Accelerating Regular-Expression Matching on FPGAs with High-Level Synthesis

The importance of security infrastructures for high-throughput networks has rapidly grown as a result of expanding internet traffic and increasingly high-bandwidth connections. Intrusion-detection systems (IDSs), such as SNORT, rely upon rule sets designed to alert system administrators of malicious packets. Methods for deep-packet inspection, which often depend upon regular-expression searches, can be accelerated on programmable-logic (PL) architectures using non-deterministic finite automata (NFAs). Prior designs have relied upon register-transfer level (RTL) design descriptions and have achieved efficient resource utilization through fine-grained optimizations. New advances made by field-programmable gate array (FPGA) vendors have led to powerful compiler toolchains for OpenCL and SYCL that allow for rapid development on PL architectures while generating competitive designs in terms of performance. The goal of this research is to evaluate performance differences between a custom, SYCL- and OpenCL-based, acceleration architecture for regular expressions and comparable RTL-based designs. The simplicity of the application, which requires only basic hardware building blocks, adds to the novelty of the comparison. In contrast to prior RTL-based solutions, which show frequency degradation with bandwidth scaling, this approach is able to maintain stable and high operating frequencies at the cost of resource usage. By scaling input bandwidth with multi-character transformations, high-throughput designs can be realized.Using Intel's OpenCL compiler, throughputs in excess of 17 Gbps can be achieved on Intel’s Arria 10 Programmable Acceleration Card and 19.4 Gbps with Intel's Stratix 10 Programmable Acceleration Card, outperforming similar designs with RTL, as reported in the literature. SYCL-based designs, synthesized with Intel's oneAPI compiler show performance degradation but still achieve higher throughput, up to 15.6 Gbps, than past RTL-based implementations. Overall, OpenCL and SYCL development yields both competitive results, when compared to the fine-grained RTL development process, and many ease-of-use improvements and design abstractions

Parallelization of dynamic programming recurrences in computational biology

The rapid growth of biosequence databases over the last decade has led to a performance bottleneck in the applications analyzing them. In particular, over the last five years DNA sequencing capacity of next-generation sequencers has been doubling every six months as costs have plummeted. The data produced by these sequencers is overwhelming traditional compute systems. We believe that in the future compute performance, not sequencing, will become the bottleneck in advancing genome science. In this work, we investigate novel computing platforms to accelerate dynamic programming algorithms, which are popular in bioinformatics workloads. We study algorithm-specific hardware architectures that exploit fine-grained parallelism in dynamic programming kernels using field-programmable gate arrays: FPGAs). We advocate a high-level synthesis approach, using the recurrence equation abstraction to represent dynamic programming and polyhedral analysis to exploit parallelism. We suggest a novel technique within the polyhedral model to optimize for throughput by pipelining independent computations on an array. This design technique improves on the state of the art, which builds latency-optimal arrays. We also suggest a method to dynamically switch between a family of designs using FPGA reconfiguration to achieve a significant performance boost. We have used polyhedral methods to parallelize the Nussinov RNA folding algorithm to build a family of accelerators that can trade resources for parallelism and are between 15-130x faster than a modern dual core CPU implementation. A Zuker RNA folding accelerator we built on a single workstation with four Xilinx Virtex 4 FPGAs outperforms 198 3 GHz Intel Core 2 Duo processors. Furthermore, our design running on a single FPGA is an order of magnitude faster than competing implementations on similar-generation FPGAs and graphics processors. Our work is a step toward the goal of automated synthesis of hardware accelerators for dynamic programming algorithms

ClickINC: In-network Computing as a Service in Heterogeneous Programmable Data-center Networks

In-Network Computing (INC) has found many applications for performance boosts or cost reduction. However, given heterogeneous devices, diverse applications, and multi-path network typologies, it is cumbersome and error-prone for application developers to effectively utilize the available network resources and gain predictable benefits without impeding normal network functions. Previous work is oriented to network operators more than application developers. We develop ClickINC to streamline the INC programming and deployment using a unified and automated workflow. ClickINC provides INC developers a modular programming abstractions, without concerning to the states of the devices and the network topology. We describe the ClickINC framework, model, language, workflow, and corresponding algorithms. Experiments on both an emulator and a prototype system demonstrate its feasibility and benefits

Scaling Up Delay Tolerant Networking

Delay Tolerant Networks (DTN) introduce a networking paradigm based on store, carry and forward. This makes DTN ideal for situations where nodes experience intermittent connectivity due to movement, less than ideal infrastructure, sparse networks or other challenging environmental conditions. Standardization efforts focused around the Bundle Protoocol (BP) (RFC 5050) aim to provide a generic set of protocols and technologies to build DTNs. However, there are several challenges when trying to apply the BP to the Internet as a whole that are tackled in this thesis: There is no DTN routing mechanism that can work in Internet-scale networks. Similarly, available discovery mechanisms for opportunistic contacts do not scale to the Internet. This work presents a solution offering pull-based name resolution that is able to represent the flat unstructured BP namespace in a distributed data structure and leaves routing through the Internet to the underlying IP layer. A second challenge is the large amount of data stored by DTN nodes in large-scale applications. Reconciling two large sets of data during an opportunistic contact without any previous state in a space efficient manner is a non-trivial problem. This thesis will present a very robust solution that is almost as efficient as Bloom filters while being able to avoid false positives that would prevent full reconciliation of the sets. Lastly, when designing networks that are based on agents willing to carry information, incentives are an important factor. This thesis proposes a financially sustainable system to incentive users to participate in a DTN with their private smartphones. A user study is conducted to get a lead on the main motivational factors that let people participate in a DTN. The study gives some insight under what conditions relying on continuous motivation and cooperation from private users is a reasonable assumption when designing a DTN.Delay Tolerant Networks (DTN) sind ein Konzept für Netzwerke, das auf der Idee beruht, Datenpakete bei Bedarf längere Zeit zu speichern und vor der Weiterleitung an einen anderen Knoten physikalisch zu transportieren. Diese Vorgehensweise erlaubt den Einsatz von DTN in Netzen, die häufige Unterbrechungen aufweisen. Mit dem Bundle Protocol (BP) (RFC 5050) wird ein Satz von Standardprotokollen für DTNs entwickelt. Wenn man das BP im Internet einsetzen möchte ergeben sich einige Herausforderungen: Es existiert kein DTN Routingverfahren, das skalierbar genug ist um im Internet eingesetzt zu werden. Das Gleiche trifft auf verfügbare Discovery Mechanismen für opportunistische Netze zu. In dieser Arbeit wird ein verteilter, reaktiver Mechanismus zur Namensauflösung im DTN vorgestellt, der den flachen, unstrukturierten Namensraum des BP abbilden kann und es ermöglicht das Routing komplett der IP Schicht zu überlassen. Eine weitere Herausforderung ist die große Menge an Nachrichten, die Knoten puffern müssen. Die effiziente Synchronisierung von zwei Datensets während eines opportunistischen Kontaktes, ohne Zustandsinformationen, ist ein komplexes Problem. Diese Arbeit schlägt einen robusten Algorithmus vor, der die Effizienz eines Bloom Filters hat, dabei jedoch die False Positives vermeidet, die normalerweise eine komplette Synchronisation verhindern würden. Ein DTN basiert darauf, dass Teilnehmer Daten puffern und transportieren. Wenn diese Teilnehmer z.B. private User mit Smarpthones sind, ist es essentiell diese Benutzer zu einer dauerhaften Teilnahme am Netzwerk zu motivieren. In dieser Arbeit wird ein finanziell tragfähiges System entwickelt, welches Benutzer für eine Teilnahme am DTN belohnt. Eine Benutzerstudie wurde durchgeführt, um herauszufinden, welche Faktoren Benutzer motivieren und unter welchen Umständen davon auszugehen ist, dass Benutzer wenn man das BP im Internet einsetzen möchte dauerhaft in einem DTN kooperieren und Resourcen zur Verfügung stellen

Event Generators for High-Energy Physics Experiments

We provide an overview of the status of Monte-Carlo event generators for high-energy particle physics. Guided by the experimental needs and requirements, we highlight areas of active development, and opportunities for future improvements. Particular emphasis is given to physics models and algorithms that are employed across a variety of experiments. These common themes in event generator development lead to a more comprehensive understanding of physics at the highest energies and intensities, and allow models to be tested against a wealth of data that have been accumulated over the past decades. A cohesive approach to event generator development will allow these models to be further improved and systematic uncertainties to be reduced, directly contributing to future experimental success. Event generators are part of a much larger ecosystem of computational tools. They typically involve a number of unknown model parameters that must be tuned to experimental data, while maintaining the integrity of the underlying physics models. Making both these data, and the analyses with which they have been obtained accessible to future users is an essential aspect of open science and data preservation. It ensures the consistency of physics models across a variety of experiments

Dependable Embedded Systems

This Open Access book introduces readers to many new techniques for enhancing and optimizing reliability in embedded systems, which have emerged particularly within the last five years. This book introduces the most prominent reliability concerns from today’s points of view and roughly recapitulates the progress in the community so far. Unlike other books that focus on a single abstraction level such circuit level or system level alone, the focus of this book is to deal with the different reliability challenges across different levels starting from the physical level all the way to the system level (cross-layer approaches). The book aims at demonstrating how new hardware/software co-design solution can be proposed to ef-fectively mitigate reliability degradation such as transistor aging, processor variation, temperature effects, soft errors, etc. Provides readers with latest insights into novel, cross-layer methods and models with respect to dependability of embedded systems; Describes cross-layer approaches that can leverage reliability through techniques that are pro-actively designed with respect to techniques at other layers; Explains run-time adaptation and concepts/means of self-organization, in order to achieve error resiliency in complex, future many core systems

Performance engineering of data-intensive applications

Data-intensive programs deal with big chunks of data and often contain compute-intensive characteristics. Among various HPC application domains, big data analytics, machine learning and the more recent deep-learning models are well-known data-intensive applications. An efficient design of such applications demands extensive knowledge of the target hardware and software, particularly the memory/cache hierarchy and the data communication among threads/processes. Such a requirement makes code development an arduous task, as inappropriate data structures and algorithm design may result in superfluous runtime, let alone hardware incompatibilities while porting the code to other platforms. In this dissertation, we introduce a set of tools and methods for the performance engineering of parallel data-intensive programs. We start with performance profiling to gain insights on thread communications and relevant code optimizations. Then, by narrowing down our scope to deep-learning applications, we introduce our tools for enhancing the performance portability and scalability of convolutional neural networks (ConvNet) at inference and training phases. Our first contribution is a novel performance-profiling method to unveil potential communication bottlenecks caused by data-access patterns and thread interactions. Our findings show that the data shared between a pair of threads should be reused with a reasonably short intervals to preserve data locality, yet existing profilers neglect them and mainly report the communication volume. We propose new hardware-independent metrics to characterize thread communication and provide suggestions for applying appropriate optimizations on a specific code region. Our experiments show that applying relevant optimizations improves the performance in Rodinia benchmarks by up to 56%. For the next contribution, we developed a framework for automatic generation of efficient and performance-portable convolution kernels, including Winograd convolutions, for various GPU platforms. We employed a synergy of meta-programming, symbolic execution, and auto-tuning. The results demonstrate efficient kernels generated through an automated optimization pipeline with runtimes close to vendor deep-learning libraries, and the minimum required programming effort confirms the performance portability of our approach. Furthermore, our symbolic execution method exploits repetitive patterns in Winograd convolutions, enabling us to reduce the number of arithmetic operations by up to 62% without compromising the numerical stability. Lastly, we investigate possible methods to scale the performance of ConvNets in training and inference phases. Our specialized training platform equipped with a novel topology-aware network pruning algorithm enables rapid training, neural architecture search, and network compression. Thus, an AI model training can be easily scaled to a multitude of compute nodes, leading to faster model design with less operating costs. Furthermore, the network compression component scales a ConvNet model down by removing redundant layers, preparing the model for a more pertinent deployment. Altogether, this work demonstrates the necessity and shows the benefit of performance engineering and parallel programming methods in accelerating emerging data-intensive workloads. With the help of the proposed tools and techniques, we pinpoint data communication bottlenecks and achieve performance portability and scalability in data-intensive applications

A framework for multidimensional indexes on distributed and highly-available data stores

Spatial Big Data is considered an essential trend in future scientific and business applications. Indeed, research instruments, medical devices, and social networks generate hundreds of peta bytes of spatial data per year. However, as many authors have pointed out, the lack of specialized frameworks dealing with such kind of data is limiting possible applications and probably precluding many scientific breakthroughs. In this thesis, we describe three HPC scientific applications, ranging from molecular dynamics, neuroscience analysis, and physics simulations, where we experience first hand the limits of the existing technologies. Thanks to our experience, we define the desirable missing functionalities, and we focus on two features that when combined significantly improve the way scientific data is analyzed. On one side, scientific simulations generate complex datasets where multiple correlated characteristics describe each item. For instance, a particle might have a space position (x,y,z) at a given time (t). If we want to find all elements within the same area and period, we either have to scan the whole dataset, or we must organize the data so that all items in the same space and time are stored together. The second approach is called Multidimensional Indexing (MI), and it uses different techniques to cluster and to organize similar data together. On the other side, approximate analytics has been often indicated as a smart and flexible way to explore large datasets in a short period. Approximate analytics includes a broad family of algorithms which aims to speed up analytical workloads by relaxing the precision of the results within a specific interval of confidence. For instance, if we want to know the average age in a group with 1-year precision, we can consider just a random fraction of all the people, thus reducing the amount of calculation. But if we also want less I/O operations, we need efficient data sampling, which means organizing data in a way that we do not need to scan the whole data set to generate a random sample of it. According to our analysis, combining Multidimensional Indexing with efficient data Sampling (MIS) is a vital missing feature not available in the current distributed data management solutions. This thesis aims to solve such a shortcoming and it provides novel scalable solutions. At first, we describe the existing data management alternatives; then we motivate our preference for NoSQL key-value databases. Secondly, we propose an analytical model to study the influence of data models on the scalability and performance of this kind of distributed database. Thirdly, we use the analytical model to design two novel multidimensional indexes with efficient data sampling: the D8tree and the AOTree. Our first solution, the D8tree, improves state of the art for approximate spatial queries on static and mostly read dataset. Later, we enhanced the data ingestion capability or our approach by introducing the AOTree, an algorithm that enables the query performance of the D8tree even for HPC write-intensive applications. We compared our solution with PostgreSQL and plain storage, and we demonstrate that our proposal has better performance and scalability. Finally, we describe Qbeast, the novel distributed system that implements the D8tree and the AOTree using NoSQL technologies, and we illustrate how Qbeast simplifies the workflow of scientists in various HPC applications providing a scalable and integrated solution for data analysis and management.La gestión de BigData con información espacial está considerada como una tendencia esencial en el futuro de las aplicaciones científicas y de negocio. De hecho, se generan cientos de petabytes de datos espaciales por año mediante instrumentos de investigación, dispositivos médicos y redes sociales. Sin embargo, tal y como muchos autores han señalado, la falta de entornos especializados en manejar este tipo de datos está limitando sus posibles aplicaciones y está impidiendo muchos avances científicos. En esta tesis, describimos 3 aplicaciones científicas HPC, que cubren los ámbitos de dinámica molecular, análisis neurocientífico y simulaciones físicas, donde hemos experimentado en primera mano las limitaciones de las tecnologías existentes. Gracias a nuestras experiencias, hemos podido definir qué funcionalidades serían deseables y no existen, y nos hemos centrado en dos características que, al combinarlas, mejoran significativamente la manera en la que se analizan los datos científicos. Por un lado, las simulaciones científicas generan conjuntos de datos complejos, en los que cada elemento es descrito por múltiples características correlacionadas. Por ejemplo, una partícula puede tener una posición espacial (x, y, z) en un momento dado (t). Si queremos encontrar todos los elementos dentro de la misma área y periodo, o bien recorremos y analizamos todo el conjunto de datos, o bien organizamos los datos de manera que se almacenen juntos todos los elementos que comparten área en un momento dado. Esta segunda opción se conoce como Indexación Multidimensional (IM) y usa diferentes técnicas para agrupar y organizar datos similares. Por otro lado, se suele señalar que las analíticas aproximadas son una manera inteligente y flexible de explorar grandes conjuntos de datos en poco tiempo. Este tipo de analíticas incluyen una amplia familia de algoritmos que acelera el tiempo de procesado, relajando la precisión de los resultados dentro de un determinado intervalo de confianza. Por ejemplo, si queremos saber la edad media de un grupo con precisión de un año, podemos considerar sólo un subconjunto aleatorio de todas las personas, reduciendo así la cantidad de cálculo. Pero si además queremos menos operaciones de entrada/salida, necesitamos un muestreo eficiente de datos, que implica organizar los datos de manera que no necesitemos recorrerlos todos para generar una muestra aleatoria. De acuerdo con nuestros análisis, la combinación de Indexación Multidimensional con Muestreo eficiente de datos (IMM) es una característica vital que no está disponible en las soluciones actuales de gestión distribuida de datos. Esta tesis pretende resolver esta limitación y proporciona unas soluciones novedosas que son escalables. En primer lugar, describimos las alternativas de gestión de datos que existen y motivamos nuestra preferencia por las bases de datos NoSQL basadas en clave-valor. En segundo lugar, proponemos un modelo analítico para estudiar la influencia que tienen los modelos de datos sobre la escalabilidad y el rendimiento de este tipo de bases de datos distribuidas. En tercer lugar, usamos el modelo analítico para diseñar dos novedosos algoritmos IMM: el D8tree y el AOTree. Nuestra primera solución, el D8tree, mejora el estado del arte actual para consultas espaciales aproximadas, cuando el conjunto de datos es estático y mayoritariamente de lectura. Después, mejoramos la capacidad de ingestión introduciendo el AOTree, un algoritmo que conserva el rendimiento del D8tree incluso para aplicaciones HPC intensivas en escritura. Hemos comparado nuestra solución con PostgreSQL y almacenamiento plano demostrando que nuestra propuesta mejora tanto el rendimiento como la escalabilidad. Finalmente, describimos Qbeast, el sistema que implementa los algoritmos D8tree y AOTree, e ilustramos cómo Qbeast simplifica el flujo de trabajo de los científicos ofreciendo una solución escalable e integraPostprint (published version

Helmholtz Portfolio Theme Large-Scale Data Management and Analysis (LSDMA)

The Helmholtz Association funded the "Large-Scale Data Management and Analysis" portfolio theme from 2012-2016. Four Helmholtz centres, six universities and another research institution in Germany joined to enable data-intensive science by optimising data life cycles in selected scientific communities. In our Data Life cycle Labs, data experts performed joint R&D together with scientific communities. The Data Services Integration Team focused on generic solutions applied by several communities