Programming Persistent Memory

Beginning and experienced programmers will use this comprehensive guide to persistent memory programming. You will understand how persistent memory brings together several new software/hardware requirements, and offers great promise for better performance and faster application startup times—a huge leap forward in byte-addressable capacity compared with current DRAM offerings. This revolutionary new technology gives applications significant performance and capacity improvements over existing technologies. It requires a new way of thinking and developing, which makes this highly disruptive to the IT/computing industry. The full spectrum of industry sectors that will benefit from this technology include, but are not limited to, in-memory and traditional databases, AI, analytics, HPC, virtualization, and big data. Programming Persistent Memory describes the technology and why it is exciting the industry. It covers the operating system and hardware requirements as well as how to create development environments using emulated or real persistent memory hardware. The book explains fundamental concepts; provides an introduction to persistent memory programming APIs for C, C++, JavaScript, and other languages; discusses RMDA with persistent memory; reviews security features; and presents many examples. Source code and examples that you can run on your own systems are included. What You’ll Learn Understand what persistent memory is, what it does, and the value it brings to the industry Become familiar with the operating system and hardware requirements to use persistent memory Know the fundamentals of persistent memory programming: why it is different from current programming methods, and what developers need to keep in mind when programming for persistence Look at persistent memory application development by example using the Persistent Memory Development Kit (PMDK) Design and optimize data structures for persistent memory Study how real-world applications are modified to leverage persistent memory Utilize the tools available for persistent memory programming, application performance profiling, and debugging Who This Book Is For C, C++, Java, and Python developers, but will also be useful to software, cloud, and hardware architects across a broad spectrum of sectors, including cloud service providers, independent software vendors, high performance compute, artificial intelligence, data analytics, big data, etc

ADDING PERSISTENCE TO MAIN MEMORY PROGRAMMING

Unlocking the true potential of the new persistent memories (PMEMs) requires eliminating traditional persistent I/O abstractions altogether, by introducing persistent semantics directly into main memory programming. Such a programming model elevates failure atomicity to a first-class application property in addition to in-memory data layout, concurrency-control, and fault tolerance, and therefore requires redesign of programming abstractions for both program correctness and maximum performance gains. To address these challenges, this thesis proposes a set of system software designs that integrate persistence with main memory programming, and makes the following contributions. First, this thesis proposes a PMEM-aware I/O runtime, NVStream, that supports fast durable streaming I/O. NVStream uses a memory-based I/O interface that integrates with existing I/O data movement operations of an application to accelerate persistent data writes. NVStream carefully designs its persistent data storage layout and crash-consistent semantics to match both application and PMEM characteristics. Specifically, we leverage the streaming nature of I/O in HPC workflows, to benefit from using a log-structured PMEM storage engine design, that uses relaxed write orderings and append-only failure-atomic semantics to form strongly consistent application checkpoints. Furthermore, we identify that optimizing the I/O software stack exposes the PMEM bandwidth limitations as a bottleneck during parallel HPC I/O writes, and propose a novel data movement design – PHX. PHX uses alternative network data movement paths available in datacenters to ease up the bandwidth pressure on the PMEM memory interconnects, all while maintaining the correctness of the persistent data. Next, the thesis explores the challenges and opportunities of using PMEM for true main memory persistent programming – a single data domain for both runtime and persistent applicationstate. Such a programming model includes maintaining ACID properties during each and every update to applications persistent structures. ACID-qualified persistent programming for multi-threaded applications is hard, as the programmer has to reason about both crash-consistency and synchronization – crash-sync – semantics for programming correctness. The thesis contributes new understanding of the correctness requirements for mixing different crash-consistent and synchronization protocols, characterizes the performance of different crash-sync realizations for different applications and hardware architectures, and draws actionable insights for future designs of PMEM systems. Finally, the application state stored on node-local persistent memory is still vulnerable to catastrophic node failures. The thesis proposes a replicated persistent memory runtime, Blizzard, that supports truly fault tolerant, concurrent and persistent data-structure programming. Blizzard carefully integrates userspace networking with byte addressable PMEM for a fast, persistent memory replication runtime. The design also incorporates a replication-aware crash-sync protocol that supports consistent and concurrent updates on persistent data-structures. Blizzard offers applications the flexibility to use the data structures that best match their functional requirements, while offering better performance, and providing crucial reliability guarantees lacking from existing persistent memory runtimes.Ph.D

Architectural Principles for Database Systems on Storage-Class Memory

Database systems have long been optimized to hide the higher latency of storage media, yielding complex persistence mechanisms. With the advent of large DRAM capacities, it became possible to keep a full copy of the data in DRAM. Systems that leverage this possibility, such as main-memory databases, keep two copies of the data in two different formats: one in main memory and the other one in storage. The two copies are kept synchronized using snapshotting and logging. This main-memory-centric architecture yields nearly two orders of magnitude faster analytical processing than traditional, disk-centric ones. The rise of Big Data emphasized the importance of such systems with an ever-increasing need for more main memory. However, DRAM is hitting its scalability limits: It is intrinsically hard to further increase its density. Storage-Class Memory (SCM) is a group of novel memory technologies that promise to alleviate DRAM’s scalability limits. They combine the non-volatility, density, and economic characteristics of storage media with the byte-addressability and a latency close to that of DRAM. Therefore, SCM can serve as persistent main memory, thereby bridging the gap between main memory and storage. In this dissertation, we explore the impact of SCM as persistent main memory on database systems. Assuming a hybrid SCM-DRAM hardware architecture, we propose a novel software architecture for database systems that places primary data in SCM and directly operates on it, eliminating the need for explicit IO. This architecture yields many benefits: First, it obviates the need to reload data from storage to main memory during recovery, as data is discovered and accessed directly in SCM. Second, it allows replacing the traditional logging infrastructure by fine-grained, cheap micro-logging at data-structure level. Third, secondary data can be stored in DRAM and reconstructed during recovery. Fourth, system runtime information can be stored in SCM to improve recovery time. Finally, the system may retain and continue in-flight transactions in case of system failures. However, SCM is no panacea as it raises unprecedented programming challenges. Given its byte-addressability and low latency, processors can access, read, modify, and persist data in SCM using load/store instructions at a CPU cache line granularity. The path from CPU registers to SCM is long and mostly volatile, including store buffers and CPU caches, leaving the programmer with little control over when data is persisted. Therefore, there is a need to enforce the order and durability of SCM writes using persistence primitives, such as cache line flushing instructions. This in turn creates new failure scenarios, such as missing or misplaced persistence primitives. We devise several building blocks to overcome these challenges. First, we identify the programming challenges of SCM and present a sound programming model that solves them. Then, we tackle memory management, as the first required building block to build a database system, by designing a highly scalable SCM allocator, named PAllocator, that fulfills the versatile needs of database systems. Thereafter, we propose the FPTree, a highly scalable hybrid SCM-DRAM persistent B+-Tree that bridges the gap between the performance of transient and persistent B+-Trees. Using these building blocks, we realize our envisioned database architecture in SOFORT, a hybrid SCM-DRAM columnar transactional engine. We propose an SCM-optimized MVCC scheme that eliminates write-ahead logging from the critical path of transactions. Since SCM -resident data is near-instantly available upon recovery, the new recovery bottleneck is rebuilding DRAM-based data. To alleviate this bottleneck, we propose a novel recovery technique that achieves nearly instant responsiveness of the database by accepting queries right after recovering SCM -based data, while rebuilding DRAM -based data in the background. Additionally, SCM brings new failure scenarios that existing testing tools cannot detect. Hence, we propose an online testing framework that is able to automatically simulate power failures and detect missing or misplaced persistence primitives. Finally, our proposed building blocks can serve to build more complex systems, paving the way for future database systems on SCM

tlCell: a software transactional memory for the cell broadband engine architecture

Dissertação apresentada na Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa para a obtenção do Grau de Mestre em Engenharia InformáticaOs computadores evoluíram exponencialmente na ultima década. A performance tem sido o principal objectivo resultando no aumento do frequência dos processadores, situação que já não é fazível devido ao consumo de energia exagerado dos processadores actuais. A arquitectura Cell Broadband Engine começou com o objectivo de providenciar alta capacidade computacional com um baixo consumo energético. O resultado é uma arquitectura com multiprocessadores heterogéneos e uma distribuição de memória única com vista a alto desempenho e redução da complexidade do hardware para reduzir o custo de produção. Espera-se que as técnicas de concorrência e paralelismo aumentem a performance desta arquitectura, no entanto as soluções de alto desempenho apresentadas s˜ao sempre muito especificas e devido à sua arquitectura e distribuição de memória inovadora ´e ainda difícil apresentar ferramentas passíveis de explorar concorrência e paralelismo como um camada de abstracção. Memória Transaccional por Software é um modelo de programação que propõe este nível de abstracção e tem vindo a ganhar popularidade existindo já variadas implementações com performance perto de soluções específicas de grão fino. A possibilidade de usar Memória Transaccional por Software nesta arquitectura inovadora, desenvolvendo uma ferramenta capaz de abstrair o programador da consistência e gestão de memória é apelativo. Neste documento especifica-se uma plataforma deffered-update de Memória Transactional por Software para a arquitectura Cell Broadband Engine que tira partido da capacidade computacional dos Synergistic Processing Elements (SPEs) usando locks em commit-time. São propostos dois modelos diferentes, fully local e multi-buffered de forma a poder estudar as implicações das escolhas feitas no desenho da plataforma

Design and evaluation of a Thread-Level Speculation runtime library

En los próximos años es más que probable que máquinas con cientos o incluso miles de procesadores sean algo habitual. Para aprovechar estas máquinas, y debido a la dificultad de programar de forma paralela, sería deseable disponer de sistemas de compilación o ejecución que extraigan todo el paralelismo posible de las aplicaciones existentes. Así en los últimos tiempos se han propuesto multitud de técnicas paralelas. Sin embargo, la mayoría de ellas se centran en códigos simples, es decir, sin dependencias entre sus instrucciones. La paralelización especulativa surge como una solución para estos códigos complejos, posibilitando la ejecución de cualquier tipo de códigos, con o sin dependencias. Esta técnica asume de forma optimista que la ejecución paralela de cualquier tipo de código no de lugar a errores y, por lo tanto, necesitan de un mecanismo que detecte cualquier tipo de colisión. Para ello, constan de un monitor responsable que comprueba constantemente que la ejecución no sea errónea, asegurando que los resultados obtenidos de forma paralela sean similares a los de cualquier ejecución secuencial. En caso de que la ejecución fuese errónea los threads se detendrían y reiniciarían su ejecución para asegurar que la ejecución sigue la semántica secuencial. Nuestra contribución en este campo incluye (1) una nueva librería de ejecución especulativa fácil de utilizar; (2) nuevas propuestas que permiten reducir de forma significativa el número de accesos requeridos en las peraciones especulativas, así como consejos para reducir la memoria a utilizar; (3) propuestas para mejorar los métodos de scheduling centradas en la gestión dinámica de los bloques de iteraciones utilizados en las ejecuciones especulativas; (4) una solución híbrida que utiliza memoria transaccional para implementar las secciones críticas de una librería de paralelización especulativa; y (5) un análisis de las técnicas especulativas en uno de los dispositivos más vanguardistas del momento, los coprocesadores Intel Xeon Phi. Como hemos podido comprobar, la paralelización especulativa es un campo de investigación activo. Nuestros resultados demuestran que esta técnica permite obtener mejoras de rendimiento en un gran número de aplicaciones. Así, esperamos que este trabajo contribuya a facilitar el uso de soluciones especulativas en compiladores comerciales y/o modelos de programación paralela de memoria compartida.Departamento de Informática (Arquitectura y Tecnología de Computadores, Ciencias de la Computación e Inteligencia Artificial, Lenguajes y Sistemas Informáticos

Data-intensive Systems on Modern Hardware : Leveraging Near-Data Processing to Counter the Growth of Data

Over the last decades, a tremendous change toward using information technology in almost every daily routine of our lives can be perceived in our society, entailing an incredible growth of data collected day-by-day on Web, IoT, and AI applications. At the same time, magneto-mechanical HDDs are being replaced by semiconductor storage such as SSDs, equipped with modern Non-Volatile Memories, like Flash, which yield significantly faster access latencies and higher levels of parallelism. Likewise, the execution speed of processing units increased considerably as nowadays server architectures comprise up to multiple hundreds of independently working CPU cores along with a variety of specialized computing co-processors such as GPUs or FPGAs. However, the burden of moving the continuously growing data to the best fitting processing unit is inherently linked to today’s computer architecture that is based on the data-to-code paradigm. In the light of Amdahl's Law, this leads to the conclusion that even with today's powerful processing units, the speedup of systems is limited since the fraction of parallel work is largely I/O-bound. Therefore, throughout this cumulative dissertation, we investigate the paradigm shift toward code-to-data, formally known as Near-Data Processing (NDP), which relieves the contention on the I/O bus by offloading processing to intelligent computational storage devices, where the data is originally located. Firstly, we identified Native Storage Management as the essential foundation for NDP due to its direct control of physical storage management within the database. Upon this, the interface is extended to propagate address mapping information and to invoke NDP functionality on the storage device. As the former can become very large, we introduce Physical Page Pointers as one novel NDP abstraction for self-contained immutable database objects. Secondly, the on-device navigation and interpretation of data are elaborated. Therefore, we introduce cross-layer Parsers and Accessors as another NDP abstraction that can be executed on the heterogeneous processing capabilities of modern computational storage devices. Thereby, the compute placement and resource configuration per NDP request is identified as a major performance criteria. Our experimental evaluation shows an improvement in the execution durations of 1.4x to 2.7x compared to traditional systems. Moreover, we propose a framework for the automatic generation of Parsers and Accessors on FPGAs to ease their application in NDP. Thirdly, we investigate the interplay of NDP and modern workload characteristics like HTAP. Therefore, we present different offloading models and focus on an intervention-free execution. By propagating the Shared State with the latest modifications of the database to the computational storage device, it is able to process data with transactional guarantees. Thus, we achieve to extend the design space of HTAP with NDP by providing a solution that optimizes for performance isolation, data freshness, and the reduction of data transfers. In contrast to traditional systems, we experience no significant drop in performance when an OLAP query is invoked but a steady and 30% faster throughput. Lastly, in-situ result-set management and consumption as well as NDP pipelines are proposed to achieve flexibility in processing data on heterogeneous hardware. As those produce final and intermediary results, we continue investigating their management and identified that an on-device materialization comes at a low cost but enables novel consumption modes and reuse semantics. Thereby, we achieve significant performance improvements of up to 400x by reusing once materialized results multiple times

Guided Automatic Binary Parallelisation

For decades, the software industry has amassed a vast repository of pre-compiled libraries and executables which are still valuable and actively in use. However, for a significant fraction of these binaries, most of the source code is absent or is written in old languages, making it practically impossible to recompile them for new generations of hardware. As the number of cores in chip multi-processors (CMPs) continue to scale, the performance of this legacy software becomes increasingly sub-optimal. Rewriting new optimised and parallel software would be a time-consuming and expensive task. Without source code, existing automatic performance enhancing and parallelisation techniques are not applicable for legacy software or parts of new applications linked with legacy libraries. In this dissertation, three tools are presented to address the challenge of optimising legacy binaries. The first, GBR (Guided Binary Recompilation), is a tool that recompiles stripped application binaries without the need for the source code or relocation information. GBR performs static binary analysis to determine how recompilation should be undertaken, and produces a domain-specific hint program. This hint program is loaded and interpreted by the GBR dynamic runtime, which is built on top of the open-source dynamic binary translator, DynamoRIO. In this manner, complicated recompilation of the target binary is carried out to achieve optimised execution on a real system. The problem of limited dataflow and type information is addressed through cooperation between the hint program and JIT optimisation. The utility of GBR is demonstrated by software prefetch and vectorisation optimisations to achieve performance improvements compared to their original native execution. The second tool is called BEEP (Binary Emulator for Estimating Parallelism), an extension to GBR for binary instrumentation. BEEP is used to identify potential thread-level parallelism through static binary analysis and binary instrumentation. BEEP performs preliminary static analysis on binaries and encodes all statically-undecided questions into a hint program. The hint program is interpreted by GBR so that on-demand binary instrumentation codes are inserted to answer the questions from runtime information. BEEP incorporates a few parallel cost models to evaluate identified parallelism under different parallelisation paradigms. The third tool is named GABP (Guided Automatic Binary Parallelisation), an extension to GBR for parallelisation. GABP focuses on loops from sequential application binaries and automatically extracts thread-level parallelism from them on-the-fly, under the direction of the hint program, for efficient parallel execution. It employs a range of runtime schemes, such as thread-level speculation and synchronisation, to handle runtime data dependences. GABP achieves a geometric mean of speedup of 1.91x on binaries from SPEC CPU2006 on a real x86-64 eight-core system compared to native sequential execution. Performance is obtained for SPEC CPU2006 executables compiled from a variety of source languages and by different compilers.St John's Benefactor Scholarship ARM Sponsorshi

Lightweight speculative support for aggressive auto-parallelisation tools

With the recent move to multi-core architectures it has become important to create the means to exploit the performance made available to us by these architectures. Unfortunately parallel programming is often a difficult and time-intensive process, even to expert programmers. Auto-parallelisation tools have aimed to fill the performance gap this has created, but static analysis commonly employed by such tools are unable to provide the performance improvements required due to lack of information at compile-time. More recent aggressive parallelisation tools use profiled-execution to discover new parallel opportunities, but these tools are inherently unsafe. They require either manual confirmation that their changes are safe, completely ruling out auto-parallelisation, or they rely upon speculative execution such as software thread-level speculation (SW-TLS) to confirm safe execution at runtime. SW-TLS schemes are currently very heavyweight and often fail to provide speedups for a program. Performance gains are dependent upon suitable parallel opportunities, correct selection and configuration, and appropriate execution platforms. Little research has been completed into the automated implemention of SW-TLS programs. This thesis presents an automated, machine-learning based technique to select and configure suitable speculation schemes when appropriate. This is performed by extracting metrics from potential parallel opportunities and using them to determine if a loop is suitable for speculative execution and if so, which speculation policy should be used. An extensive evaluation of this technique is presented, verifying that SW-TLS configuration can indeed be automated and provide reliable performance gains. This work has shown that on an 8-core machine, up to 7.75X and a geometric mean of 1.64X speedups can be obtained through automatic configuration, providing on average 74% of the speedup obtainable through manual configuration. Beyond automated configuration, this thesis explores the idea that many SW-TLS schemes focus too heavily on recovery from detecting a dependence violation. Doing so often results in worse than sequential performance for many real-world applications, therefore this work hypothesises that for many highly-likely parallel candidates, discovered through aggressive parallelisation techniques, would benefit from a simple dependence check without the ability to roll back. Dependence violations become extremely expensive in this scenario, however this would be incredibly rare. With a thorough evaluation of the technique this thesis confirms the hypothesis whilst achieving speedups of up to 22.53X, and a geometric mean of 2.16X on a 32-core machine. In a competitive scheduling scenario performance loss can be restricted to at least sequential speeds, even when a dependence has been detected. As a means to lower costs further this thesis explores other platforms to aid in the execution of speculative error checking. Introduced is the use of a GPU to offload some of the costs to during execution that confirms that using an auxiliary device is a legitimate means to obtain further speedup. Evaluation demonstrates that doing so can achieve up to 14.74X and a geometric mean of 1.99X speedup on a 12-core hyperthreaded machine. Compared to standard CPU-only techniques this performs slightly slower with a geometric mean of 0.96X speedup, however this is likely to improve with upcoming GPU designs. With the knowledge that GPU’s can be used to reduce speculation costs, this thesis also investigates their use to speculatively improve execution times also. Presented is a novel SW-TLS scheme that targets GPU-based execution for use with aggressive auto-parallelisers. This scheme is executed using a competitive scheduling model, ensuring performance is no lower than sequential execution, whilst being able to provide speedups of up to 99X and on average 3.2X over sequential. On average this technique outperformed static analysis alone by a factor of 7X and achieved approximately 99% of the speedup obtained from manual parallel implementations and outperformed the state-of-the-art in GPU SW-TLS by a factor of 1.45

Personalized large scale classification of public tenders on hadoop

Ce projet a été réalisé dans le cadre d’un partenariat entre Fujitsu Canada et Université Laval. Les besoins du projets ont été centrés sur une problématique d’affaire définie conjointement avec Fujitsu. Le projet consistait à classifier un corpus d’appels d’offres électroniques avec une approche orienté big data. L’objectif était d’identifier avec un très fort rappel les offres pertinentes au domaine d’affaire de l’entreprise. Après une séries d’expérimentations à petite échelle qui nous ont permise d’illustrer empiriquement (93% de rappel) l’efficacité de notre approche basé sur l’algorithme BNS (Bi-Normal Separation), nous avons implanté un système complet qui exploite l’infrastructure technologique big data Hadoop. Nos expérimentations sur le système complet démontrent qu’il est possible d’obtenir une performance de classification tout aussi efficace à grande échelle (91% de rappel) tout en exploitant les gains de performance rendus possible par l’architecture distribuée de Hadoop.This project was completed as part of an innovation partnership with Fujitsu Canada and Université Laval. The needs and objectives of the project were centered on a business problem defined jointly with Fujitsu. Our project aimed to classify a corpus of electronic public tenders based on state of the art Hadoop big data technology. The objective was to identify with high recall public tenders relevant to the IT services business of Fujitsu Canada. A small scale prototype based on the BNS algorithm (Bi-Normal Separation) was empirically shown to classify with high recall (93%) the public tender corpus. The prototype was then re-implemented on a full scale Hadoop cluster using Apache Pig for the data preparation pipeline and using Apache Mahout for classification. Our experimentation show that the large scale system not only maintains high recall (91%) on the classification task, but can readily take advantage of the massive scalability gains made possible by Hadoop’s distributed architecture