrives is one building block of this platform; it supports conducting real-driving emissions tests and provides feedback to the user in how far a trip satisfies driving conditions that are defined by official regulations.Software ist gedopt wenn sie eine versteckte Funktionalität enthält, die vom Hersteller beabsichtigt ist und deren Existenz nicht im Interesse des Benutzers oder der Gesellschaft ist. Die vorliegende Arbeit ergänzt diese nicht formale Definition um eine Menge von Cleanness-Definitionen, die die Abwesenheit von Software Doping charakterisieren. Diese Definitionen spiegeln allgemeine Erwartungen an "sauberes" Softwareverhalten wider und sie sind auf viele Arten von Software anwendbar, vom Drucker über Autos bis hin zu diskriminierenden KI-Systemen. Wir verwenden diese Definitionen um sowohl white-box, als auch black-box Analyseverfahren zur Verfügung zu stellen, die in der Lage sind Software Doping zu erkennen. Insbesondere stellen wir einen korrekt bewiesenen Algorithmus für modellbasierte Tests vor, der eng verflochten ist mit einer Test-Input-Generierung basierend auf einer Probabilistic-Falsification-Technik. Wir identifizieren Hürden hinsichtlich Software-Doping-Tests in der echten Welt und erklären, wie diese bewältigt werden können. Das bekannteste Beispiel für Software Doping in den letzten Jahren ist der Diesel-Abgasskandal. Wir demonstrieren die Fähigkeiten unserer Cleanness-Definitionen und Analyseverfahren, indem wir diese auf Abgasreinigungssystem von Dieselfahrzeugen anwenden. Unsere gesamte auto-basierte Forschung kommt in der Car Data Platform zusammen. Die mobile App LolaDrives ist eine Kernkomponente dieser Plattform; sie unterstützt bei der Durchführung von Abgasmessungen auf der Straße und gibt dem Fahrer Feedback inwiefern eine Fahrt den offiziellen Anforderungen der EU-Norm der Real-Driving Emissions entspricht