Doctor of Philosophy

dissertationServing as a record of what happened during a scientific process, often computational, provenance has become an important piece of computing. The importance of archiving not only data and results but also the lineage of these entities has led to a variety of systems that capture provenance as well as models and schemas for this information. Despite significant work focused on obtaining and modeling provenance, there has been little work on managing and using this information. Using the provenance from past work, it is possible to mine common computational structure or determine differences between executions. Such information can be used to suggest possible completions for partial workflows, summarize a set of approaches, or extend past work in new directions. These applications require infrastructure to support efficient queries and accessible reuse. In order to support knowledge discovery and reuse from provenance information, the management of those data is important. One component of provenance is the specification of the computations; workflows provide structured abstractions of code and are commonly used for complex tasks. Using change-based provenance, it is possible to store large numbers of similar workflows compactly. This storage also allows efficient computation of differences between specifications. However, querying for specific structure across a large collection of workflows is difficult because comparing graphs depends on computing subgraph isomorphism which is NP-Complete. Graph indexing methods identify features that help distinguish graphs of a collection to filter results for a subgraph containment query and reduce the number of subgraph isomorphism computations. For provenance, this work extends these methods to work for more exploratory queries and collections with significant overlap. However, comparing workflow or provenance graphs may not require exact equality; a match between two graphs may allow paired nodes to be similar yet not equivalent. This work presents techniques to better correlate graphs to help summarize collections. Using this infrastructure, provenance can be reused so that users can learn from their own and others' history. Just as textual search has been augmented with suggested completions based on past or common queries, provenance can be used to suggest how computations can be completed or which steps might connect to a given subworkflow. In addition, provenance can help further science by accelerating publication and reuse. By incorporating provenance into publications, authors can more easily integrate their results, and readers can more easily verify and repeat results. However, reusing past computations requires maintaining stronger associations with any input data and underlying code as well as providing paths for migrating old work to new hardware or algorithms. This work presents a framework for maintaining data and code as well as supporting upgrades for workflow computations

Prefetching techniques for client server object-oriented database systems

The performance of many object-oriented database applications suffers from the page fetch latency which is determined by the expense of disk access. In this work we suggest several prefetching techniques to avoid, or at least to reduce, page fetch latency. In practice no prediction technique is perfect and no prefetching technique can entirely eliminate delay due to page fetch latency. Therefore we are interested in the trade-off between the level of accuracy required for obtaining good results in terms of elapsed time reduction and the processing overhead needed to achieve this level of accuracy. If prefetching accuracy is high then the total elapsed time of an application can be reduced significantly otherwise if the prefetching accuracy is low, many incorrect pages are prefetched and the extra load on the client, network, server and disks decreases the whole system performance. Access pattern of object-oriented databases are often complex and usually hard to predict accurately. The ..

Understanding and Optimizing Flash-based Key-value Systems in Data Centers

Flash-based key-value systems are widely deployed in today’s data centers for providing high-speed data processing services. These systems deploy flash-friendly data structures, such as slab and Log Structured Merge(LSM) tree, on flash-based Solid State Drives(SSDs) and provide efficient solutions in caching and storage scenarios. With the rapid evolution of data centers, there appear plenty of challenges and opportunities for future optimizations. In this dissertation, we focus on understanding and optimizing flash-based key-value systems from the perspective of workloads, software, and hardware as data centers evolve. We first propose an on-line compression scheme, called SlimCache, considering the unique characteristics of key-value workloads, to virtually enlarge the cache space, increase the hit ratio, and improve the cache performance. Furthermore, to appropriately configure increasingly complex modern key-value data systems, which can have more than 50 parameters with additional hardware and system settings, we quantitatively study and compare five multi-objective optimization methods for auto-tuning the performance of an LSM-tree based key-value store in terms of throughput, the 99th percentile tail latency, convergence time, real-time system throughput, and the iteration process, etc. Last but not least, we conduct an in-depth, comprehensive measurement work on flash-optimized key-value stores with recently emerging 3D XPoint SSDs. We reveal several unexpected bottlenecks in the current key-value store design and present three exemplary case studies to showcase the efficacy of removing these bottlenecks with simple methods on 3D XPoint SSDs. Our experimental results show that our proposed solutions significantly outperform traditional methods. Our study also contributes to providing system implications for auto-tuning the key-value system on flash-based SSDs and optimizing it on revolutionary 3D XPoint based SSDs

Efficient I/O for Computational Grid Applications

High-performance computing increasingly occurs on computational grids composed of heterogeneous and geographically distributed systems of computers, networks, and storage devices that collectively act as a single virtual computer. A key challenge in this environment is to provide efficient access to data distributed across remote data servers. This dissertation explores some of the issues associated with I/O for wide-area distributed computing and describes an I/O system, called Armada, with the following features: a framework to allow application and dataset providers to flexibly compose graphs of processing modules that describe the distribution, application interfaces, and processing required of the dataset before or after computation; an algorithm to restructure application graphs to increase parallelism and to improve network performance in a wide-area network; and a hierarchical graph-partitioning scheme that deploys components of the application graph in a way that is both beneficial to the application and sensitive to the administrative policies of the different administrative domains. Experiments show that applications using Armada perform well in both low- and high-bandwidth environments, and that our approach does an exceptional job of hiding the network latency inherent in grid computing

Sixth Goddard Conference on Mass Storage Systems and Technologies Held in Cooperation with the Fifteenth IEEE Symposium on Mass Storage Systems

This document contains copies of those technical papers received in time for publication prior to the Sixth Goddard Conference on Mass Storage Systems and Technologies which is being held in cooperation with the Fifteenth IEEE Symposium on Mass Storage Systems at the University of Maryland-University College Inn and Conference Center March 23-26, 1998. As one of an ongoing series, this Conference continues to provide a forum for discussion of issues relevant to the management of large volumes of data. The Conference encourages all interested organizations to discuss long term mass storage requirements and experiences in fielding solutions. Emphasis is on current and future practical solutions addressing issues in data management, storage systems and media, data acquisition, long term retention of data, and data distribution. This year's discussion topics include architecture, tape optimization, new technology, performance, standards, site reports, vendor solutions. Tutorials will be available on shared file systems, file system backups, data mining, and the dynamics of obsolescence

Towards Design and Analysis For High-Performance and Reliable SSDs

NAND Flash-based Solid State Disks have many attractive technical merits, such as low power consumption, light weight, shock resistance, sustainability of hotter operation regimes, and extraordinarily high performance for random read access, which makes SSDs immensely popular and be widely employed in different types of environments including portable devices, personal computers, large data centers, and distributed data systems. However, current SSDs still suffer from several critical inherent limitations, such as the inability of in-place-update, asymmetric read and write performance, slow garbage collection processes, limited endurance, and degraded write performance with the adoption of MLC and TLC techniques. To alleviate these limitations, we propose optimizations from both specific outside applications layer and SSDs\u27 internal layer. Since SSDs are good compromise between the performance and price, so SSDs are widely deployed as second layer caches sitting between DRAMs and hard disks to boost the system performance. Due to the special properties of SSDs such as the internal garbage collection processes and limited lifetime, traditional cache devices like DRAM and SRAM based optimizations might not work consistently for SSD-based cache. Therefore, for the outside applications layer, our work focus on integrating the special properties of SSDs into the optimizations of SSD caches. Moreover, our work also involves the alleviation of the increased Flash write latency and ECC complexity due to the adoption of MLC and TLC technologies by analyzing the real work workloads

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

Network Repository for Performance Evaluation Results

For performance evaluation of software systems, benchmarking is used. Benchmarking generates a large amount of output data, which is necessary to store, process and evaluate it. Network Repository serves as a repository of benchmark results. The goal of the master thesis is to design and implement the data storage with a support of various result types with the possibility of the format configuration. Stored results can be processed, evaluated, or used as a source for plotting. As part of the master thesis, the design and implementation of a general framework for benchmark storage and evaluation is developed and a sample configuration for the selected benchmark result data format is established.Pro měření výkonu softwarových systemů se používá benchmarkovaní. Benchmarkovaní vytváří velké množství dat, které je třeba ukládat, zpracovávat a vyhodnocovat. Network Repository slouží jako úložiště výsledků vznikajících během benchmarkovani. Cílem diplomové práce je navrhnout a naimplementovat datové úložiště podporujicí různé druhy výsledků s možností konfigurace jejich formátu. Uložené výsledky je možné dále zpracovávat, vyhodnocovat a používat jako zdroj pro generovaní grafických výstupů. Součástí diplomové práce je návrh a implementace obecného frameworku pro ukládání a vyhodnocovaní dat benchmarků a vytvoření vzorové konfigurace pro vybrané formáty dat výsledků benchmarků.Katedra softwarového inženýrstvíDepartment of Software EngineeringFaculty of Mathematics and PhysicsMatematicko-fyzikální fakult

Supercomputing Frontiers

This open access book constitutes the refereed proceedings of the 6th Asian Supercomputing Conference, SCFA 2020, which was planned to be held in February 2020, but unfortunately, the physical conference was cancelled due to the COVID-19 pandemic. The 8 full papers presented in this book were carefully reviewed and selected from 22 submissions. They cover a range of topics including file systems, memory hierarchy, HPC cloud platform, container image configuration workflow, large-scale applications, and scheduling